10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington D.C. 20549

FORM 10-Q

(Mark One)

x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended March 31, 2017

OR

o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from              to

Commission File Number: 001-34885

AMYRIS, INC.

(Exact name of registrant as specified in its charter)

Delaware	55-0856151
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

(510) 450-0761

(Address and telephone number of principal executive offices)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuance to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    No  o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, or a non-accelerated filer.

Large accelerated filer	o	Accelerated filer	o
Non-accelerated filer	o	Smaller reporting company	x
Emerging growth company	o

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  o    No  x

Indicate the number of shares outstanding of each of the issuer’s classes of common stock, as of the latest practicable date.

Class	Outstanding at April 30, 2017
Common Stock, $0.0001 par value per share	297,086,351

AMYRIS, INC.

QUARTERLY REPORT ON FORM 10-Q

For the Quarterly Period Ended March 31, 2017

INDEX

		Page
PART I - FINANCIAL INFORMATION
Item 1.	Financial Statements (unaudited)	3
Item 2.	Management’s  Discussion and Analysis of Financial Condition and Results of Operations	68
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	85
Item 4.	Controls and Procedures	86
PART II - OTHER INFORMATION
Item 1.	Legal Proceedings	88
Item 1A.	Risk Factors	88
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	120
Item 3.	Defaults Upon Senior Securities	121
Item 4.	Mine Safety Disclosures	121
Item 5.	Other Information	121
Item 6.	Exhibits	121
	Signatures
	Exhibit Index

PART I

ITEM 1. FINANCIAL STATEMENTS

Amyris, Inc.

Condensed Consolidated Balance Sheets

(In Thousands, Except Shares and Per Share Amounts)

(Unaudited)

	March 31, 2017			December 31, 2016
Assets
Current assets:
Cash and cash equivalents	$	1,297		$	27,150
Restricted cash		301			4,326
Short-term investments		1,188			1,374
Accounts receivable, net of allowance of $478 and $478, respectively		8,122			13,105
Related party accounts receivable, net of allowance of $23 and $23, respectively		416			872
Inventories, net		7,077			6,213
Prepaid expenses and other current assets		5,652			6,083
Total current assets		24,053			59,123
Property, plant and equipment, net		53,045			53,735
Restricted cash		958			957
Equity and loans in affiliates		34			34
Other assets		16,794			15,464
Goodwill and intangible assets		560			560
Total assets	$	95,444		$	129,873
Liabilities, Mezzanine Equity and Stockholders' Deficit
Current liabilities:
Accounts payable	$	16,453		$	15,315
Deferred revenue		3,487			5,288
Accrued and other current liabilities		31,806			29,188
Capital lease obligation, current portion		405			922
Debt, current portion		15,290			25,853
Related party debt		34,165			33,302
Total current liabilities		101,606			109,868
Capital lease obligation, net of current portion		405			334
Long-term debt, net of current portion		131,759			128,744
Related party debt		39,724			39,144
Deferred rent, net of current portion		8,691			8,906
Deferred revenue, net of current portion		6,650			6,650
Derivative liabilities		5,144			6,894
Other liabilities		7,716			7,841
Total liabilities		301,695			308,381
Commitments and contingencies (Note 6)
Mezzanine Equity
Contingently redeemable common stock (Note 8)		5,000			5,000
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding		—			—
Common stock - $0.0001 par value, 500,000,000 and 500,000,000 shares authorized as of March 31, 2017 and December 31, 2016, respectively; 287,973,020 and 274,108,808 shares issued and outstanding as of March 31, 2017 and December 31, 2016, respectively		28			27
Additional paid-in capital		1,000,174			990,870
Accumulated other comprehensive loss		(40,581	)		(40,904	)
Accumulated deficit		(1,171,809	)		(1,134,438	)
Total Amyris, Inc. stockholders’ deficit		(212,188	)		(184,445	)
Noncontrolling interest		937			937
Total stockholders' deficit		(211,251	)		(183,508	)
Total liabilities, mezzanine equity and stockholders' deficit	$	95,444		$	129,873

See the accompanying notes to the unaudited condensed consolidated financial statements.

3

Amyris, Inc.

Condensed Consolidated Statements of Operations

(In Thousands, Except Shares and Per Share Amounts)

(Unaudited)

	Three Months Ended March 31,
	2017			2016
Revenues
Renewable product sales	$	8,292		$	3,140
Grants and collaborations revenue		4,688			5,671
Total revenues		12,980			8,811
Cost and operating expenses
Cost of products sold		12,768			11,178
Research and development		14,778			11,906
Sales, general and administrative		12,778			12,266
Total cost and operating expenses		40,324			35,350
Loss from operations		(27,344	)		(26,539	)
Other income (expense):
Interest income		61			57
Interest expense		(12,184	)		(8,359	)
Gain from change in fair value of derivative instruments		2,339			21,678
Gain/(loss) upon extinguishment of debt		96			(216	)
Other expense, net		(380	)		(1,814	)
Total other income (expense)		(10,068	)		11,346
Loss before income taxes		(37,412	)		(15,193	)
(Benefit from)/provision for income taxes		41			(115	)
Net loss		(37,371	)		(15,308	)
Net loss attributable to noncontrolling interest		—			—
Net loss attributable to Amyris, Inc. common stockholders	$	(37,371	)	$	(15,308	)
Net loss per share attributable to common stockholders:
Basic	$	(0.13	)	$	(0.07	)
Diluted	$	(0.13	)	$	(0.12	)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock:
Basic		290,039,216			207,199,563
Diluted		290,039,216			260,932.09

See the accompanying notes to the unaudited condensed consolidated financial statements.

4

Amyris, Inc.

Condensed Consolidated Statements of Comprehensive Loss

(In Thousands)

(Unaudited)

	Three Months Ended March 31,
	2017			2016
Comprehensive loss:
Net loss	$	(37,371	)	$	(15,308	)
Foreign currency translation adjustment, net of tax		323			4,687
Total comprehensive loss		(37,048	)		(10,621	)
Loss attributable to noncontrolling interest		—			—
Comprehensive loss attributable to Amyris, Inc.	$	(37,048	)	$	(10,621	)

See the accompanying notes to the unaudited condensed consolidated financial statements.

5

Amyris, Inc.

Condensed Consolidated Statements of Stockholders’ Deficit

(In Thousands, Except Shares)

(Unaudited)

	Common Stock
	Shares		Amount		Additional Paid-in Capital			Accumulated Deficit			Accumulated Other Comprehensive Loss			Noncontrolling Interest		Total Deficit			Mezzanine Equity
December 31, 2016		274,108,808	$	27	$	990,870		$	(1,134,438	)	$	(40,904	)	$	937	$	(183,508	)	$	5,000
Issuance of common stock upon exercise of stock options, net of restricted stock		500		—		—			—			—			—		—			—
Issuance of common stock for settlement of debt principal payments		13,546,448		1		7,680			—			—			—		7,681			—
Shares issued from restricted stock settlement		317,264		—		(22	)		—			—			—		(22	)		—
Stock-based compensation		—		—		1,646			—			—			—		1,646			—
Foreign currency translation adjustment		—		—		—			—			323			—		323			—
Net loss		—		—		—			(37,371	)		—			—		(37,371	)		—
March 31, 2017		287,973,020	$	28	$	1,000,174		$	(1,171,809	)	$	(40,581	)	$	937	$	(211,251	)	$	5,000

See the accompanying notes to the unaudited condensed consolidated financial statements.

6

Amyris, Inc.

Condensed Consolidated Statements of Cash Flows

(In Thousands)

(Unaudited)

	Three Months Ended March 31,
	2017			2016
Operating activities
Net loss	$	(37,371	)	$	(15,308	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization		2,715			2,869
Loss on disposal of property, plant and equipment		(55	)		(37	)
Stock-based compensation		1,646			2,051
Amortization of debt discount and issuance costs		4,473			2,994
(Gain)/loss upon extinguishment of debt		(96	)		216
Gain from change in fair value of derivative instruments		(2,339	)		(21,678	)
(Gain)/loss on foreign currency exchange rates		(295	)		1,117
Changes in assets and liabilities:
Accounts receivable		4,888			(1,484	)
Related party accounts receivable		500			(300	)
Inventories, net		(867	)		3,870
Prepaid expenses and other assets		(713	)		1,288
Accounts payable		450			(810	)
Accrued and other liabilities		3,730			2,924
Deferred revenue		(1,844	)		(1,292	)
Deferred rent		(215	)		(163	)
Net cash used in operating activities		(25,393	)		(23,743	)
Investing activities
Purchase of short-term investments		(1,781	)		(1,377	)
Maturities of short-term investments		2,094			1,627
Change in restricted cash		4,040			13
Purchases of property, plant and equipment, net of disposals		(457	)		(271	)
Net cash provided by (used in) investing activities		3,896			(8	)
Financing activities
Employees' taxes paid upon vesting of restricted stock units		(22	)		(48	)
Principal payments on capital leases		(627	)		(160	)
Proceeds from debt issued		1,500			—
Proceeds from debt issued to related party		—			20,000
Principal payments on debt		(4,273	)		(729	)
Net cash provided by (used in) financing activities		(3,762	)		19,063
Effect of exchange rate changes on cash and cash equivalents		(83	)		522
Net decrease in cash and cash equivalents		(25,853	)		(4,166	)
Cash and cash equivalents at beginning of period		27,150			11,992
Cash and cash equivalents at end of period	$	1,297		$	7,826

7

Amyris, Inc.

Condensed Consolidated Statements of Cash Flows—(Continued)

(In Thousands)

	Three Months Ended March 31,
	2017			2016
Supplemental disclosures of cash flow information:
Cash paid for interest	$	1,863		$	990
Supplemental disclosures of non-cash investing and financing activities:
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	$	(821	)	$	(521	)
Financing of equipment	$	180		$	100
Financing of insurance premium under notes payable	$	(146	)	$	(159	)
Issuance of common stock for settlement of debt principal and interest payments	$	7,681		$	—
Interest capitalized to debt	$	1,115		$	1,010
Purchase of property, plant and equipment via deposit	$	—		$	24
Non-cash investment in joint venture	$	—		$	600
Cancellation of debt and accrued interest on disposal of interest in affiliate	$	—		$	4,252

See the accompanying notes to the unaudited condensed consolidated financial statements.

8

Amyris, Inc.

Notes to Unaudited Condensed Consolidated Financial Statements

1. The Company

Amyris, Inc. (or the Company) was incorporated in California on July 17, 2003 and reincorporated in Delaware on April 15, 2010 for the purpose of leveraging breakthroughs in bioscience technology to develop and provide renewable compounds for a variety of markets. The Company is currently applying its industrial synthetic biology platform to engineer, manufacture and sell high performance, low cost products into Health and Nutrition, Personal Care and Performance Material markets. The Company's first commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene (Biofene®), which forms the basis for a wide range of products including nutraceuticals, skin care, fragrances, solvents, polymers, and lubricants ingredients. In 2014, the Company began manufacturing additional molecules for the flavors and fragrance (F&F) industry, in 2015 the Company began investing to expand its capabilities to other small molecule chemical classes beyond terpenes via its collaboration with the Defense Advanced Research Project Agency, as discussed below, and in 2016 the Company expanded into proteins. While the Company's platform is able to use a wide variety of feedstocks, the Company has initially focused on Brazilian sugarcane because of its renewability, low cost and relative price stability. The Company has established one principal operating subsidiary, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., or Amyris Brasil) which oversees the Company’s production operations in Brazil.

The Company's renewable products business strategy is to generally focus on direct commercialization of specialty products while moving established commodity products into joint venture arrangements with leading industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture its products at commercial scale and on an economically viable basis (i.e., low per unit production costs) and developing sufficient sales volume for those products to support its operations. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development.

Liquidity

The Company expects to fund its operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaborations and grants, with cash contributions from product sales, with new debt and equity financings and with proceeds from strategic asset divestments. The Company's planned 2017 and 2018 working capital needs and its planned operating and capital expenditures are dependent on significant inflows of cash from new and existing collaboration partners and from cash generated from renewable product sales and from strategic asset divestments, and will also require additional funding from debt or equity financings.

The Company has incurred significant operating losses since its inception and believes that it will continue to incur losses and negative cash flow from operations into at least 2018. As of March 31, 2017, the Company had negative working capital of $77.6 million, an accumulated deficit of $1,171.8 million, and had cash, cash equivalents and short term investments of $2.5 million. The Company will need additional financing as early as the second quarter of 2017 to support its liquidity needs. See Note 18, “Subsequent Events” for details regarding financing transactions completed subsequent to March 31, 2017. These factors raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date that the financial statements are issued. The financial statements do not include any adjustments that might result from the outcome of this uncertainty. If the Company is unable to continue as a going concern, it may be unable to meet its obligations under its existing debt facilities, which could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and it may be forced to liquidate its assets.

As of March 31, 2017, the Company's debt, net of discount and issuance costs of $42.0 million, totaled $220.9 million, of which $49.5 million is classified as current. In addition to upcoming debt maturities, the Company's debt service obligations over the next twelve months are significant, including $20.8 million of anticipated cash interest payments. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults such as restrictions on additional indebtedness, material adverse effect and cross default clauses. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required would generally result in events of default under such instruments, which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of such other outstanding indebtedness. Any required repayment of such indebtedness as a result of acceleration or otherwise would consume current cash on hand such that the Company would not have those funds available for use in its business or for payment of other outstanding indebtedness. Please refer to Note 5, “Debt and Mezzanine Equity”, Note 6, “Commitments and Contingencies” and Note 18, “Subsequent Events” for further details regarding the Company's debt service obligations and commitments. The Company also has a significant working capital deficit and contractual obligations related to capital and operating leases, as well as purchase commitments.

9

In addition to the need for financing described above, the Company may take the following actions as early as the second quarter of 2017 to support its liquidity needs through the remainder of 2017 and into 2018:

• Effect significant headcount reductions, particularly with respect to employees not connected to critical or contracted activities across all functions of the Company, including employees involved in general and administrative, research and development, and production activities.

• Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.

• Reduce production activity at the Company’s Brotas manufacturing facility to levels only sufficient to satisfy volumes required for product revenues forecast from existing products and customers.

• Reduce expenditures for third party contractors, including consultants, professional advisors and other vendors.

• Reduce or delay uncommitted capital expenditures, including non-essential facility and lab equipment, and information technology projects.

• Closely monitor the Company’s working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on the Company's ability to continue its business as currently contemplated, including, without limitation, delays or failures in its ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have an adverse effect on the Company's ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

10

2. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (or “GAAP”) and with the instructions for Form 10-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form 10-K for the fiscal year ended December 31, 2016 as filed with the Securities and Exchange Commission (or the “SEC”) on April 17, 2017. The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

The Company uses the equity method to account for investments in companies, if its investments provide it with the ability to exercise significant influence over operating and financial policies of the investee. Consolidated net income or loss includes the Company’s proportionate share of the net income or loss of these companies. Judgments made by the Company regarding the level of influence over each equity method investment include considering key factors such as the Company’s ownership interest, representation on the board of directors, participation in policy-making decisions and material intercompany transactions.

Principles of Consolidation

The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated variable interest entities (or “VIEs”), with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 7, "Joint Ventures and Noncontrolling Interest."

Variable Interest Entities

The Company has interests in joint venture entities that are VIEs. Determining whether to consolidate a VIE requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

Use of Estimates

In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements, except for the impact of adoption of certain accounting standards as described below, and in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented. In the quarter ended March 31, 2017 the Company adopted Accounting Standards Update (“ASU”) No. 2015-11, Simplifying the Measurement of Inventory, ASU No. 2016-06, Contingent Put and Call Options in Debt Instruments, ASU No. 2016-09, Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting. None of the ASU’s adopted had a material impact on the Company’s condensed consolidated financial statements.

The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.

Recent Accounting Pronouncements

In November 2016, the Financial Accounting Standards Board (FASB) issued ASU 2016-18 Statement of Cash Flows - Restricted Cash. The amendments in this update require that a statement of cash flows explain the change during the period in the total of cash, cash equivalents, and amounts generally described as restricted cash or restricted cash equivalents. Therefore, amounts generally described as restricted cash and restricted cash equivalents should be included with cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. The amendments in this update are effective for public business entities for fiscal years beginning after December 15, 2017, and interim periods within those fiscal years. Early adoption is permitted, including adoption in an interim period. The amendments in this update should be applied using a retrospective transition method to each period presented. The Company has not adopted the update. Upon adoption this would result in a change in the presentation of restricted cash in the statement of cash flows.

11

In October 2016, FASB issued ASU 2016-16, Intra-Entity Transfers of Assets Other Than Inventory on simplifying the accounting for income taxes related to intra-entity asset transfers. The new guidance allows an entity to recognize the tax expense from the sale of an asset in the seller’s tax jurisdiction when the transfers occur, even though the pre-tax effects of that transaction are eliminated in consolidation. This guidance will be effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2017. Early adoption is permitted only in the first quarter of 2017. The Company does not expect a material impact on its financial statements upon adoption of this standard.

In August 2016, FASB issued ASU 2016-15 Classification of Certain Cash Receipts and Cash Payments on the statement of cash flows. The new guidance clarifies classification of certain cash receipts and cash payments in the statement of cash flows. This guidance will be effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2017 and interim periods within those fiscal years. Early adoption is permitted. The Company is evaluating the impact of adopting this accounting standard update on the financial statements and related disclosures.

In June 2016, FASB issued ASU No. 2016-13, Allowance for Loan and Lease Losses (Financial Instruments - Credit Losses Topic 326). New impairment guidance for certain financial instruments (including trade receivables) will replace the current “incurred loss” model for estimating credit losses with a forward looking “expected loss” model. The ASU is effective for the Company for fiscal years beginning after December 15, 2019, including interim periods within those fiscal years. Early application is permitted as of the fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. The Company is evaluating the impact of this standard on its financial statements.

In February 2016, FASB issued Accounting Standards Update2016-02-Leases with fundamental changes to how entities account for leases. Lessees will need to recognize a right-of-use asset and a lease liability for virtually all of their leases (other than leases that meet the definition of a short-term lease). The liability will be equal to the present value of lease payments. The asset will be based on the liability, subject to adjustment, such as for initial direct costs. Additional disclosures for leases will also be required. The standard is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. Early adoption is permitted. The new standard must be adopted using a modified retrospective transition, and provides for certain practical expedients. The new standard may materially impact the Company’s financial statements.

12

In January 2016, FASB issued Accounting Standards Update 2016-01 Financial Instruments-Overall, which address certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. The amendments in this update are effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years. Earlier application is permitted under specific circumstances. The Company expects the new standard to impact the extent of its disclosures of financial instruments, particularly in relation to fair value disclosures, but otherwise does not expect a significant impact from the new standard.

In May 2014, FASB issued new guidance related to revenue recognition. In March, April, May and December 2016, the FASB issued additional amendments to the new revenue guidance relating to reporting revenue on a gross versus net basis, identifying performance obligations, licensing arrangements, collectability, noncash consideration, presentation of sales tax, and transition. This new standard will replace all current GAAP guidance on this topic and eliminate all industry-specific guidance. The new revenue recognition update guidance provides a unified model to determine how revenue is recognized. The core principle of the guidance is that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The FASB has issued several updates to the standard which i) clarify the application of the principal versus agent guidance (ASU 2016-08); ii) clarify the guidance on inconsequential and perfunctory promises and licensing (ASU 2016-10) and iii) narrow-scope improvements and practical expedients (ASU 2016-12). On July 9, 2015, the FASB voted to defer the effective date by one year to December 15, 2017 for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of December 15, 2016. Entities have the option of using either a full retrospective or a modified retrospective approach to adopt the new standard. Therefore, the new standard will be effective commencing with our quarter ending March 31, 2018. The Company is currently assessing the potential impact of this new standard on its financial statements and has not selected the transition method. While the Company continues to assess the impact of the new guidance on its revenue recognition policies, it is expected that a key area will be the assessment of contract modifications and collaboration contracts to determine if identification of performance obligations is impacted, which may impact the timing of revenue recognition. In addition, the Company expects additional disclosures related to revenue.

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3. Fair Value of Financial Instruments

The inputs to the valuation techniques used to measure fair value are classified into the following categories:

Level 1: Quoted market prices in active markets for identical assets or liabilities.

Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data.

Level 3: Unobservable inputs that are not corroborated by market data.

There were no transfers between the levels, and as of March 31, 2017, the Company’s financial assets and financial liabilities at fair value were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of March 31, 2017
Financial Assets
Money market funds	$	297	$	—	$	—	$	297
Certificates of deposit		1,188		—		—		1,188
Total financial assets	$	1,485	$	—	$	—	$	1,485
Financial Liabilities
Loans payable (1)	$	—	$	51,378	$	—	$	51,378
Credit facilities  (1)		—		50,891		—		50,891
Convertible notes (1)		—		—		115,268		115,268
Compound embedded derivative liabilities		—		—		2,728		2,728
Currency interest rate swap derivative liability		—		2,961		—		2,961
Total financial liabilities	$	—	$	105,230	$	117,996	$	223,226

________

⁽¹⁾ These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds and certificates of deposit are based on fair values of identical assets. The fair values of the loans payable, convertible notes, credit facilities and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. The method of determining the fair value of the compound embedded derivative liabilities is described subsequently in this note. Market risk associated with the fixed and variable rate long-term loans payable, credit facilities and convertible notes relates to the potential reduction in fair value and negative impact to future earnings, from an increase in interest rates. Market risk associated with the compound embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable.

14

As of December 31, 2016, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of December 31, 2016
Financial Assets
Money market funds	$	1,549	$	—	$	—	$	1,549
Certificates of deposit		1,373		—		—		1,373
Total financial assets	$	2,922	$	—	$	—	$	2,922
Financial Liabilities
Loans payable (1)	$	—	$	53,579	$	—	$	53,579
Credit facilities  (1)		—		51,261		—		51,261
Convertible notes (1)		—		—		117,767		117,767
Compound embedded derivative liabilities		—		—		4,135		4,135
Currency interest rate swap derivative liability		—		3,343		—		3,343
Total financial liabilities	$	—	$	108,183	$	121,902	$	230,085

_______

⁽¹⁾ These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis (noting that the Remaining Notes subject to the Maturity Treatment Agreement were revalued to fair value on July 29, 2015, see Note 5 “Debt and Mezzanine Equity” and Note 18, “Subsequent Events” for details).

The following table provides a reconciliation of the beginning and ending balances for the convertible notes disclosed at fair value using significant unobservable inputs (Level 3) (in thousands):

	2017
Balance at January 1	$	117,767
New instruments		15,049
Conversion/extinguishment of convertible notes		(21,077	)
Change in fair value of convertible notes		3,529
Balance at March 31	$	115,268

Derivative Instruments

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liabilities measured at fair value using significant unobservable inputs (Level 3) (in thousands):

	2017
Balance at January 1	$	4,135
Gain from change in fair value of derivative liabilities		(1,984	)
Additions		577
Balance at March 31	$	2,728

The compound embedded derivative liabilities represent the fair value of the equity conversion options and "make-whole" provisions, as well as the down round conversion price adjustment or conversion rate adjustment provisions of the R&D Notes, the Tranche I Notes, the Tranche II Notes, the 2014 144A Notes and the 2015 144A Notes (see Note 5, “Debt and Mezzanine Equity”). There is no current observable market for these types of derivatives and, as such, the Company determined the fair value of the embedded derivatives using a Monte Carlo simulation valuation model for the R&D Notes and the binomial lattice model for the Tranche I Notes, the Tranche II Notes, the 2014 144A Notes and the 2015 144A Notes (or, collectively, Convertible Notes). A Monte Carlo simulation valuation model combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are or may be convertible. A binomial lattice model generates two probable outcomes - one up and another down - arising at each point in time, starting from the date of valuation until the maturity date. A lattice model was used to determine if the Convertible Notes would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the Convertible Notes will be converted early if the conversion value is greater than the holding value and (ii) the Convertible Notes will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the Convertible Notes are called, then the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the Convertible Notes. Using this lattice method, the Company valued the embedded derivatives using the "with-and-without method", where the fair value of the Convertible Notes including the embedded derivative is defined as the "with", and the fair value of the Convertible Notes excluding the embedded derivatives is defined as the "without". This method estimates the fair value of the embedded derivatives by looking at the difference in the values between the Convertible Notes with the embedded derivatives and the fair value of the Convertible Notes without the embedded derivatives. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company marks the compound embedded derivatives to market due to the conversion price not being indexed to the Company's own stock. As of March 31, 2017 and December 31, 2016, included in "Derivative Liabilities" on the condensed consolidated balance sheet are the Company's compound embedded derivative liabilities of $2.7 million and $4.1 million, respectively.

15

The market-based assumptions and estimates used in valuing the compound embedded derivative liabilities include amounts in the following ranges/amounts:

	March 31, 2017			March 31, 2016
Risk-free interest rate	0.74%	-	1.30%	0.80%	-	0.89%
Risk-adjusted yields	12.50%	-	22.63%	35.00%	-	45.13%
Stock-price volatility		45%			45%
Probability of change in control		5%			5%
Stock price		$0.53			$1.11
Credit spread	11.28%	-	21.35%	34.16%	-	44.25%
Estimated conversion dates	2017	-	2019	2016	-	2019

Changes in valuation assumptions can have a significant impact on the valuation of the embedded derivative liabilities. For example, all other things being equal, a decrease/increase in the Company’s stock price, probability of change of control, credit spread, term to maturity/conversion or stock price volatility decreases/increases the valuation of the liabilities, whereas a decrease/increase in risk adjusted yields or risk-free interest rates increases/decreases the valuation of the liabilities. The conversion price of certain of the Convertible Notes also include conversion price adjustment features and for, example, issuances of common stock by the Company at prices lower than the conversion price result in a reset of the conversion price of such notes, which increases the value of the embedded derivative liabilities. See Note 5, “Debt and Mezzanine Equity” for further details of conversion price adjustment features.

In June 2012, the Company entered into a loan agreement with Banco Pine S.A. (or "Banco Pine") under which Banco Pine provided the Company with a loan (or the "Banco Pine Bridge Loan") (see Note 5, “Debt and Mezzanine Equity”). At the time of the Banco Pine Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of R$22.0 million (approximately US$6.9 million based on the exchange rate as of March 31, 2017) of the Banco Pine Bridge Loan. The swap arrangement exchanges the principal and interest payments under the Banco Pine Bridge Loan for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. Changes in the fair value of the swap are recognized in “Gain (loss) from change in fair value of derivative instruments" in the condensed consolidated statements of operations are as follows (in thousands):

Type of Derivative Contract	Income Statement Classification	Three Months Ended March 31,
		2017		2016
Currency interest rate swap	Gain from change in fair value of derivative instruments	$	355	$	845

16

Derivative instruments measured at fair value as of March 31, 2017 and December 31, 2016, and their classification on the condensed consolidated balance sheets are as follows (in thousands):

	March 31, 2017		December 31, 2016
Fair market value of compound embedded derivative liabilities	$	2,150	$	4,135
Non-current fair value of  swap obligations		2,979		3,343
Total derivative liabilities	$	5,129	$	7,478

4. Balance Sheet Components

Inventories, net

Inventories, net are stated at the lower of cost or net realizable value and comprise of the following (in thousands):

	March 31,  2017		December 31,  2016
Raw materials	$	3,038	$	3,159
Work-in-process		1,343		1,848
Finished goods		2,696		1,206
Inventories, net	$	7,077	$	6,213

Property, Plant and Equipment, net

Property, plant and equipment, net is comprised of the following (in thousands):

	March 31, 2017			December 31, 2016
Machinery and equipment	$	84,853		$	82,688
Leasehold improvements		38,828			38,785
Computers and software		9,658			9,585
Buildings		4,834			4,699
Furniture and office equipment		2,350			2,333
Vehicles		136			164
Land		460			460
Construction in progress		2,465			2,216
		143,584			140,930
Less: accumulated depreciation and amortization		(90,539	)		(87,195	)
Property, plant and equipment, net	$	53,045		$	53,735

The Company's first, purpose-built, large-scale Biofene production plant in southeastern Brazil commenced operations in December 2012. This plant is located at Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Tonon Bioenergia S.A. (or “Tonon”) (formerly Paraíso Bioenergia) with which the Company has an agreement to purchase a certain number of tons of sugarcane per year, along with specified water and vapor volumes.

17

Property, plant and equipment, net includes $3.1 million and $3.1 million of machinery and equipment under capital leases as of March 31, 2017 and December 31, 2016, respectively. Accumulated amortization of assets under capital leases totaled $0.1 million and $0.6 million as of March 31, 2017 and December 31, 2016, respectively.

Depreciation and amortization expense, including amortization of assets under capital leases was $2.7 million and $2.9 million for the three months ended March 31, 2017 and 2016, respectively.

Other Assets (non-current)

Other assets are comprised of the following (in thousands):

	March 31, 2017		December 31, 2016
Recoverable taxes from Brazilian government entities	$	14,894	$	13,723
Deposits on property and equipment, including taxes		499		291
Other		1,401		1,450
Total other assets	$	16,794	$	15,464

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):

	March 31, 2017		December 31, 2016
Withholding tax related to conversion of related party notes	$	1,370	$	1,370
Professional services		5,358		6,876
SMA relocation accrual		3,746		3,641
Accrued interest		8,259		4,847
Tax-related liabilities		2,480		2,610
Accrued vacation		2,228		2,034
Payroll and related expenses		2,761		4,310
Deferred rent, current portion		1,111		1,111
Contractual obligations to contract manufacturers		381		—
Other		1,960		2,389
Total accrued and other current liabilities	$	29,654	$	29,188

18

5. Debt and Mezzanine Equity

Debt is comprised of the following (in thousands):

	March 31, 2017			December 31, 2016
Senior secured loan facility	$	27,844		$	27,658
BNDES credit facility		904			1,172
FINEP credit facility		637			696
Guanfu credit facility		19,858			19,564
Total credit facilities		49,243			49,090
Convertible notes		75,218			78,981
Related party convertible notes		43,335			42,754
Related party loan payable		30,554			29,691
Loans payable		22,588			26,527
Total debt		220,938			227,043
Less: current portion		(49,455	)		(59,155	)
Long-term debt	$	171,483		$	167,888
Mezzanine equity	$	5,000		$	5,000

Senior Secured Loan Facility

In March 2014, the Company entered into a Loan and Security Agreement (or the LSA) with Hercules Technology Growth Capital, Inc. (or Hercules) to make available to Amyris a collateralized loan facility (or the Senior Secured Loan Facility) in the aggregate principal amount of up to $25.0 million, which loan facility was fully drawn at the closing. The initial loan of $25.0 million under the Senior Secured Loan Facility accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 6.25% or 9.50%. The Company may repay the outstanding amounts under the Senior Secured Loan Facility before the maturity date (October 15, 2018) if it pays an additional fee of 1% of the outstanding loans. The Company was also required to pay a 1% facility charge at the closing of the Senior Secured Loan Facility, and is required to pay a 10% end of term charge with respect to the initial loan of $25.0 million. In connection with the entry into the LSA, Amyris agreed to certain customary representations and warranties and covenants, as well as certain covenants that were subsequently amended (as described below).

In June 2014, the Company and Hercules entered into a first amendment of the LSA. Pursuant to the first amendment, the parties agreed to extend the maturity date of the loans under the Senior Secured Loan Facility from May 31, 2015 to February 1, 2017 and remove (i) a requirement for the Company to pay a forbearance fee of $10.0 million in the event certain covenants were not satisfied, (ii) a covenant that the Company maintain positive cash flow commencing with the fiscal quarter beginning October 1, 2014, (iii) a covenant that, commencing with the fiscal quarter beginning July 1, 2014, the Company and its subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for the Company to file a registration statement on Form S-3 with the SEC by no later than June 30, 2014 and complete an equity financing of more than $50.0 million by no later than September 30, 2014. The Company further agreed to include a new covenant in the LSA requiring the Company to maintain unrestricted, unencumbered cash in defined U.S. bank accounts in an amount equal to at least 50% of the principal amount of the loans then outstanding under the Senior Secured Loan Facility (or the “Minimum Cash Covenant”) and borrow an additional $5.0 million. The additional $5.0 million borrowing under the Senior Secured Loan Facility was completed in June 2014, and accrues interest at a rate per annum equal to the greater of (i) the prime rate reported in the Wall Street Journal plus 5.25% and (ii) 8.5%.

19

In March 2015, the Company and Hercules entered into a second amendment of the LSA. Pursuant to the second amendment, the parties agreed to, among other things, establish an additional credit facility in the principal amount of up to $15.0 million, which would be available to be drawn by the Company through the earlier of March 31, 2016 or such time as the Company raised an aggregate of at least $20.0 million through the sale of new equity securities. Under the terms of the second amendment, the Company agreed to pay Hercules a 3.0% facility availability fee on April 1, 2015. The Company had the ability to cancel the additional facility at any time prior to June 30, 2015 at its own option, and the additional facility would terminate upon the Company securing a new equity financing of at least $20.0 million. If the facility was not canceled, and any outstanding borrowings were not repaid, before June 30, 2015, an additional 5.0% facility fee would become payable on June 30, 2015. The Company did not cancel the facility prior to June 30, 2015, and the 5.0% facility fee became payable as of June 30, 2015. The Company did not pay the additional facility fee and thereafter received a waiver from Hercules with respect thereto. The additional facility was cancelled undrawn upon the completion of the Company’s private offering of common stock and warrants in July 2015.

In November 2015, the Company and Hercules entered into a third amendment of the LSA. Pursuant to the third amendment, the Company borrowed $10,960,000 (or the Third Amendment Borrowed Amount) from Hercules on November 30, 2015. As of December 1, 2015, after the funding of the Third Amendment Borrowed Amount (and including repayment of $9.1 million of principal that had occurred prior to the third amendment), the aggregate principal amount outstanding under the Senior Secured Loan Facility was approximately $31.7 million. The Third Amendment Borrowed Amount accrues interest at a rate per annum equal to the greater of (i) 9.5% and (ii) the prime rate reported in the Wall Street Journal plus 6.25%,. Upon the earlier of the maturity date, prepayment in full or such obligations otherwise becoming due and payable, in addition to repaying the outstanding Third Amendment Borrowed Amount (and all other amounts owed under the Senior Secured Loan Facility, as amended), the Company is also required to pay an end-of-term charge of $767,200. Pursuant to the third amendment, the Company also paid Hercules fees of $1.0 million, $750,000 of which was owed in connection with the expired $15.0 million facility under the second amendment and $250,000 of which was related to the Third Amendment Borrowed Amount. Under the third amendment, the parties agreed that the Company would, commencing on December 1, 2015, be required to pay only the interest accruing on all outstanding loans under the Senior Secured Loan Facility until February 29, 2016. Commencing on March 1, 2016, the Company would have been required to begin repaying principal of all loans under the Senior Secured Loan Facility, in addition to the applicable interest. However, pursuant to the third amendment, the Company could, by achieving certain cash inflow targets in 2016, extend the interest-only period to December 1, 2016. Upon the issuance and sale by the Company of $20.0 million of unsecured promissory notes and warrants in a private placement in February 2016 for aggregate cash proceeds of $20.0 million, the Company satisfied the conditions for extending the interest-only period to May 31, 2016. On June 1, 2016, the Company commenced the repayment of outstanding principal under the Senior Secured Loan Facility. In June 2016, the Company was notified by Hercules that it had transferred and assigned its rights and obligations under the Senior Secured Loan Facility to Stegodon Corporation (Stegodon), an affiliate of Ginkgo Bioworks, Inc. (Ginkgo). On June 29, 2016, in connection with the execution by the Company and Ginkgo of an initial strategic partnership agreement, the Company received a deferment from Stegodon of all scheduled principal repayments under the Senior Secured Loan Facility, as well as a waiver of the Minimum Cash Covenant, through October 31, 2016. Refer to Note 8, “Significant Agreements” for additional details. On October 6, 2016, in connection with the execution by the Company and Ginkgo of a definitive collaboration agreement (or the Ginkgo Collaboration Agreement), the Company and Stegodon entered into a fourth amendment of the LSA, pursuant to which the parties agreed to (i) subject to the Company extending the maturity of certain of its other outstanding indebtedness (or the Extension Condition), extend the maturity date of the Senior Secured Loan Facility, (ii) make the Senior Secured Loan Facility interest-only until maturity, subject to the requirement that the Company apply certain monies received by it under the Ginkgo Collaboration Agreement to repay the amounts outstanding under the Senior Secured Loan Facility, up to a maximum amount of $1 million per month and (iii) waive the Minimum Cash Covenant until the maturity date of the Senior Secured Loan Facility. On January 11, 2017, the maturity date of the Senior Secured Loan Facility was extended to October 15, 2018 due to the Extension Condition being met as a result of the Fidelity Exchange (as defined below). See below under “Fidelity” for additional details. This modification of the Senior Secured Loan Facility was accounted for as a troubled debt restructuring with the future undiscounted cash flows being greater than the carrying value of the debt prior to extension. No gain was recorded and a new effective interest rate was established based on the carrying value of the debt and the revised cash flows. In December 2016, in connection with Stegodon granting certain waivers and releases under the LSA in connection with the Company’s formation of its Neossance joint venture with Nikko, as described in more detail in Note 7, “Joint Ventures and Noncontrolling Interest”, the Company agreed to pay to Stegodon (i) a fee of $425,000 on or prior to December 31, 2017 and (ii) a fee of $450,000 on or prior to the maturity date of the loans under the Senior Secured Loan Facility. Subsequently, in January 2017, in connection with Stegodon granting certain waivers of the debt and transfer covenants under the LSA, the Company, certain of its subsidiaries and Stegodon entered into a fifth amendment of the LSA. Pursuant to the fifth amendment, the Company agreed to apply additional monies received by the Company under the Ginkgo Collaboration Agreement towards repayment of the outstanding loans under the Senior Secured Loan Facility, up to a maximum amount of $3 million, to the extent any such monies are received by the Company.

20

As of March 31, 2017, $27.8 million was outstanding under the Senior Secured Loan Facility, net of discount and issuance costs of $0.7 million. The Senior Secured Loan Facility is collateralized by liens on the Company's assets, including on certain Company intellectual property. The Senior Secured Loan Facility includes customary events of default, including failure to pay amounts due, breaches of covenants and warranties, material adverse effect events, certain cross defaults and judgments, and insolvency. If an event of default occurs, Stegodon may require immediate repayment of all amounts outstanding under the Senior Secured Loan Facility.

BNDES Credit Facility

In December 2011, the Company entered into a credit facility with the Brazilian Development Bank (or “BNDES” and such credit facility is the “BNDES Credit Facility”) in the amount of R$22.4 million (approximately US$7.1 million based on the exchange rate as of March 31, 2017). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line was divided into an initial tranche of up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that would become available upon delivery of additional guarantees. The credit line was cancelled in 2013.

The principal of the loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment paid in January 2013 and the last due in December 2017. Interest was due initially on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments are due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per annum. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately $7.9 million based on the exchange rate as of March 31, 2017). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company was required to provide a bank guarantee equal to 10% of the total approved amount (R$22.4 million in total debt) available under the BNDES Credit Facility. For advances of the second tranche (above R$19.1 million), the Company is required to provide additional bank guarantees equal to 90% of each such advance, plus additional Company guarantees equal to at least 130% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, BNDES may terminate its commitments and declare immediately due all borrowings under the facility. As of March 31, 2017 and December 31, 2016, the Company had R$2.9 million (approximately US$0.9 million based on the exchange rate as of March 31, 2017) and R$3.8 million (approximately US$1.2 million based on the exchange rate as of December 31, 2016), respectively, in outstanding advances under the BNDES Credit Facility.

FINEP Credit Facility

In November 2010, the Company entered into a credit facility with Financiadora de Estudos e Projetos (or the “FINEP Credit Facility”). The FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (or the “FINEP Project”) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.0 million based on the exchange rate as of March 31, 2017), which is secured by a chattel mortgage on certain equipment of Amyris Brasil as well as by bank letters of guarantee. All available credit under this facility is fully drawn.

21

Interest on loans drawn under the FINEP Credit Facility is fixed at 5% per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the “TJLP”). If the TJLP at the time of default is greater than 6%, then the interest will be 5% plus a TJLP adjustment factor, otherwise the interest will be 11% per annum. In addition, a fine of up to 10% shall apply to the amount of any obligation in default. Interest on late balances will be 1% per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of March 31, 2017 and December 31, 2016, the total outstanding loan balance under this credit facility was R$2.0 million (approximately US$0.7 million based on the exchange rate as of March 31, 2017) and R$2.3 million (approximately US$0.7 million based on exchange rate as of December 31, 2016), respectively.

Guanfu Credit Facility

On October 26, 2016, the Company and Guanfu Holding Co., Ltd. (or, together with its subsidiaries, Guanfu), an existing commercial partner of the Company, entered into a credit agreement (or the Guanfu Credit Agreement) to make available to the Company an unsecured credit facility (or the Guanfu Credit Facility) with an aggregate principal amount of up to $25.0 million, which the Company could borrow from time to time in up to three closings. The effectiveness of the Guanfu Credit Agreement was subject to the parties obtaining certain required approvals, which occurred on November 16, 2016, and upon the effectiveness of the Guanfu Credit Agreement, the Company granted to Guanfu the global exclusive purchase right with respect to the Company products subject to the parties’ pre-existing commercial relationship. The initial funding of the Guanfu Credit Facility was scheduled to occur on December 1, 2016, subject to Guanfu’s right to extend such initial funding to a date no later than December 31, 2016. Guanfu exercised its right to extend the initial funding to December 31, 2016, and on such date the Company borrowed the full amount under the Guanfu Credit Facility and issued to Guanfu a note in the principal amount of $25.0 million (or the Guanfu Note). The Guanfu Note has a term of five years and will accrue interest at a rate of 10% per annum, payable quarterly beginning March 31, 2017. The Company may, at its option, repay the Guanfu Note before its maturity date, in whole or in part, at a price equal to 100% of the amount being repaid plus accrued and unpaid interest on such amount to the date of repayment.

Upon the occurrence of certain specified events of default under the Guanfu Credit Facility, the Company will grant to Guanfu an exclusive, royalty-free, global license to certain intellectual property useful in connection with Guanfu’s existing commercial relationship with the Company. In addition, in the event the Company fails to pay interest or principal under the Guanfu Note within ten days of when due, the Company will also be required, subject to applicable laws and regulations, to repay the outstanding principal amount under the Guanfu Note, together with accrued and unpaid interest, in the form of shares of the Company’s common stock at a per share price equal to 90% of the volume weighted average closing sale price of the Company’s common stock for the 90 trading days ending on and including the trading day that is two trading days preceding such default.

Convertible Notes

Fidelity

In February 2012, the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million pursuant to a securities purchase agreement between the Company and certain investment funds affiliated with FMR LLC (or the Fidelity Securities Purchase Agreement). The offering consisted of the sale of 3% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock, subject to proportional adjustment for adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions (or the Fidelity Notes). In October 2015, the Company issued and sold $57.6 million of convertible senior notes and used approximately $8.8 million of the proceeds therefrom to repurchase $9.7 million aggregate principal amount of outstanding Fidelity Notes. As of March 31, 2017, the Fidelity Notes were convertible into an aggregate of up to 2,165,898 shares of the Company's common stock. The holders of the Fidelity Notes have a right to require repayment of 101% of the principal amount of the Fidelity Notes in an acquisition of the Company, and the Fidelity Notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment. The Fidelity Securities Purchase Agreement and Fidelity Notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of corporate existence, and timely filing of SEC reports. The Fidelity Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults and breaches of the covenants in the Fidelity Securities Purchase Agreement and Fidelity Notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the Fidelity Notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the Fidelity Notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million in October 2013 (or the Temasek Bridge Note), holders of the Fidelity Notes waived compliance with the debt limitations outlined above as to the Temasek Bridge Note and the August 2013 Financing (as defined below). In consideration for such waiver, the Company granted to holders of the Fidelity Notes or their affiliates the right to purchase up to an aggregate of $7.6 million worth of convertible promissory notes in the first tranche of the August 2013 Financing (as defined below). See "Related Party Convertible Notes" in this Note 5, "Debt and Mezzanine Equity" for additional details. On December 28, 2016, the Company entered into an Exchange Agreement (or the Fidelity Exchange Agreement) with the holders of the outstanding Fidelity Notes. Pursuant to the Fidelity Exchange Agreement, the Company and the holders agreed to exchange (or the Fidelity Exchange) all outstanding Fidelity Notes, together with accrued and unpaid interest thereon, for approximately $19.1 million in aggregate principal amount of additional 2015 144A Notes (as defined below), representing an exchange ratio of approximately 1:1.25 (i.e., each $1.00 of Fidelity Notes was exchanged for approximately $1.25 of additional 2015 144A Notes), in a private placement exempt from registration under the Securities Act of 1933, as amended (or the Securities Act). The closing of the Fidelity Exchange occurred on January 11, 2017. At the closing, the Company issued approximately $19.1 million in aggregate principal amount of its 2015 144A Notes (or the Additional 2015 144A Notes) to the holders in exchange for the cancellation of the outstanding Fidelity Notes. The Company did not receive any cash proceeds from the Fidelity Exchange. The exchange has been accounted for as an extinguishment of the Fidelity Notes and issuance of the Additional 2015 144A Notes. A gain of approximately $0.1 million was recognized in the first quarter to recognize the deficit of the fair value of the Additional 2015 144A Notes (including related embedded derivatives) compared to the carrying value of the Fidelity Notes at the time of extinguishment. Pursuant to the Fidelity Exchange Agreement, upon the closing of the Fidelity Exchange, the Fidelity Securities Purchase Agreement terminated. In addition, upon the closing of the Fidelity Exchange, in accordance with the terms of the fourth amendment to the LSA, the maturity date of all outstanding loans under the LSA was extended to October 15, 2018. See above under “Senior Secured Loan Facility” for details regarding the fourth amendment to the LSA.

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2014 Rule 144A Convertible Note Offering

In May 2014, the Company entered into a Purchase Agreement with Morgan Stanley & Co. LLC, as the initial purchaser (or the Initial Purchaser), relating to the sale of $75.0 million aggregate in principal amount of 6.50% Convertible Senior Notes due 2019 (or the 2014 144A Notes) to the Initial Purchaser in a private placement, and for initial resale by the Initial Purchaser to certain qualified institutional buyers (or the 2014 144A Convertible Note Offering). In addition, the Company granted the Initial Purchaser an option to purchase up to an additional $15.0 million aggregate principal amount of 2014 144A Notes, which option expired unexercised according to its terms. Under the terms of the purchase agreement for the 2014 144A Notes, the Company agreed to customary indemnification of the Initial Purchaser against certain liabilities. The Notes were issued pursuant to an Indenture, dated as of May 29, 2014 (or the 2014 Indenture), between the Company and Wells Fargo Bank, National Association, as trustee. The net proceeds from the offering of the 2014 144A Notes were approximately $72.0 million after payment of the Initial Purchaser’s discounts and offering expenses. In addition, in connection with obtaining a waiver from Total of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by the Company for new notes issued in the 2014 144A Convertible Note Offering, the Company used approximately $9.7 million of the net proceeds to repay previously issued notes (representing the amount of 2014 144A Notes purchased by Total from the Initial Purchaser). Certain of the Company's affiliated entities purchased $24.7 million in aggregate principal amount of 2014 144A Notes from the Initial Purchaser (described further below under "Related Party Convertible Notes"). In October 2015, as discussed below, the Company issued $57.6 million of convertible senior notes and used approximately $18.3 million of the net proceeds therefrom to repurchase $22.9 million aggregate principal amount of outstanding 2014 144A Notes. The 2014 144A Notes bear interest at a rate of 6.50% per year, payable semiannually in arrears on May 15 and November 15 of each year, beginning November 15, 2014. The 2014 144A Notes mature on May 15, 2019, unless earlier converted or repurchased. The 2014 144A Notes are convertible into shares of the Company's common stock at any time prior to the close of business on the business day immediately preceding the maturity date of the 2014 144A Notes, at the initial conversion rate of 267.037 shares of Common Stock per $1,000 principal amount of 2014 144A Notes (subject to adjustment in certain circumstances). This represents an effective conversion price of approximately $3.74 per share of common stock. For any conversion on or after May 15, 2015, in the event that the last reported sale price of the Company’s common stock for 20 or more trading days (whether or not consecutive) in a period of 30 consecutive trading days ending within five trading days immediately prior to the date the Company receives a notice of conversion exceeds the then-applicable conversion price per share on each such trading day, the holders, in addition to the shares deliverable upon conversion, noteholders will be entitled to receive a cash payment equal to the present value of the remaining scheduled payments of interest that would have been made on the 2014 144A Notes being converted from the conversion date to the earlier of the date that is three years after the date the Company receives such notice of conversion and maturity (May 15, 2019), which will be computed using a discount rate of 0.75%. In the event of a fundamental change, as defined in the 2014 Indenture, holders of the 2014 144A Notes may require the Company to purchase all or a portion of the 2014 144A Notes at a price equal to 100% of the principal amount of the 2014 144A Notes, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. In addition, holders of the 2014 144A Notes who convert their 2014 144A Notes in connection with a make-whole fundamental change will, under certain circumstances, be entitled to an increase in the conversion rate of such notes. Refer to the “Exchange” and “Maturity Treatment Agreement” sections of this Note 5, "Debt and Mezzanine Equity", as well as Note 18, “Subsequent Events”, for details of the impact of the Maturity Treatment and Exchange Agreements on the 2014 144A Notes.

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2015 Rule 144A Convertible Note Offering

In October 2015, the Company entered into a purchase agreement with certain qualified institutional buyers relating to the sale of $57.6 million aggregate principal amount of 9.50% Convertible Senior Notes due 2019 (or the 2015 144A Notes) to the purchasers in a private placement (or the 2015 144A Offering). The 2015 144A Notes were issued pursuant to an Indenture, dated as of October 20, 2015 (or the 2015 Indenture), between the Company and Wells Fargo Bank, National Association, as trustee. The net proceeds from the offering of the 2015 144A Notes were approximately $54.4 million after payment of the offering expenses and placement agent fees. The Company used approximately $18.3 million of the net proceeds to repurchase $22.9 million aggregate principal amount of outstanding 2014 144A Notes and approximately $8.8 million to repurchase $9.7 million aggregate principal amount of outstanding Fidelity Notes, in each case held by purchasers of the 2015 144A Notes. The 2015 144A Notes bear interest at a rate of 9.50% per year, payable semiannually in arrears on April 15 and October 15 of each year, beginning April 15, 2016. Interest on the 2015 144A Notes is payable, at the Company’s option, entirely in cash or entirely in common stock. The Company elected to make the April 15, 2016 interest payment in shares of common stock, the October 15, 2016 interest payment in cash and the April 15, 2017 interest payment in shares of common stock. The 2015 144A Notes will mature on April 15, 2019 unless earlier converted or repurchased.

The 2015 144A Notes are convertible into shares of the Company's common stock at any time prior to the close of business on April 15, 2019. The 2015 144A Notes had an initial conversion rate of 443.6557 shares of Common Stock per $1,000 principal amount of 2015 144A Notes (subject to adjustment in certain circumstances). This represented an initial effective conversion price of approximately $2.25 per share of common stock. Following the issuance by the Company of warrants to purchase common stock in a private placement transaction in February 2016 and the issuance by the Company of convertible notes in May, September and October 2016, as described below, the conversion rate of the 2015 144A Notes was 446.8707 shares of Common Stock per $1,000 principal amount of 2015 144A Notes as of December 31, 2016. Furthermore, following the issuance by the Company of shares of convertible preferred stock and warrants to purchase common stock in May 2017, the conversion rate of the 2015 144A Notes is 711.1209 shares of Common Stock per $1,000 principal amount of 2015 144A Notes as of May 11, 2017, representing an effective conversion price of approximately $1.41 per share of common stock. For any conversion on or after November 27, 2015, in addition to the shares deliverable upon conversion, noteholders will be entitled to receive a payment equal to the present value of the remaining scheduled payments of interest that would have been made on the 2015 144A Notes being converted from the conversion date to the earlier of the date that is three years after the date the Company receives such notice of conversion and maturity (April 15, 2019), which will be computed using a discount rate of 0.75%. The Company may make such payment (the “Early Conversion Payment”) either in cash or in common stock, at its election, provided that it may only make such payment in common stock if such common stock is not subject to restrictions on transfer under the Securities Act by persons other than the Company’s affiliates. If the Company elects to pay an Early Conversion Payment in common stock, then the stock will be valued at 92.5% of the simple average of the daily volume-weighted average price per share for the 10 trading days ending on and including the trading day immediately preceding the conversion date. Through March 31, 2017, the Company has elected to make each Early Conversion Payment in shares of common stock. In the event of a fundamental change, as defined in the 2015 Indenture, holders of the 2015 144A Notes may require the Company to purchase all or a portion of the 2015 144A Notes at a price equal to 100% of the principal amount of the 2015 144A Notes, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. In addition, holders of the 2015 144A Notes who convert their 2015 144A Notes in connection with a make-whole fundamental change will, under certain circumstances, be entitled to an increase in the conversion rate. The issuance of shares of common stock upon conversion of the 2015 144A Notes, upon the Company’s election to pay interest on the 2015 144A Notes in shares of common stock and upon the Company’s election to pay the Early Conversion Payment in shares of common stock in an aggregate amount in excess of 38,415,626 shares of the Company’s common stock was subject to stockholder approval, which was obtained on May 17, 2016. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the 2015 144A Notes provide that, as long as the aggregate outstanding principal amount of the 2015 144A Notes exceeds $25.0 million, the Company's outstanding unsecured debt at any time cannot exceed $200.0 million and its secured debt cannot exceed the greater of $65.0 million or 30% of its consolidated total assets. In January 2017, the Company issued an additional $19.1 million in aggregate principal amount of 2015 144A Notes (or the Additional 2015 144A Notes) in exchange for the cancellation of $15.3 million in aggregate principal amount of outstanding Fidelity Notes. The Additional 2015 144A Notes were issued pursuant to the 2015 Indenture, as amended by the First Supplemental Indenture thereto, dated as of January 11, 2017, which amended the 2015 Indenture to clarify the Exchange Cap (as defined below) for the Additional 2015 144A Notes. Unless and until the Company obtains stockholder approval to issue a number of shares of the Company’s common Stock in excess of the Exchange Cap (as defined below), holders of the Additional 2015 144A Notes will not have the right to receive shares of the Company’s common stock upon conversion of the Additional 2015 144A Notes, and the Company will not have the right to issue shares of common stock as payment of interest on the Additional 2015 144A Notes, including any Early Conversion Payment, if the aggregate number of shares issued with respect to the Additional 2015 144A Notes (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed 19.99% of the number of shares of the Company’s common stock outstanding as of December 28, 2016 (or the Exchange Cap). The Company will pay cash in lieu of any shares that would otherwise be deliverable in excess of the Exchange Cap.

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May 2016 Convertible Note Offering

In May 2016, the Company entered into a securities purchase agreement (or the May 2016 Purchase Agreement) between the Company and a private investor relating to the sale of up to $15.0 million aggregate principal amount of convertible notes (or the May 2016 Convertible Notes) that are convertible into shares of the Company’s common stock at an initial conversion price of $1.90 per share. The conversion price will be subject to adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar transaction. The May 2016 Purchase Agreement includes customary representations, warranties and covenants by the Company. The May 2016 Purchase Agreement also provides the purchaser with a right of first refusal with respect to any variable rate transaction on the same terms and conditions as are offered to a third-party purchaser for as long as the purchaser holds any May 2016 Convertible Notes or shares of the Company’s common stock underlying the May 2016 Convertible Notes.

Pursuant to the May 2016 Purchase Agreement, the May 2016 Convertible Notes were to be issued and sold in two separate closings. The initial closing occurred on May 10, 2016. At the initial closing, the Company issued and sold a May 2016 Convertible Note in a principal amount of $10.0 million to the purchaser, resulting in net proceeds to the Company of approximately $9.9 million. The second closing was to occur on the first trading day following the completion of the first three installment periods under the May 2016 Convertible Notes and the satisfaction or waiver of certain other closing conditions, including certain equity conditions, such as that no Triggering Event (as defined below) had occurred. At the second closing, the Company was to issue and sell a May 2016 Convertible Note in a principal amount of $5.0 million to the purchaser, resulting in expected net proceeds to the Company of approximately $5.0 million. On September 2, 2016, in connection with the Company and the purchaser waiving certain conditions to the second closing under the May 2016 Purchase Agreement, the Company issued and sold an additional May 2016 Convertible Note in the principal amount of $3.0 million to the purchaser, for proceeds to the Company of approximately $3.0 million, and granted the purchaser the option to purchase a further May 2016 Convertible Note in the principal amount of $2.0 million (or the Remaining May 2016 Note), representing the remaining May 2016 Convertible Notes provided for in the May 2016 Purchase Agreement, on or before December 31, 2016. On October 13, 2016, the Company issued and sold the Remaining May 2016 Note to the purchaser for proceeds to the Company of $2.0 million.

The May 2016 Convertible Notes are general unsecured obligations of the Company. Unless earlier converted or redeemed, the May 2016 Convertible Notes will mature on the 18-month anniversary of their respective issuance, subject to the rights of the holders to extend the maturity date in certain circumstances.

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The May 2016 Convertible Notes are payable in monthly installments, in either cash at 118% of such installment amount or, at the Company’s option, subject to the satisfaction of certain equity conditions, shares of common stock at a discount to the then-current market price, subject to a price floor. In addition, in the event that the Company elects to pay all or any portion of a monthly installment in common stock, the holders of the May 2016 Convertible Notes shall have the right to require that the Company repay in common stock an additional amount of the May 2016 Convertible Notes not to exceed 50% of the cumulative sum of the aggregate amounts by which the dollar-weighted trading volume of the Company’s common stock for all trading days during the applicable installment period exceeds $200,000. The Company elected to make the May, June, July, August, September and October 2016 installment payments on the May 2016 Convertible Notes in shares of common stock. As of October 31, 2016, all May 2016 Convertible Notes had been repaid in full.

The May 2016 Convertible Notes contain customary terms and covenants, including certain events of default, including failure to pay amounts due, breaches of warranties, material adverse effect events, certain cross defaults and judgments, and insolvency, after which the holders may require the Company to redeem all or any portion of their May 2016 Convertible Notes in cash at a price equal to the greater of (i) 118% of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

In the event of a Fundamental Transaction (as defined in the May 2016 Convertible Notes), holders of the May 2016 Convertible Notes may require the Company to redeem all or any portion of their May 2016 Convertible Notes at a price equal to the greater of (i) 118% of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

The Company has the right to redeem the May 2016 Convertible Notes for cash, in whole, at any time, or in part, from time to time, at a redemption price equal to 118% of the principal amount of the May 2016 Convertible Notes being redeemed. In addition, if the volume-weighted average price of the Company’s common stock is (i) less than $1.00 for 30 consecutive trading days or (ii) less than $0.50 for five consecutive trading days (each, a “Triggering Event”) within four months of the issuance of any 2016 Convertible Notes, the Company will have the option to redeem such May 2016 Convertible Notes in whole for cash at a redemption price equal to 112% of the principal amount of such May 2016 Convertible Notes.

Notwithstanding the foregoing, the holders will not have the right to convert any portion of a May 2016 Convertible Note, and the Company may not issue shares of common stock upon conversion or repayment of the May 2016 Convertible Notes, if (a) the holder, together with its affiliates, would beneficially own in excess of 4.99% (or such other percentage as determined by the holder and notified to the Company in writing, not to exceed 9.99%, provided that any increase of such percentage will not be effective until 61 days after notice thereof) of the number of shares of the Company’s common stock outstanding immediately after giving effect to such conversion or payment, as applicable, or (b) the aggregate number of shares issued with respect to the May 2016 Convertible Notes after giving effect to such conversion or payment, as applicable, would exceed 19.99% of the number of shares of the Company’s common stock outstanding as of May 10, 2016. In the event that the Company is prohibited from issuing any shares of common stock in respect of the May 2016 Convertible Notes as a result of such limits, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess thereof.

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For as long as they hold the May 2016 Convertible Notes or shares of common stock issued under the May 2016 Convertible Notes, the holders may not sell any shares of the Company’s common stock at a price less than $1.05 per share; provided, that with respect to any shares of common stock issued under the May 2016 Convertible Notes at a price less than $1.00, the holders may sell such shares at a price not less than the price floor applicable to the installment period with respect to which such shares were issued.

The May 2016 Convertible Notes had been fully repaid as of March 31, 2017.

December 2016 Convertible Note Offering

On December 1, 2016, the Company entered into a securities purchase agreement (or the December 2016 Purchase Agreement) with a private investor relating to the sale of a convertible note in the original principal amount $10.0 million (or the December 2016 Convertible Note) that is convertible into shares of the Company’s common stock at an initial conversion price of $1.90 per share. The conversion price will be subject to adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar transaction. The December 2016 Purchase Agreement includes customary representations, warranties and covenants by the Company. The Purchase Agreement also provides the purchaser with a right of first refusal with respect to any variable rate transaction, subject to certain exceptions, on the same terms and conditions as are offered to a third-party purchaser for as long as the purchaser holds the December 2016 Convertible Note or shares of common stock underlying the December 2016 Convertible Note.

The December 2016 Convertible Note was issued on December 2, 2016, resulting in net proceeds to the Company of approximately $9.9 million.

The December 2016 Convertible Note is a general unsecured obligation of the Company. Unless earlier converted or redeemed, the December 2016 Convertible Note will mature on May 1, 2018, subject to the rights of the holder to extend the maturity date in certain circumstances.

The December 2016 Convertible Note is payable in monthly installments, beginning January 1, 2017, in either cash at 118% of such installment amount or, at the Company’s option, subject to the satisfaction of certain equity conditions, shares of common stock at a discount to the then-current market price, subject to a price floor. In addition, between December 1, 2016 and December 31, 2016, or in the event that the Company elects to pay all or any portion of a monthly installment in common stock, the holder of the December 2016 Convertible Note shall have the right to require that the Company repay in common stock an additional amount of the December 2016 Convertible Note not to exceed 50% of the cumulative sum of the aggregate amounts by which the dollar-weighted trading volume of the Company’s common stock for all trading days during the applicable period exceeds $200,000.

The December 2016 Convertible Note contains customary terms and covenants, including certain events of default, including failure to pay amounts due, breaches of warranties, material adverse effect events, certain cross defaults and judgments, and insolvency, after which the holders may require the Company to redeem all or any portion of their December 2016 Convertible Note in cash at a price equal to the greater of (i) 118% of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

In the event of a Fundamental Transaction (as defined in the December 2016 Convertible Note), the holder of the December 2016 Convertible Note may require the Company to purchase all or any portion of its December 2016 Convertible Note at a price equal to the greater of (i) 118% of the amount being redeemed and (ii) the intrinsic value of the shares of Common Stock issuable upon an installment payment of the amount being redeemed in shares.

The Company has the right to redeem the December 2016 Convertible Note for cash, in whole, at any time, or in part, from time to time, at a redemption price equal to 118% of the principal amount of the December 2016 Convertible Note to be redeemed.

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Notwithstanding the foregoing, the holder will not have the right to convert any portion of the December 2016 Convertible Note, and the Company will not have the option to pay any amount in shares of common stock, if (a) the holder, together with its affiliates, would beneficially own in excess of 4.99% (or such other percentage as determined by the holder and notified to the Company in writing, not to exceed 9.99%, provided that any increase of such percentage will not be effective until 61 days after notice thereof) of the number of shares of the Company’s common stock outstanding immediately after giving effect to such conversion or payment, as applicable, or (b) the aggregate number of shares issued with respect to the December 2016 Convertible Note (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed 19.99% of the number of shares of the Company’s common stock outstanding as of December 1, 2016. In the event that the Company is prohibited from issuing any shares of common stock in respect of the December 2016 Convertible Note as a result of such limits, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess thereof.

For as long as it holds the December 2016 Convertible Note or shares of common stock issued under the December 2016 Convertible Note, the holder may not sell any shares of the Company’s common stock at a price less than $1.05 per share; provided, that with respect to any shares of common stock issued under the December 2016 Convertible Note at a price less than $1.00, the holder may sell such shares at a price not less than the price floor applicable to the period with respect to which such shares were issued. The embedded derivative features in this instrument are separately accounted for and the fair value of such features was not material at March 31, 2017 and December 31, 2016.

In May 2017, the Company agreed to amend the December 2016 Convertible Note, as described in more detail in Note 18, “Subsequent Events.”

See Note 18, “Subsequent Events” for details regarding financing transactions completed subsequent to March 31, 2017.

Related Party Convertible Notes

Total R&D Convertible Notes

In July 2012 and December 2013, the Company entered into a series of agreements (or the Total Fuel Agreements) with Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, and referred to as Total) to establish a research and development program (or the Program) and form a joint venture (or the Fuels JV) with Total to produce and commercialize farnesene- or farnesane-based diesel and jet fuels, and established a convertible debt structure for the collaboration funding from Total.

The purchase agreement for the notes related to the funding from Total (or the Total Purchase Agreement) provided for the sale of an aggregate of $105.0 million in 1.5% Senior Unsecured Convertible Notes due March 2017 (or the Unsecured R&D Notes) as follows:

• As part of an initial closing under the purchase agreement (which was completed in two installments), (i) on July 30, 2012, the Company sold an Unsecured R&D Note with a principal amount of $38.3 million, including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012, the Company sold another Unsecured R&D Note for $15.0 million in new funds from Total. These Unsecured R&D Notes had an initial conversion price of $7.0682 per share.

• At a second closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional Unsecured R&D Notes for an aggregate of $30.0 million in new funds from Total ($10.0 million in June 2013 and $20.0 million in July 2013). These Unsecured R&D Notes had an initial conversion price of $3.08 per share, as described below.

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• At a third closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional Unsecured R&D Notes for an aggregate of $21.7 million in new funds from Total ($10.85 million in July 2014 and $10.85 million in January 2015). These Unsecured R&D Notes had an initial conversion price of $4.11 per share, as described below.

In March 2013, the Company entered into a letter agreement with Total (or the March 2013 Letter Agreement) under which Total agreed to waive its right to cease its participation in the parties' fuels collaboration at the July 2013 decision point and committed to proceed with the July 2013 funding tranche of $30.0 million (subject to the Company's satisfaction of the relevant closing conditions for such funding in the Total Purchase Agreement). As consideration for this waiver and commitment, the Company agreed to:

• Reduce the conversion price for the $30.0 million in principal amount of Unsecured R&D Notes to be issued in connection with the second closing of the Unsecured R&D Notes (as described above) from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the March 2013 Letter Agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price would not be reduced by more than the maximum possible amount permitted under the rules of The NASDAQ Stock Market (or NASDAQ) such that the new conversion price would require the Company to obtain stockholder consent; and

• Grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the second closing.

In June 2013, the Company sold and issued $10.0 million in principal amount of Unsecured R&D Notes to Total pursuant to the second closing of the Unsecured R&D Notes as discussed above. In accordance with the March 2013 Letter Agreement, this Unsecured R&D Note had an initial conversion price equal to $3.08 per share of the Company's common stock.

In July 2013, the Company sold and issued $20.0 million in principal amount of Unsecured R&D Notes to Total pursuant to the Total second closing of the Unsecured R&D Notes as discussed above. This purchase and sale completed Total's commitment to purchase $30.0 million of the Unsecured R&D Notes in the second closing by July 2013. In accordance with the March 2013 Letter Agreement, this Unsecured R&D Note has an initial conversion price equal to $3.08 per share of the Company's common stock.

In December 2013, in connection with the Company's entry into a Shareholders Agreement dated December 2, 2013 and License Agreement dated December 2, 2013 (or, collectively, the JV Documents) with Total and Total Amyris BioSolutions B.V. (or TAB) relating to the establishment of TAB (see Note 7, "Joint Ventures and Noncontrolling Interest"), the Company (i) exchanged the $69.0 million of the then-outstanding Unsecured R&D Notes issued pursuant to the Total Purchase Agreement for replacement 1.5% Senior Secured Convertible Notes due March 2017 (or the Secured R&D Notes, and together with the Unsecured R&D Notes, the R&D Notes), in principal amounts equal to the principal amount of each cancelled note and with substantially similar terms except that such replacement notes were secured, (ii) in connection therewith, granted to Total a security interest in and lien on all of the Company’s rights, title and interest in and to the Company’s shares in the capital of TAB as security for such Secured R&D Notes and (iii) agreed that any securities to be purchased and sold at the third closing under the Total Purchase Agreement by Total would be Secured R&D Notes instead of Unsecured R&D Notes. As a consequence of executing the JV Documents and forming TAB, the security interest in all of the Company's intellectual property, granted by the Company in favor of Total, Maxwell (Mauritius) Pte Ltd (or Temasek), and certain entities affiliated with FMR LLC (or the Fidelity Entities) pursuant to the Restated Intellectual Property Security Agreement dated as of October 16, 2013, was automatically terminated effective as of December 2, 2013 upon Total’s and the Company’s joint written notice to Temasek and the Fidelity Entities.

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In April 2014, the Company and Total entered into a letter agreement dated as of March 29, 2014 (or the March 2014 Total Letter Agreement) to amend the Amended and Restated Master Framework Agreement entered into as of December 2, 2013 (included as part of JV Documents) and the Total Purchase Agreement. Under the March 2014 Total Letter Agreement, the Company agreed to (i) amend the conversion price of the Secured R&D Notes to be issued in the third closing under the Total Purchase Agreement from $7.0682 per share to $4.11 per share subject to stockholder approval at the Company's 2014 annual meeting (which was obtained in May 2014), (ii) extend the period during which Total may exchange for other Company securities Secured R&D Notes issued under the Total Fuel Agreements from June 30, 2014 to the later of December 31, 2014 and the date on which the Company shall have raised $75.0 million of equity and/or convertible debt financing (excluding any convertible promissory notes issued pursuant to the Total Purchase Agreement), (iii) eliminate the Company’s ability to qualify, in a disclosure letter to Total, certain of the representations and warranties that the Company must make at the closing of any third closing sale, and (iv) beginning on March 31, 2014, provide Total with monthly reporting on the Company’s cash, cash equivalents and short-term investments. In consideration of these agreements, Total agreed to waive its right not to consummate the third closing under the Total Purchase Agreement if it had decided not to proceed with the collaboration and had made a "No-Go" decision with respect thereto.

In July 2014, the Company sold and issued a Secured R&D Note to Total with a principal amount of $10.85 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement. This purchase and sale constituted the initial installment of the $21.7 million third closing described above. In accordance with the March 2014 Total Letter Agreement, this Secured R&D Note had an initial conversion price equal to $4.11 per share of the Company's common stock.

In January 2015, the Company sold and issued a Secured R&D Note to Total with a principal amount of $10.85 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement. This purchase and sale constituted the final installment of the $21.7 million third closing described above. In accordance with the March 2014 Total Letter Agreement, this Secured R&D Note had an initial conversion price equal to $4.11 per share of the Company's common stock.

In July 2015, Total exchanged all but $5.0 million of Secured R&D Notes then held by Total, such cancelled notes having an aggregate principal amount of $70 million, in exchange for approximately 30.4 million shares of the Company’s common stock in connection with the Exchange. Refer to the “Exchange” section of this Note 5, "Debt and Mezzanine Equity", for additional details of the impact of the Exchange on the R&D Notes.

In March 2016, in connection with the restructuring of TAB (see Note 7, "Joint Ventures and Noncontrolling Interest"), the Company sold to Total one half of the Company’s ownership stake in TAB (giving Total an aggregate ownership stake of 75% of TAB and giving the Company an aggregate ownership stake of 25% of TAB) in exchange for Total cancelling (i) approximately $1.3 million of Secured R&D Notes, plus all paid-in-kind and accrued interest under all outstanding Secured R&D Notes ($2.8 million, including all such interest that was outstanding as of July 29, 2015) and (ii) a note in the principal amount of Euro 50,000, plus accrued interest, issued to Total in connection with the original capitalization of TAB. To satisfy its purchase obligation above, Total surrendered to the Company the remaining Secured R&D Note of approximately $5.0 million in principal amount, and the Company executed and delivered to Total a new Unsecured R&D Note in the principal amount of $3.7 million. The disposal of the 25% ownership stake in the Fuels JV resulted in a gain to the Company of $4.2 million, which was recognized as a capital contribution from Total within equity.

As of March 31, 2017 and December 31, 2016, $3.7 million and $3.7 million, respectively, of R&D Notes were outstanding. In February 2017, the Company and Total agreed to extend the maturity of the outstanding R&D Notes from March 1, 2017 to May 15, 2017. The R&D Notes bear interest of 1.5% per annum (with a default rate of 2.5%), accruing from the date of issuance and payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes, as described below.

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The R&D Notes become convertible into the Company's common stock (i) within 10 trading days prior to maturity, (ii) on a change of control of the Company, and (iii) on a default by the Company. The conversion price of the R&D Notes are subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the R&D Notes in the event of a change of control of the Company and the R&D Notes provide for payment of unpaid future interest through the maturity date on conversion following such a change of control, subject to a cap, if Total does not require such repayment. The Total Purchase Agreement and R&D Notes include covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The R&D Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the Total Purchase Agreement and R&D Notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, with exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the R&D Notes provide that the Company's total outstanding debt at any time may not exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt may not exceed the greater of $125.0 million or 30% of its consolidated total assets.

August 2013 Financing Convertible Notes and Temasek Bridge Note

In August 2013, the Company entered into a Securities Purchase Agreement (or the August 2013 SPA) with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements (or the August 2013 Financing), with such notes to be sold and issued over a period of up to 24 months from the date of signing. The August 2013 SPA provided for the August 2013 Financing to be divided into two tranches (the first tranche for $42.6 million and the second tranche for $30.4 million), each with differing closing conditions. Of the total possible purchase price in the financing, $25.0 million was to be paid in the form of cash by Temasek ($25.0 million in the second tranche), $35.0 million was to be paid by the exchange and cancellation of the Temasek Bridge Note, as described below, and $13.0 million was to be paid by the exchange and cancellation of outstanding R&D Notes held by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche). The August 2013 SPA included requirements that the Company meet certain production milestones before the second tranche would become available, obtain stockholder approval prior to completing any closing of the transaction, and issue a warrant to Temasek to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share, initially exercisable only if Total converted R&D Notes previously issued to Total in the second closing under the Total Purchase Agreement. In September 2013, prior to the initial closing of the August 2013 Financing, the Company's stockholders approved the issuance in a private placement of up to $110.0 million aggregate principal amount of senior convertible promissory notes, the issuance of a warrant to purchase 1,000,000 shares of the Company's common stock and the issuance of the common stock issuable upon conversion or exercise of such notes and warrant, which approval included the transactions contemplated by the August 2013 Financing.

In October 2013, the Company sold and issued a senior secured promissory note to Temasek (or the Temasek Bridge Note) in exchange for a bridge loan of $35.0 million. The Temasek Bridge Note was due on February 2, 2014 and accrued interest at a rate of 5.5% quarterly from the October 4, 2013 date of issuance. The Temasek Bridge Note was cancelled on October 16, 2013 as payment for Temasek’s purchase of Tranche I Notes in the first tranche of the August 2013 Financing, as further described below.

In October 2013, the Company amended the August 2013 SPA to include the investment by the Fidelity Entities in the first tranche of the August 2013 Financing of $7.6 million, and to proportionally increase the amount of first tranche notes acquired by exchange and cancellation of outstanding R&D Notes held by Total in connection with its exercise of pro rata rights up to $9.2 million in the first tranche. Also in October 2013, the Company completed the closing of the first tranche of senior convertible notes provided for in the August 2013 Financing (or the Tranche I Notes), issuing a total of $51.8 million in Tranche I Notes for cash proceeds of $7.6 million and exchange and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from the exchange and cancellation of the Temasek Bridge Note and the remaining $9.2 million from the exchange and cancellation of an outstanding R&D Note held by Total. As a result of the exchange and cancellation of the $35.0 million Temasek Bridge Note and the $9.2 million R&D Note held by Total for the Tranche I Notes, the Company recorded a loss from extinguishment of debt of $19.9 million. The Tranche I Notes are due sixty months from the date of issuance and were initially convertible into the Company’s common stock at a conversion price equal to $2.44 per share, which represents a 15% discount to the trailing 60-day weighted-average closing price of the common stock on The NASDAQ Stock Market (or NASDAQ) through August 7, 2013, subject to certain adjustments as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues on the Tranche I Notes at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or of 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six months or may elect to pay interest in cash. Through March 31, 2017, the Company has elected to pay interest on the Tranche I Notes in kind. The Tranche I Notes may be prepaid by the Company on the 30-month anniversary of the issuance date, and thereafter every six months at the date of payment of the semi-annual coupon.

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In December 2013, the Company further amended the August 2013 SPA to sell $3.0 million of senior convertible notes under the second tranche of the August 2013 Financing (or the Tranche II Notes) to funds affiliated with Wolverine Asset Management, LLC (or Wolverine) and the Company elected to call $25.0 million in additional funds from Temasek pursuant to its previous commitment to purchase such amount of Tranche II Notes. In January 2014, the Company sold and issued, for face value, approximately $34.0 million of Tranche II Notes in the second tranche of the August 2013 Financing. At the closing, Temasek purchased $25.0 million of the Tranche II Notes and funds affiliated with Wolverine purchased $3.0 million of the Tranche II Notes, each for cash. Total purchased approximately $6.0 million of the Tranche II Notes through exchange and cancellation of the same amount of principal of previously outstanding R&D Notes held by Total. As a result of the exchange and cancellation of the $6.0 million R&D Note held by Total for the Tranche II Notes, the Company recorded a loss from extinguishment of debt of $9.4 million. The Tranche II Notes will be due sixty months from the date of issuance and were initially convertible into shares of common stock at a conversion price equal to $2.87 per share, which represents the trailing 60-day weighted-average closing price of the common stock on NASDAQ through August 7, 2013, subject to certain adjustments as described below. The Tranche II Notes are convertible at the option of the holder (i) at any time after the 12 month anniversary of the issue date, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. Each Tranche II Note will accrue interest from the date of issuance until the earlier of the date that such Tranche II Note is converted into common stock or repaid in full. Interest will accrue on the Tranche II Notes at a rate per annum equal to 10%, compounded annually (with graduated interest rates of 13% applicable to the first 180 days and 16% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or of 12% for all other defaults). Interest for the first 36 months shall be payable in kind and added to principal every year following the issue date and thereafter, the Company may continue to pay interest in kind by adding to the principal on every year anniversary of the issue date or may elect to pay interest in cash.

The conversion prices of the Tranche I Notes and Tranche II Notes are subject to adjustment (i) according to proportional adjustments to outstanding common stock of the Company in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the Company in connection with future financing transactions in excess of its pro rata amount. The holders have a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment. The August 2013 SPA, Tranche I Notes and Tranche II Notes include covenants regarding payment of interest, maintenance of the Company’s listing status, limitations on debt and on certain liens, maintenance of corporate existence, and filing of SEC reports. The Tranche I Notes and Tranche II Notes include standard events of default including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the August 2013 SPA, Tranche I Notes and Tranche II Notes, after which such notes may be due and payable immediately, as well as associated default interest rates as set forth above.

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In July 2015, Temasek exchanged all of the Tranche I and Tranche II Notes then held by Temasek, such notes having an aggregate principal amount of approximately $71.0 million, in exchange for approximately 30.86 million shares of the Company’s common stock in connection with the Exchange. Refer to the “Exchange” section of this Note 5, "Debt and Mezzanine Equity", for additional details of the impact of the Exchange on the Tranche I Notes and Tranche II Notes.

The conversion price of the Tranche I Notes and Tranche II Notes was reduced to approximately $1.42 per share upon the completion of a private placement of common stock and warrants to purchase common stock in July 2015, as described below. Following the issuance by the Company of warrants to purchase common stock in a private placement transaction in February 2016, the conversion price of the Tranche I Notes and Tranche II Notes was further adjusted to $1.40 per share, and following the sale by the Company of shares of common stock to the Bill & Melinda Gates Foundation in May 2016, as described below, the conversion price of the Tranche I Notes and Tranche II Notes was further adjusted to $1.14 per share. Furthermore, following the issuance by the Company of shares of convertible preferred stock and warrants to purchase common stock in May 2017, as described in Note 18, “Subsequent Events,” the conversion price of the Tranche I Notes and Tranche II Notes was further adjusted to approximately $0.50 per share.

As of March 31, 2017 and December 31, 2016, the related party convertible notes outstanding under the Tranche I Notes and Tranche II Notes were $22.1 million and $21.8 million, respectively, net of debt discount of $0.0 million and $0.0 million, respectively. Refer to the “Exchange” and “Maturity Treatment Agreement” sections of this Note 5, "Debt and Mezzanine Equity", for details of the impact of the Maturity Treatment and Exchange agreements on the Tranche I and II Notes.

2014 144A Notes Sold to Related Parties

As of March 31, 2017 and December 31, 2016, the related party convertible notes outstanding under the 2014 Rule 144A Convertible Note Offering were $17.6 million and $17.3 million, respectively, net of discount and issuance costs of $7.1 million and $7.4 million, respectively.

As of March 31, 2017 and December 31, 2016, the total related party convertible notes outstanding were $43.3 million and $42.8 million, respectively, net of discount and issuance costs of $5.6 million and $5.4 million, respectively.

Loans Payable

In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods Agreement (together, the "July 2012 Bank Agreements") with each of Nossa Caixa Desenvolvimento (or “Nossa Caixa”) and Banco Pine S.A. (or “Banco Pine”). Under the July 2012 Bank Agreements, the Company pledged certain farnesene production assets as collateral for the loans of R$52.0 million. The Company's total acquisition cost for such pledged assets was approximately R$68.0 million (approximately US$21.5 million based on the exchange rate as of March 31, 2017). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. Under the July 2012 Bank Agreements, the Company could borrow an aggregate of R$52.0 million (approximately US$16.4 million based on the exchange rate as of March 31, 2017) as financing for capital expenditures relating to the Company's manufacturing facility located in Brotas, Brazil. Specifically, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million. The funds for the loans are provided by BNDES, but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at the Company's manufacturing facility in Brotas, Brazil for more than 30 days, except during the sugarcane off-season. For the first two years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis. Since August 15, 2014, the Company has been required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. As of March 31, 2017 and December 31, 2016, a principal amount of $10.9 million and $11.1 million, respectively, was outstanding under these loan agreements.

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Exchange (Debt Conversion - Related Party Transaction)

On July 29, 2015, the Company closed the "Exchange" pursuant to that certain Exchange Agreement, dated as of July 26, 2015 (or the Exchange Agreement), among the Company, Temasek and Total.

Under the Exchange Agreement, at the closing of the Exchange, Temasek exchanged $71.0 million in principal amount of outstanding Tranche I and Tranche II Notes (including paid-in-kind and accrued interest through July 29, 2015) and Total exchanged $70.0 million in principal amount of outstanding R&D Notes for shares of the Company’s common stock. The exchange price was $2.30 per share (or the Exchange Price) and was paid by the exchange and cancellation of such outstanding convertible promissory notes, and Temasek and Total received 30,860,633 and 30,434,782 shares of the Company’s common stock, respectively, in the Exchange. As a result of the Exchange, accretion of debt discount was accelerated based on the Company’s estimate of the expected conversion date, resulting in an additional interest expense of $39.2 million for the year ended December 31, 2015.

Under the Exchange Agreement, Total also received the following warrants, each with a five-year term, at the closing of the Exchange:

• A warrant to purchase 18,924,191 shares of the Company’s Common Stock (or the Total Funding Warrant).

• A warrant to purchase 2,000,000 shares of the Company’s common stock that would only be exercisable if the Company failed, as of March 1, 2017, to achieve a target cost per liter to manufacture farnesene (or the Total R&D Warrant). The Total Funding Warrant and the Total R&D Warrant are collectively referred to as the “Total Warrants.”

Additionally, under the Exchange Agreement, Temasek received the following warrants:

• A warrant to purchase 14,677,861 shares of the Company’s common stock (or the Temasek Exchange Warrant).

• A warrant exercisable for that number of shares of the Company’s common stock equal to (1) (A) the number of shares for which Total exercises the Total Funding Warrant plus (B) the number of additional shares for which the certain convertible notes remaining outstanding following the completion of the Exchange may become exercisable as a result of a reduction in the conversion price of such remaining notes as of a result of and/or subsequent to the date of the Exchange plus (C) that number of additional shares in excess of 2,000,000, if any, for which the Total R&D Warrant becomes exercisable multiplied by a fraction equal to 30.6% divided by 69.4% plus (2) (A) the number of any additional shares for which certain other outstanding convertible promissory notes may become exercisable as a result of a reduction to the conversion price of such notes multiplied by (B) a fraction equal to 13.3% divided by 86.7% (or the Temasek Funding Warrant).

• A warrant exercisable for that number of shares of the Company’s common stock equal to 880,339 multiplied by a fraction equal to the number of shares for which Total exercises the Total R&D Warrant divided by 2,000,000 (or the Temasek R&D Warrant). If Total is entitled to, and does, exercise the Total R&D Warrant in full, the Temasek R&D Warrant would be exercisable for 880,339 shares.

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The Temasek Exchange Warrant, the Temasek Funding Warrant and the Temasek R&D Warrant each have ten-year terms and are referred to herein as the “Temasek Warrants” and, the Temasek Warrants and Total Warrants are hereinafter collectively referred to as the “Exchange Warrants”. All of the Exchange Warrants have an exercise price of $0.01 per share.

In addition to the grant of the Exchange Warrants, a warrant issued by the Company to Temasek in October 2013 in conjunction with a prior convertible debt financing (or the 2013 Warrant) became exercisable in full upon the completion of the Exchange. There were 1,000,000 shares underlying the 2013 Warrant, with an exercise price of $0.01 per share.

The exercisability of all of the Exchange Warrants was subject to stockholder approval, which was obtained on September 17, 2015.

In February and May 2016, as a result of adjustments to the conversion price of the Tranche Notes discussed above, the Temasek Funding Warrant became exercisable for an additional 127,194 and 2,335,342 shares of common stock, respectively. Following the issuance by the Company of shares of convertible preferred stock and warrants to purchase common stock in May 2017, as described in Note 18, “Subsequent Events,” and a corresponding adjustment to the conversion price of the Tranche I Notes and Tranche II Notes, as described above, the Temasek Funding Warrant became exercisable for an additional 16,886,320 shares of common stock.

As of March 1, 2017, the Company had not achieved the target cost per liter to manufacture farnesene provided in the Total R&D Warrant, and as a result, on March 1, 2017 the Total R&D Warrant became exercisable in accordance with its terms. In addition, upon any exercise by Total of the Total R&D Warrant, the Temasek R&D Warrant will become exercisable for that number of shares of the Company's common stock equal to 880,339 multiplied by a fraction equal to the number of shares for which Total exercises the Total R&D Warrant divided by 2,000,000.

As of March 31, 2017, the Total Funding Warrant, the Temasek Exchange Warrant, and the 2013 Warrant had been fully exercised and Temasek had exercised the Temasek Funding Warrant with respect to 12,700,244 shares of common stock. Neither the Total R&D Warrant nor the Temasek R&D Warrant had been exercised as of March 31, 2017. Warrants to purchase 2,462,536 shares of common stock under the Temasek Funding Warrant were unexercised as of March 31, 2017

Maturity Treatment Agreement

At the closing of the Exchange, the Company, Total and Temasek also entered into a Maturity Treatment Agreement, dated as of July 29, 2015, pursuant to which Total and Temasek agreed to convert any Tranche I Notes, Tranche II Notes or 2014 144A Notes held by them that were not cancelled in the Exchange (or the Remaining Notes) into shares of the Company’s common stock in accordance with the terms of such Remaining Notes upon maturity, provided that certain events of default had not occurred with respect to the applicable Remaining Notes prior to such maturity. As of immediately following the closing of the Exchange, Temasek held $10.0 million in aggregate principal amount of Remaining Notes (consisting of 2014 144A Notes) and Total held approximately $25.0 million in aggregate principal amount of Remaining Notes (consisting of $9.7 million of 2014 144A Notes and $15.3 million of Tranche I and II Notes). See Note 18, “Subsequent Events” for additional details regarding the Remaining Notes.

February 2016 Private Placement - Related Party Transaction

On February 12, 2016, the Company entered into a Note and Warrant Purchase Agreement (or the February 2016 Purchase Agreement) with the purchasers named therein for the sale of $18.0 million in aggregate principal amount of unsecured promissory notes (or the February 2016 Notes) to the purchasers, as well as warrants to purchase 2,571,428 shares of the Company’s common stock at an exercise price of $0.01 per share, representing aggregate proceeds to the Company of $18 million (or the Initial Sale). On February 15, 2016, an additional purchaser joined the February 2016 Purchase Agreement and purchased $2.0 million in aggregate principal amount of the February 2016 Notes, as well as warrants to purchase 285,714 shares of the Company’s common stock at an exercise price of $0.01 per share, representing aggregate proceeds to the Company of $2 million (or the Subsequent Sale and together with the Initial Sale, the February 2016 Private Placement). The February 2016 Notes and the warrants were issued in a private placement exempt from registration under the Securities Act. The purchasers are existing stockholders of the Company and affiliated with certain members of the Company’s Board of Directors: Foris Ventures, LLC (or Foris, an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder), which purchased $16.0 million aggregate principal amount of the February 2016 Notes and warrants to purchase 2,285,714 shares of the Company’s common stock; Naxyris S.A. (an investment vehicle owned by Naxos Capital Partners SCA Sicar; director Carole Piwnica is Director of NAXOS UK, which is affiliated with Naxos Capital Partners SCA Sicar), which purchased $2.0 million aggregate principal amount of the February 2016 Notes and warrants to purchase 285,714 shares of the Company’s common stock; and Biolding Investment SA, a fund affiliated with director HH Sheikh Abdullah bin Khalifa Al Thani, which purchased $2.0 million aggregate principal amount of the February 2016 Notes and warrants to purchase 285,714 shares of the Company’s common stock. The Initial Sale closed on February 12, 2016, and the Subsequent Sale closed on February 15, 2016.

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The February 2016 Notes are unsecured obligations of the Company and are subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to a Subordination Agreement, dated as of February 12, 2016, by and among the Company, the purchasers and the administrative agent under the Senior Secured Loan Facility. Interest will accrue on the February 2016 Notes from and including, with respect to the Initial Sale, February 12, 2016, and with respect to the Subsequent Sale, February 15, 2016, at a rate of 13.50% per annum and is payable on May 15, 2017, the maturity date of the February 2016 Notes, unless the February 2016 Notes are prepaid in accordance with their terms prior to such date. The February 2016 Purchase Agreement and the February 2016 Notes contain customary terms, provisions, representations and warranties, including certain events of default after which the February 2016 Notes may be due and payable immediately, as set forth in the February 2016 Notes.

The exercisability of the warrants issued in the February 2016 Private Placement, which each have a term of five years, was subject to stockholder approval, which was obtained on May 17, 2016. As of March 31, 2017, the carrying amount of the February 2016 Notes was $19.6 million.

In May 2017, in connection with the issuance and sale of convertible preferred stock and warrants to purchase common stock, as described in more detail below in Note 18, “Subsequent Events,” $18.0 million of the February 2016 Notes were exchanged for shares of convertible preferred stock and warrants to purchase common stock in the offering.

June 2016 Private Placement - Related Party Transaction

On June 24, 2016, the Company entered into a Note Purchase Agreement (or the June 2016 Purchase Agreement) with Foris for the sale of $5.0 million in aggregate principal amount of secured promissory notes (or the June 2016 Notes) to Foris in exchange for aggregate proceeds to the Company of $5.0 million (or the June 2016 Private Placement). The June 2016 Notes were issued in a private placement exempt from registration under the Securities Act. The June 2016 Private Placement closed on June 24, 2016.

The June 2016 Notes are collateralized by a second priority lien on the assets securing the Company’s obligations under the Senior Secured Loan Facility, and are subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to a Subordination Agreement, dated as of June 24, 2016, by and among the Company, Foris and the administrative agent under the Company’s Senior Secured Loan Facility. Interest will accrue on the June 2016 Notes from and including June 24, 2016 at a rate of 13.50% per annum and is payable in full on May 15, 2017, the maturity date of the June 2016 Notes, unless the June 2016 Notes are prepaid in accordance with their terms prior to such date. The June 2016 Purchase Agreement and the June 2016 Notes contain customary terms, provisions, representations and warranties, including certain events of default after which the June 2016 Notes may be due and payable immediately, as set forth in the June 2016 Notes.

In May 2017, in connection with the issuance and sale of convertible preferred stock and warrants to purchase common stock, as described in more detail below in Note 18, “Subsequent Events,” the June 2016 Notes were exchanged for shares of convertible preferred stock and warrants to purchase common stock in the offering.

October 2016 Private Placements

On October 21 and October 27, 2016, the Company entered into separate Note Purchase Agreements (or the October 2016 Purchase Agreements) with Foris and Ginkgo, respectively, for the sale of $6.0 million and $8.5 million, respectively, in aggregate principal amount of secured promissory notes (or the October 2016 Notes) in exchange for aggregate proceeds to the Company of $6.0 million and $8.5 million, respectively (or the October 2016 Private Placements). The October 2016 Notes were issued in private placements exempt from registration under the Securities Act. The October 2016 Private Placements closed on October 21 and October 27, 2016, respectively.

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The October 2016 Notes are collateralized by a second priority lien on the assets securing the Company’s obligations under the Senior Secured Loan Facility, and are subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to Subordination Agreements, dated as of the respective dates of the October 2016 Purchase Agreements, by and among the Company, the applicable purchaser and the administrative agent under the Company’s Senior Secured Loan Facility. Interest will accrue on the October 2016 Notes from and including October 21 and 27, 2016, respectively, at a rate of 13.50% per annum and is payable in full on May 15, 2017, the maturity date of the October 2016 Notes, unless the October 2016 Notes are prepaid in accordance with their terms prior to such date. The October 2016 Purchase Agreements and the October 2016 Notes contain customary terms, provisions, representations and warranties, including certain events of default after which the October 2016 Notes may be due and payable immediately, as set forth in the October 2016 Notes.

In May 2017, in connection with the issuance and sale of convertible preferred stock and warrants to purchase common stock, as described in more detail below in Note 18, “Subsequent Events,” the October 2016 Notes purchased by Foris in the October 2016 Private Placements were exchanged for shares of convertible preferred stock and warrants to purchase common stock in the offering.

Salisbury Note

In December 2016, in connection with the Company’s purchase of a manufacturing facility in Leland, North Carolina and related assets (Glycotech Assets), as discussed in more detail in Note 7, “Joint Venture and Noncontrolling Interests,” the Company issued a purchase money promissory note in the principal amount of $3.5 million (Salisbury Note) in favor of Salisbury Partners, LLC (Salisbury). The Salisbury Note (i) bears interest at a rate of 5% per year, (ii) has a term of 13 years, (iii) is payable in equal monthly installments of principal and interest beginning on January 1, 2017 (which payments are subject to a penalty of 5% if delinquent more than 5 days) and (iv) is secured by a purchase money lien on the Glycotech Assets. The Salisbury Note contains customary terms and provisions, including certain events of default after which the Salisbury Note may become immediately due and payable. In addition, the Salisbury Note may be prepaid in full or in part at any time without penalty or premium. In January 2017, the Salisbury Note was repaid with proceeds from the Nikko Note (as defined below).

Nikko Note

In December 2016, in connection with the Company’s formation of its cosmetics joint venture (or the Aprinnova JV) with Nikko Chemicals Co., Ltd. (or Nikko), an existing commercial partner of the Company, and Nippon Surfactant Industries Co., Ltd., an affiliate of Nikko, as discussed in more detail in Note 7, “Joint Venture and Noncontrolling Interests,” Nikko made a loan to the Company in the principal amount of $3.9 million, and the Company in consideration therefor issued a promissory note (or the Nikko Note) to Nikko in an equal principal amount. The proceeds of the Nikko Note were used to satisfy the Company’s remaining liabilities relating to the Company’s purchase of the Glycotech Assets, including liabilities under the Salisbury Note. The Nikko Note (i) bears interest at a rate of 5% per year, (ii) has a term of 13 years, (iii) is payable in equal monthly installments of principal and interest beginning on January 1, 2017 (which payments are subject to a penalty of 5% if delinquent more than 5 days) and (iv) is collateralized by a first-priority lien on 10% of the Aprinnova JV interests owned by the Company. In addition to the payments under the Nikko Note set forth in the preceding sentence, the Company is required to (i) repay $400,000 of the Nikko Note in equal monthly installments of $100,000 on January 1, 2017, February 1, 2017, March 1, 2017 and April 1, 2017 and (ii) commencing with the distributions from the Aprinnova JV to its members relating to the fourth fiscal year of the Aprinnova JV and continuing for each fiscal year thereafter until the Nikko Note is fully repaid, repay the Nikko Note in an amount equal to the profits, if any, distributed to the Company by the Aprinnova JV. The Note contains customary terms and provisions, including certain events of default after which the Note may become immediately due and payable. In addition, the Nikko Note may be prepaid in full or in part at any time without penalty or premium.

In February 2017, in connection with the Aprinnova JV, Nikko made an unsecured loan to Aprinnova JV in the principal amount of $1.5 million and the Aprinnova issued a promissory note (Aprinnova Note) to Nikko in an equal principal amount. The proceeds of the Aprinnova Note will be used as working capital for Aprinnova JV and are repayable in $375,000 instalments on the following dates: May 1, 2017, August, 2017, November 1, 2018 and February 1, 2018. The Aprinnova Note bears interest at 2.75% annually payable on the principal installment dates.

Letters of Credit

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord of its headquarters in Emeryville, California, in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has $1.0 million as restricted cash under this arrangement as of March 31, 2017 and December 31, 2016.

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Future minimum payments under the debt agreements as of March 31, 2017 are as follows (in thousands):

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Related Party Loans payable			Credit Facility			Total
2017 (remaining nine months)	$	4,537		$	12,677		$	11,899		$	31,511		$	5,271		$	65,895
2018		16,290			21,803			2,878			—			33,710			74,681
2019		34,913			93,287			2,766			—			2,580			133,546
2020		—			—			2,656			—			2,500			5,156
2021		—			—			2,543			—			27,396			29,939
Thereafter		—			—			1,442			—			—			1,442
Total future minimum payments(1)		55,740			127,767			24,184			31,511			71,457			310,659
Less: amount representing interest(2)		(12,405	)		(52,549	)		(1,596	)		(957	)		(22,214	)		(89,721	)
Present value of minimum debt payments		43,335			75,218			22,588			30,554			49,243			220,938
Less: current portion		(3,611	)		(2,288	)		(11,780	)		(30,554	)		(1,222	)		(49,455	)
Noncurrent portion of debt	$	39,724		$	72,930		$	10,808		$	—		$	48,021		$	171,483

______________

(1) Including $3.9 million in 2017 related to Nomis Bay convertible note which, at the Company’s election, may be settled in shares or cash, and $46.8 million between 2018 and 2019 subject to the Maturity Treatment Agreement, which will be converted to common stock at maturity, subject to there being no default under the terms of the debt. See Note 18, “Subsequent Events” for additional details regarding the notes subject to the Maturity Treatment Agreement.

(2) Including debt discount and issuance cost of $42.0 million associated with the related party and non-related party debt which will be accreted to interest expense under the effective interest method over the term of the debt.

6. Commitments and Contingencies

Lease Obligations

The Company leases certain facilities and finances certain equipment under operating and capital leases, respectively. Operating leases include leased facilities and capital leases include leased equipment (see Note 4, "Balance Sheet Components"). The Company recognizes rent expense on a straight-line basis over the non-cancellable lease term and records the difference between rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applies them as a straight-line rent expense over the lease term. The Company has non-cancellable operating lease agreements for office, research and development, and manufacturing space that expire at various dates, with the latest expiration in February 2031. Rent expense under operating leases was $1.3 million for each of the three months ended March 31, 2017 and 2016, respectively.

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Future minimum payments under the Company's lease obligations as of March 31, 2017, are as follows (in thousands):

Years ending December 31:	Capital Leases			Operating Leases		Total Lease Obligations
2017 (remaining nine months)	$	734		$	5,194	$	5,928
2018		106			6,909		7,015
2019		9			6,782		6,791
2020		—			7,012		7,012
2021		—			7,248		7,248
Thereafter		—			10,993		10,993
Total future minimum lease payments		849		$	44,138	$	44,987
Less: amount representing interest		(39	)
Present value of minimum lease payments		810
Less: current portion		(405	)
Long-term portion	$	405

Guarantor Arrangements

The Company has agreements whereby it indemnifies its officers and directors for certain events or occurrences while the officer or director is serving in his or her official capacity. The indemnification period remains enforceable for the officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future payments. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of March 31, 2017 and December 31, 2016.

The Company entered into the FINEP Credit Facility to finance a research and development project on sugarcane-based biodiesel (see Note 5, "Debt and Mezzanine Equity"). The FINEP Credit Facility is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately R$6.0 million (approximately US$1.9 million based on the exchange rate as of March 31, 2017).

The Company entered into the BNDES Credit Facility to finance a production site in Brazil (see Note 5, "Debt and Mezzanine Equity").The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets with a total acquisition cost of R$24.9 million (approximately US$7.9 million based on the exchange rate as of March 31, 2017). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide certain bank guarantees under the BNDES Credit Facility.

The Company entered into loan agreements and security agreements whereby the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Nossa Caixa and Banco Pine (see Note 5, "Debt and Mezzanine Equity"). The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately R$68.0 million (approximately US$21.5 million based on the exchange rate as of March 31, 2017). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

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In December 2013, in connection with the execution of the JV Documents entered into by and among the Company, Total and TAB relating to the establishment of TAB (see Note 5, "Debt and Mezzanine Equity" and Note 7, “Joint Venture and Noncontrolling Interests”), the Company agreed to exchange the $69.0 million of outstanding Unsecured R&D Notes issued pursuant to the Total Purchase Agreement for replacement 1.5% Senior Secured Convertible Notes due March 2017, and grant a security interest to Total in and lien on all the Company’s rights, title and interest in and to the Company’s shares in the capital of TAB. Following execution of the JV Documents, all Unsecured R&D Notes that had been issued were exchanged for Secured R&D Notes. Further, the $10.85 million in principal amount of such notes issued in the initial tranche of the third closing under the Total Purchase Agreement in July 2014 and the $10.85 million in principal amount of such notes issued in the second tranche of the third closing in January 2015 were Secured R&D Notes instead of Unsecured R&D Notes. See Note 5,"Debt and Mezzanine Equity" for details regarding the impact of the Exchange and Maturity Treatment Agreement on the R&D Notes. In March 2016, as a result of the restructuring of TAB discussed under Note 5, “Debt and Mezzanine Equity” and Note 7, “Joint Venture and Noncontrolling Interests,” the remaining Secured R&D Notes were exchanged for an Unsecured R&D Note in the principal amount of $3.7 million. Further, in February 2017, the Company and Total agreed to extend the maturity of the outstanding R&D Notes from March 1, 2017 to May 15, 2017.

The Senior Secured Loan Facility and the June 2016 Notes and October 2016 Notes (see Note 5, "Debt and Mezzanine Equity") are collateralized by first- and second- priority liens, respectively, on substantially all of the Company's assets, including Company intellectual property. In addition, as discussed above, the Nikko Note is collateralized by a first-priority lien on 10% of the Aprinnova JV interests owned by the Company.

Purchase Obligations

As of March 31, 2017 and December 31, 2016, the Company had $3.7 million and $0.8 million, respectively, in purchase obligations which included zero and $0.6 million, respectively, of non-cancellable contractual obligations and construction commitments.

Production Cost Commitment

As of March 31, 2017, the Company committed to manufacture Squalane and Hemisqualane supplied to our Aprinnova JV at specified cost targets. The Company is obligated to pay all manufacturing costs above the production cost target but is not obligated to produce squalane and hemisqualane at a loss. The Company’s obligations under this arrangement for the quarter ended March 31, 2017 were offset by its entitlement to all of the profits of Aprinnova for the same period, which entitlement continues for the three year period following the date of the Joint Venture Agreement, up to a maximum of $10 million.

Other Matters

Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be reasonably estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed. The Company has levied indirect taxes on sugarcane-based biodiesel sales by Amyris Brasil to customers in Brazil based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate we levied.

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In April 2017, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and CFO, Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all individuals who acquired our common stock between March 2, 2017 and April 17, 2017. The complaint alleges securities law violations based on statements made by the Company in its earnings press release issued on March 2, 2017 and Form 12b-25 filed with the SEC on April 3, 2017. The Company believes that the complaint lacks merit, and intends to defend itself vigorously.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with reasonable assurance and therefore an estimate of all the reasonably possible losses cannot be determined at this time. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s condensed consolidated financial statements for the relevant reporting period could be materially adversely affected.

7. Joint Ventures and Noncontrolling Interests

Novvi LLC

In September 2011, the Company and Cosan US, Inc. (Cosan U.S.) formed Novvi LLC (or Novvi), a U.S. entity that was initially jointly owned by the Company and Cosan U.S. In March 2013, the Company and Cosan U.S. entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi (or the Novvi Operating Agreement), which sets forth the governance procedures for Novvi and the parties' initial contribution. The Company also entered into an IP License Agreement with Novvi (as amended, the Novvi IP License Agreement) under which the Company granted Novvi (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in automotive, commercial, and industrial lubricants markets, and (ii) a non-exclusive, royalty free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan U.S. granted Novvi certain rights of first refusal with respect to alternative base oil and additive technologies that may be acquired by the Company or Cosan U.S. during the term of the IP License Agreement. Under these agreements, through December 31, 2015 the Company and Cosan U.S. each owned 50% of Novvi and each party shared equally in any costs and any profits ultimately realized by the joint venture. Novvi is governed by a six member Board of Managers (or the Board of Managers). The Board of Managers appoints the officers of Novvi, who are responsible for carrying out the daily operating activities of Novvi as directed by the Board of Managers. The Novvi IP License Agreement has an initial term of 20 years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency. Under the terms of the Novvi Operating Agreement, Cosan U.S. was obligated to fund its initial 50% ownership share of Novvi in cash in the amount of $10.0 million and the Company was obligated to fund its initial 50% ownership share of Novvi through the granting of an intellectual property license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets, which Cosan U.S. and Amyris agreed was valued at $10.0 million. In March 2013, the Company measured its initial contribution of intellectual property to Novvi at the Company's carrying value of the licenses granted under the Novvi IP License Agreement, which was zero.

In April 2014, the Company, via its forgiveness of existing receivables due from Novvi related to rent and other services performed by the Company, purchased additional membership units of Novvi for a purchase price of $0.2 million. Concurrently, Cosan U.S. purchased an equal amount of additional membership units of Novvi. Also in April 2014, the Company and Cosan U.S. each contributed $2.1 million in cash in exchange for receiving additional membership units in Novvi. Following such transactions, the Company and Cosan U.S. continued to each own 50% of Novvi's issued and outstanding membership units.

In September 2014, the Company and Cosan U.S. entered into a member senior loan agreement to grant Novvi a loan amounting to approximately $3.7 million. The loan is due on September 1, 2017 and bears interest at a rate of 0.36% per annum. Interest accrues daily and is due and payable in arrears on September 1, 2017. The Company and Cosan U.S. each agreed to provide 50% of the loan. The Company's share of approximately $1.8 million was disbursed in two installments. The first installment of $1.2 million was made in September 2014 and the second installment of $0.6 million was made in October 2014. In November 2014, the Company and Cosan U.S. entered into a second member senior loan agreement to grant Novvi a loan of approximately $1.9 million on the same terms as the loan issued in September 2014, except that the due date is November 10, 2017. The Company and Cosan U.S. each agreed to provide 50% of the loan. The Company disbursed its share of the loan (i.e., approximately $1.0 million) in November 2014. In May 2015, the Company and Cosan U.S. entered into a third member senior loan agreement to grant Novvi a loan of approximately $1.1 million on the same terms as the loan issued in September 2014, except that the due date is May 14, 2018. The Company and Cosan U.S. each agreed to provide 50% of the loan.

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In the fourth quarter of 2015, the Company and Cosan U.S. entered into four additional member senior loan agreements to grant Novvi an aggregate loan of approximately $1.6 million on the same terms as the loan issued in September 2014, except that the respective due dates are August 19, 2018, October 15, 2018, November 12, 2018 and December 17, 2018. The Company and Cosan U.S. each agreed to provide 50% of each of these four loans. In July 2016, the Company contributed all outstanding amounts owing by Novvi to the Company under the seven member senior loan agreements in exchange for receiving additional membership units in Novvi.

In February 2016, the Company purchased additional membership units of Novvi for an aggregate purchase price of approximately $0.6 million in the form of forgiveness of existing receivables due from Novvi related to rent and other services performed by the Company, and Cosan U.S. purchased an equal number of additional membership units in Novvi for approximately $0.6 million in cash. Following such transactions, each member continued to own 50% of Novvi's issued and outstanding membership units.

On July 19, 2016, American Refining Group, Inc. (ARG) agreed to make a capital contribution of up to $10.0 million in cash to Novvi, subject to certain conditions, in exchange for a one third ownership stake in Novvi. In connection with such investment, the Company agreed to contribute all outstanding amounts owed by Novvi to the Company under the seven existing member senior loan agreements between the Company and Novvi, as well as certain existing receivables due from Novvi to the Company related to rent and other services performed by the Company, in exchange for receiving additional membership units in Novvi. Likewise, Cosan U.S. contributed an equal amount to Novvi as the Company in exchange for receiving an equal amount of additional membership interests in Novvi. Following the ARG investment, assuming it is made in full, and the capital contributions of the Company and Cosan U.S., each of Novvi’s three members (i.e., ARG, the Company and Cosan U.S.) would own one third of Novvi’s issued and outstanding membership units and would each be represented by two members of the Board of Managers. In order to reflect the ARG investment in Novvi and related transactions, the Novvi Operating Agreement was amended and restated on July 19, 2016. In addition, the Novvi IP License Agreement was also amended on July 19, 2016. As of March 31, 2017, all of the $10.0 million of ARG's capital contribution to Novvi had been funded.

In November 2016, Chevron U.S.A. Inc. (Chevron) made a capital contribution of $1.0 million in cash to Novvi in exchange for 20,000 membership units, representing an approximately 3% ownership stake in Novvi, which reduced the ownership interests of the Company, Cosan U.S. and ARG pro rata. In connection with its investment in Novvi, for so long as Chevron or its affiliates owns any membership units in Novvi, Chevron shall have the right to purchase up to such additional membership units as would result in Chevron owning the greater of (i) 25% of the aggregate membership units then outstanding held by Chevron, the Company, Cosan U.S. and ARG (including their affiliates and successors-in-interest) following such purchase and (ii) the highest percentage of such membership units held by the Company, Cosan U.S. and ARG (including their affiliates and successors-in-interest) following such purchase. In addition, Chevron shall have the right to purchase up to its pro rata share (as determined by the then issued and outstanding membership units, excluding any such units beneficially owned by Novvi) of all additional membership units that Novvi may, from time to time, propose to sell or issue.

Additional funding requirements to finance the ongoing operations of Novvi are expected to happen through revolving credit or other loan facilities provided by unrelated parties (i.e., such as financial institutions); cash advances or other credit or loan facilities provided by Novvi’s members or their affiliates; or additional capital contributions by the existing Novvi members or new investors.

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The Company has identified Novvi as a VIE and determined that the power to direct activities which most significantly impact the economic success of the joint venture (i.e., continuing research and development, marketing, sales, distribution and manufacturing of Novvi products) are shared among the Company, Cosan U.S. and ARG. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi under the equity method of accounting. The Company will continue to reassess its primary beneficiary analysis of Novvi if there are changes in events and circumstances impacting the power to direct activities that most significantly affect Novvi's economic success. Under the equity method, the Company's share of profits and losses and impairment charges on investments in affiliates (nil for both periods presented) are included in “Loss from investments in affiliates” in the condensed consolidated statements of operations. The carrying amount of the Company's equity investment in Novvi was zero as of each of March 31, 2017 and 2016.

Total Amyris BioSolutions B.V.

In November 2013, the Company and Total formed Total Amyris BioSolutions B.V. (TAB), a joint venture to produce and commercialize farnesene- or farnesane-based jet and diesel fuels. Prior to the restructuring of TAB in March 2016 as described below, the common equity of TAB was owned equally by the Company and Total, and TAB’s purpose was limited to executing the License Agreement dated December 2, 2013 between the Company, Total and TAB and maintaining such licenses under it, unless and until either (i) Total elected to go forward with either the full (diesel and jet fuel) TAB commercialization program (R&D Program) or the jet fuel component of the R&D Program (or a Go Decision), (ii) Total elected to not continue its participation in the R&D Program and TAB (or a No-Go Decision), or (iii) Total exercised any of its rights to buy out the Company’s interest in TAB. Following a Go Decision, the articles and shareholders’ agreement of TAB would be amended and restated to be consistent with the shareholders’ agreement contemplated by the Total Fuel Agreements (see Note 5, "Debt and Mezzanine Equity" and Note 8, "Significant Agreements").

In July 2015, the Company and Total entered into a Letter Agreement (or, as amended in February 2016, the TAB Letter Agreement) regarding the restructuring of the ownership and rights of TAB (Restructuring), pursuant to which the parties agreed to, among other things, enter into an Amended & Restated Jet Fuel License Agreement between the Company and TAB (Jet Fuel Agreement), a License Agreement regarding Diesel Fuel in the European Union (EU) between the Company and Total (EU Diesel Fuel Agreement), and an Amended and Restated Shareholders’ Agreement among the Company, Total and TAB, and file a Deed of Amendment of Articles of Association of TAB, all in order to reflect certain changes to the ownership structure of TAB and license grants and related rights pertaining to TAB.

On February 12, 2016, the Company and Total entered into an amendment to the TAB Letter Agreement, pursuant to which the parties agreed that, upon the closing of the Restructuring, Total would cancel R&D Notes in an aggregate principal amount of approximately $1.3 million, plus all paid-in-kind and accrued interest as of the closing of the Restructuring under all outstanding R&D Notes (including all such interest that was outstanding as of July 29, 2015), and a note in the principal amount of Euro 50,000, plus accrued interest, issued by the Company to Total in connection with the existing TAB capitalization, in exchange for an additional 25% ownership interest of TAB (giving Total an aggregate ownership stake of 75% of TAB and giving the Company an aggregate ownership stake of 25% of TAB). In connection therewith, Total would surrender to the Company the remaining R&D Notes and the Company would provide to Total a new R&D Note containing substantially similar terms and conditions to the outstanding R&D Notes other than it would be unsecured and its payment terms would be severed from TAB’s business performance, in the principal amount of $3.7 million (collectively, the “TAB Share Purchase”).

On March 21, 2016, the Company, Total and TAB closed the Restructuring and the TAB Share Purchase. See Note 5, “Debt and Mezzanine Equity” for further details of these transactions and the impact of these transaction on the Company’s condensed consolidated financial statements.

Under the Jet Fuel Agreement, (a) the Company granted exclusive (co-exclusive in Brazil), world-wide, royalty-free rights to TAB for the production and commercialization of farnesene- or farnesane-based jet fuel, (b) the Company granted TAB the option, until March 1, 2018, to purchase the Company’s Brazil jet fuel business at a price based on the fair value of the commercial assets and on the Company’s investment in other related assets, (c) the Company granted TAB the right to purchase farnesene or farnesane for its jet fuel business from us on a “most-favored” pricing basis and (d) all rights to farnesene- or farnesane-based diesel fuel the Company previously granted to TAB reverted back to the Company. As a result of the Jet Fuel Agreement, the Company generally no longer has an independent right to make or sell, without the approval of TAB, farnesene- or farnesane-based jet fuels outside of Brazil.

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Upon all farnesene-or farnesane-based diesel fuel rights reverting back to the Company, the Company granted to Total, pursuant to the EU Diesel Fuel Agreement, (a) an exclusive, royalty-free license to offer for sale and sell farnesene- or farnesane-based diesel fuel in the EU, (b) the non-exclusive right to make farnesene or farnesane anywhere in the world, but Total must (i) use such farnesene or farnesane to produce only diesel fuel to offer for sale or sell in the EU and (ii) pay the Company a to-be-negotiated, commercially reasonable, “most-favored” basis royalty and (c) the right to purchase farnesene or farnesane for its EU diesel fuel business from the Company on a “most-favored” pricing basis. As a result of the EU Diesel Fuel Agreement, the Company generally no longer has an independent right to make or sell, without the approval of Total, farnesene- or farnesane-based diesel fuels in the EU.

As a result of, and in order to reflect, the changes to the ownership structure of TAB described above, on March 21, 2016, (a) the Company, Total and TAB entered into an Amended and Restated Shareholders’ Agreement and filed a Deed of Amendment of Articles of Association of TAB and (b) the Company and Total terminated the Amended and Restated Master Framework Agreement, dated December 2, 2013 and amended on April 1, 2015, between the Company and Total.

As of March 31, 2017, the common equity of TAB was owned 25% by the Company and 75% by Total. TAB has a capitalization as of March 31, 2017 of €0.1 million (approximately US$0.1 million based on the exchange rate as of March 31, 2017). The Company has identified TAB as a VIE and determined that the Company is not the primary beneficiary and therefore accounts for its investment in TAB under the equity method of accounting. Under the equity method, the Company's share of profits and losses (nil for both periods presented) are included in “Loss from investment in affiliate” in the condensed consolidated statements of operations.

SMA Indústria Química S.A.

In April 2010, the Company established SMA Indústria Química (or SMA), a joint venture with São Martinho S.A. (or SMSA), to build a production facility in Brazil. SMA is located at the SMSA mill in Pradópolis, São Paulo state. The joint venture agreements establishing SMA had a 20 year initial term.

SMA was initially managed by a three member executive committee, of which the Company appointed two members, one of whom is the plant manager who is the most senior executive responsible for managing the construction and operation of the facility. SMA was initially governed by a four member board of directors, of which the Company and SMSA each appointed two members. The board of directors had certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee.

The joint venture agreements required the Company to fund the construction costs of the new facility and SMSA would reimburse the Company up to R$61.8 million (approximately US$19.5 million based on the exchange rate as of March 31, 2017) of the construction costs after SMA commences production. After commercialization, the Company would market and distribute Amyris renewable products produced by SMA and SMSA would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that SMSA could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the first four years at a price that guarantees the return of SMSA’s investment plus a fixed interest rate. After this four year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return.

Under the terms of the joint venture agreements, if the Company became controlled, directly or indirectly, by a competitor of SMSA, then SMSA would have the right to acquire the Company’s interest in SMA. If SMSA became controlled, directly or indirectly, by a competitor of the Company, then the Company would have the right to sell its interest in SMA to SMSA. In either case, the purchase price would be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management.

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The Company initially had a 50% ownership interest in SMA. The Company had identified SMA as a VIE pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk was not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, the Company directed the design and construction activities, as well as production and distribution. In addition, the Company had the obligation to fund the design and construction activities until commercialization was achieved. Subsequent to the construction phase, both parties equally would fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. As of March 31, 2017, the Company indirectly owned 100% of the equity interest in SMA and as a wholly owned subsidiary its financial results are included in the Company’s condensed consolidated financial statements.

The Company completed a significant portion of the construction of the new facility in 2012. The Company suspended construction of the facility in 2013 in order to focus on completing and operating the Company's smaller production facility in Brotas, Brazil. In February 2014, the Company entered into an amendment to the joint venture agreement with SMSA which updated and documented certain preexisting business plan requirements related to the recommencement of construction at the joint venture operated plant and sets forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than 18 months following the construction of the plant no later than March 31, 2017, and (ii) the extension of an option held by SMSA to build a second large-scale farnesene production facility to no later than December 31, 2018 with the commencement of operations at such second facility to occur no later than April 1, 2019. On July 1, 2015 SMSA filed a material fact document with CVM, the Brazilian securities regulator, that announced that certain contractual targets undertaken by the Company have not been achieved, which affects the feasibility of the project. Therefore, SMSA decided not to approve continuing construction of the plant for the joint venture with the Company and its Brazilian subsidiary Amyris Brasil. In July 2015, the Company announced that it was in discussions with SMSA regarding the continuation of the joint venture. In December 2015, the Company and SMSA entered into a Termination Agreement and a Share Purchase and Sale Agreement relating to the termination of the joint venture. Under the Termination Agreement, the parties agreed that the joint venture would be terminated effective upon the closing of a purchase by Amyris Brasil of SMSA’s shares of SMA. Under the Share Purchase and Sale Agreement, Amyris Brasil agreed to purchase, for R$50,000 (approximately US$15,780 based on the exchange rate as of March 31, 2017), 50,000 shares of SMA (representing all the outstanding shares of SMA held by SMSA), which purchase and sale was consummated on January 11, 2016. The Share Purchase and Sale Agreement also provided that the Company and Amyris Brasil would have 12 months following the closing of the share purchase to remove assets from SMSA’s site, and enter into an extension of the lease for such 12 month period for monthly rental payments of R$9,853 (approximately US$3,110 based on the exchange rate as of March 31, 2017). The Share Purchase and Sale Agreement also clarified that the Company and Amyris Brasil would not be required to demolish or remove the foundations of the plant at the SMSA site. On September 1, 2016, the parties entered into an addendum to the Share Purchase and Sale Agreement (and a corresponding amendment to the lease) which extended the deadline for the Company and Amyris Brasil to remove assets from SMSA’s site until December 31, 2017.

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Salisbury transaction

In January 2011, the Company entered into a production service agreement (Glycotech Agreement) with Glycotech, Inc. (or Glycotech), under which Glycotech provides process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina (Glycotech Facility). The Company products manufactured by Glycotech are owned and distributed by the Company. Pursuant to the terms of the Glycotech Agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility, which is dedicated solely to the manufacture of Amyris products. The initial term of the Glycotech Agreement was for a two year period commencing on February 1, 2011 and the Glycotech Agreement renews automatically for successive one-year terms, unless terminated by the Company. Concurrent with the Glycotech Agreement, the Company also entered into a Right of First Refusal Agreement with Salisbury Partners, LLC (or Salisbury), the lessor of the facility and site leased by Glycotech (ROFR Agreement). Per conditions of the ROFR Agreement, Salisbury agreed not to sell the facility and site leased by Glycotech during the term of the Glycotech Agreement. In the event that Salisbury was presented with an offer to sell or decides to sell an adjacent parcel, the Company had the right of first refusal to acquire it.

On November 10, 2016, the Company, Glycotech and Salisbury entered into a Purchase and Sale Agreement (PSA) for the purchase and sale of the Glycotech Facility, the real property on which the Glycotech Facility is located and the fixtures, equipment, materials and supplies and other tangible assets located at or used in connection with the Facility (collectively, the Glycotech Assets). Pursuant to the PSA, on December 5, 2016, the Company purchased the Glycotech Assets from Glycotech and Salisbury for an aggregate purchase price of $4.35 million, of which $3.5 million was paid in the form of a purchase money promissory note in favor of Salisbury, as described in more detail in Note 5, “Debt.” In connection with the closing of the purchase and sale of the Glycotech Assets under the PSA, the Company, Glycotech and Salisbury terminated the current lease of the Glycotech Facility and the Glycotech Agreement and modified the ROFR Agreement such that the Company’s right of first refusal with respect to certain parcels of real property owned by Salisbury adjacent to the Glycotech Facility would be an appurtenant right running with the ownership of the real property on which the Glycotech Facility is located. The Glycotech Assets were subsequently transferred to the Company’s cosmetics joint venture with Nikko Chemicals Co., Ltd. and Nippon Surfactant Industries Co., Ltd. in connection with the formation of such joint venture, as described below under “Aprinnova JV.”

Aprinnova JV

On December 12, 2016, the Company, Nikko Chemicals Co., Ltd. an existing commercial partner of the Company, and Nippon Surfactant Industries Co., Ltd., an affiliate of Nikko (collectively, Nikko) entered into a Joint Venture Agreement (Aprinnova JV Agreement), pursuant to which the Company and Nikko agreed to form a joint venture under the name Neossance, LLC, a Delaware limited liability company (Aprinnova JV). Pursuant to the Aprinnova JV Agreement, the Company agreed to initially form the Aprinnova JV and contribute certain assets of the Company, including certain intellectual property and other commercial assets relating to its Neossance cosmetic ingredients business (Aprinnova JV Business), as well as the Glycotech Assets. The Company also agreed to provide the Aprinnova JV with exclusive (to the extent not already granted to a third party), royalty-free licenses to certain intellectual property of the Company necessary to make and sell products associated with the Aprinnova JV Business (Aprinnova JV Products), and, in the event the Company is unable to meet its supply commitments under the Aprinnova JV Supply Agreement (as defined below), or Nikko terminates the Aprinnova JV Supply Agreement due to a material breach or default thereunder by the Company, the Company would be required to grant to the Aprinnova JV and Nikko additional non-exclusive, royalty-free licenses to certain intellectual property rights of the Company related to the production of farnesene in connection with the manufacture, production and sale of the Aprinnova JV Products. In March 2017, the name of the Aprinnova JV was changed to Aprinnova, LLC.

At the closing of the formation of the Neossance JV, which occurred on December 19, 2016, Nikko purchased a 50% interest in the Aprinnova JV in exchange for the following payments to the Company: (i) an initial payment of $10 million and (ii) the profits, if any, distributed to Nikko in cash as members of the Aprinnova JV during the three year period following the date of the Joint Venture Agreement, up to a maximum of $10 million.

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Pursuant to the Joint Venture Agreement, the Company and Nikko agreed to make working capital loans to the Aprinnova JV in the amounts of $500,000 and $1,500,000, respectively. In addition, the Company agreed to execute, and cause Amyris Brasil to execute, a supply agreement (Aprinnova JV Supply Agreement) to supply farnesene to the Aprinnova JV, and further agreed to conduct its business in the Aprinnova JV Products through the Aprinnova JV, to purchase all of its requirements for the Aprinnova JV Products from the Neossance JV and to transfer all of its customers for the Aprinnova JV Products to the Aprinnova JV. In addition, the Company agreed to guarantee a maximum production cost for certain Aprinnova JV Products to be produced by the Aprinnova JV and to bear any cost of production above such guaranteed costs.

Under the Aprinnova JV Agreement, in the event of a merger, acquisition, sale or other similar reorganization, or a bankruptcy, dissolution, insolvency or other similar event, of the Company, on the one hand, or Nikko, on the other hand, the other member will have a right of first purchase with respect to such member’s interest in the Aprinnova JV, at the fair market value of such interest, in the case of a merger, acquisition, sale or other similar reorganization, and at the lower of the fair market value or book value of such interest, in the case of a bankruptcy, dissolution, insolvency or other similar event.

In connection with the formation of the Aprinnova JV, the members entered into a First Amended and Restated LLC Operating Agreement of the Aprinnova JV (Operating Agreement). Pursuant to the Operating Agreement, the Aprinnova JV will be managed by a Board of Directors, which shall initially consist of four directors, two of which will be appointed by the Company and two of which will be appointed by Nikko. In addition, Nikko will have the right to designate the Chief Executive Officer of the Aprinnova JV from among the directors and the Company will have the right to designate the Chief Financial Officer. Pursuant to the Joint Venture Agreement, Nikko designated John Melo, the President and CEO of the Company, to serve as the initial CEO of the Aprinnova JV for a period of one year and the Company designated Shizuo Ukaji, the President and CEO of Nikko, to serve as the initial CFO of the Aprinnova JV for a period of one year. The Company has determined that it controls the Aprinnova JV because of its significant ongoing involvement in operational decision making and its guarantee of production costs for squalane/hemisqualane.

Under the Operating Agreement, profits from the operations of the Aprinnova JV, if any, will be distributed as follows: (i) first, to the members in proportion to their respective unreturned capital contribution balances, until each member’s unreturned capital contribution balance equals zero and (ii) second, to the members in proportion to their respective interests. In addition, future capital contributions will be made from time to time as the members shall determine, in each case on an equal (50%/50%) basis between the Company, on the one hand, and Nikko, on the other hand, unless otherwise mutually agreed by the members.

In connection with the contribution of the Glycotech Assets by the Company to the Aprinnova JV, at the closing of the formation of the Aprinnova JV, Nikko made a loan to the Company in the principal amount of $3.9 million, and the Company in consideration therefor issued a promissory note to Nikko in an equal principal amount, as described in more detail in Note 5, “Debt.”

The table below reflects the carrying amount of the assets and liabilities of the consolidated VIE for which the Company is the primary beneficiary at March 31, 2017. The creditors of each consolidated VIE have recourse only to the assets of that VIE.

(In thousands)	March 31, 2017		December 31, 2016
Assets	$	2,306	$	2,277
Liabilities	$	158	$	135

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The change in noncontrolling interest for the three months ended March 31, 2017 and 2016, is summarized below (in thousands):

	2017		2016
Balance at January 1	$	937	$	391
Acquisition of noncontrolling interest		—		(277	)
Balance at March 31	$	937	$	114

8. Significant Agreements

Research and Development Activities

Firmenich Collaboration Agreement

In March 2013, the Company entered into a Collaboration Agreement (or, as amended, the Firmenich Collaboration Agreement) with Firmenich SA (or Firmenich), a global flavors and fragrances company, to establish a collaboration arrangement for the development and commercialization of multiple renewable flavors and fragrances compounds. Under the Firmenich Collaboration Agreement, except for rights granted under pre-existing collaboration relationships, the Company granted Firmenich exclusive access to specified Company intellectual property for the development and commercialization of flavors and fragrances compounds in exchange for research and development funding and a profit sharing arrangement. The Firmenich Collaboration Agreement superseded and expanded the November 2010 Master Collaboration and Joint Development Agreement between the Company and Firmenich. Unless sooner terminated in accordance with its terms, the Firmenich Collaboration Agreement has an initial term of 10 years and will automatically renew at the end of such term (and at the end of any extension) for an additional 3-year term unless and until a party provides the other party written notice, at least twelve months before the end of the then-current term, of its desire to terminate the agreement at the end of the then-current term.

The Firmenich Collaboration Agreement provided for annual, up-front funding to the Company by Firmenich of $10.0 million for each of the first three years of the collaboration. Payments of $10.0 million were received by the Company in each of March 2013, 2014 and 2015. The Firmenich Collaboration Agreement contemplates additional funding by Firmenich of up to $5.0 million under four potential milestone payments, as well as additional funding by the collaboration partner on a discretionary basis. Through March 2017, the Company had achieved the third performance milestone under the Firmenich Collaboration Agreement and recognized collaboration revenues of $1.1 million and $3.0 million for the three months ended March 31, 2017 and 2016, respectively. The Firmenich Collaboration Agreement does not impose any specific research and development obligations on either party after year six, but provides that if the parties mutually agree to perform research and development activities after year six, the parties will fund such activities equally.

Under the Firmenich Collaboration Agreement, the parties agreed to jointly select target compounds, subject to final approval of compound specifications by Firmenich. During the development phase, the Company would be required to provide labor, intellectual property and technology infrastructure and Firmenich would be required to contribute downstream polishing expertise and market access. The Firmenich Collaboration Agreement provides that the Company will own research and development and strain engineering intellectual property, and Firmenich will own blending and, if applicable, chemical conversion intellectual property. Under certain circumstances, such as the Company’s insolvency, Firmenich would gain expanded access to the Company’s intellectual property. The Firmenich Collaboration Agreement contemplates that, following development of flavors and fragrances compounds, the Company will manufacture the initial target molecules for the compounds and Firmenich will perform any required downstream polishing and distribution, sales and marketing. The Firmenich Collaboration Agreement provides that the parties will mutually agree on a supply price for each compound developed under the agreement and, subject to certain exceptions, will share product margins from sales of each such compound on a 70/30 basis (70% for Firmenich) until Firmenich receives $15.0 million more than the Company in the aggregate from such sales, after which time the parties will share the product margins 50/50. The Company also agreed to pay a one-time success bonus to Firmenich of up to $2.5 million if certain commercialization targets are met.

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In September 2014, the Company entered into a supply agreement with Firmenich for compounds developed under the Firmenich Collaboration Agreement. The Company recognized $1.2 million and $2.0 million of revenues from product sales under this supply agreement for the three months ended March 31, 2017 and 2016, respectively.

In December 2016, the Company and Firmenich entered into an amendment of the Firmenich Collaboration Agreement, pursuant to which the parties agreed to exclude certain compounds from the scope of the agreement and to permit the Company to engage in certain activities relating to such excluded compounds with a third party, in exchange for a ten percent royalty on net sales by the Company to such third party of products related to such excluded compounds, as well as (i) the transfer of certain technical materials relating to the Firmenich Collaboration Agreement, previously held in escrow, to Firmenich, (ii) a credit to Firmenich against products previously ordered from the Company under the parties’ existing supply agreement, (iii) a reduced price for the sale of additional products to Firmenich under such supply agreement, and (iv) training for the employees of Firmenich at the Company’s manufacturing plant located in Brotas, Brazil.

Kuraray Collaboration Agreement

In July 2011, the Company entered into a collaboration agreement with Kuraray Co., Ltd (or Kuraray), with an initial focus on using farnesene-based polymers to replace petroleum-derived additives in tires. In March 2014, the Company entered into the Second Amended and Restated Collaboration Agreement with Kuraray in order to extend the term of the original collaboration agreement between the Company and Kuraray for an additional two years and add additional fields and products to the scope of development. In consideration for the Company’s agreement to extend the term of the original collaboration agreement and add additional fields and products, Kuraray agreed to pay the Company $4.0 million in two equal installments of $2.0 million. The first installment was paid on April 30, 2014 and the second installment was due on April 30, 2015. In March 2015, the Company and Kuraray entered into the First Amendment to the Second Amended and Restated Collaboration Agreement to extend the term of the collaboration agreement until December 31, 2016 and to accelerate payment to the Company of the second installment of $2.0 million due from Kuraray under the Second Amended and Restated Collaboration Agreement to March 31, 2015. Subsequently, in November 2016 the Company and Kuraray entered into Amendment #3 to the Second Amended and Restated Collaboration Agreement to, among other things, extend the term of the collaboration agreement to December 31, 2018 as well as extend certain exclusive rights granted to Kuraray under the collaboration agreement. In connection with such extensions, Kuraray agreed to pay the Company $1.0 million in two equal installments of $500,000 on or before January 15, 2017 and January 15, 2018, respectively.

The Company recognized (i) collaboration revenues of $0.1 million and $0.4 million for the three months ended March 31, 2017 and 2016, respectively, and (ii) $1.6 million and zero of revenues from product sales for the three months ended March 31, 2017 and 2016, respectively, under this agreement.

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DARPA Technology Investment Agreement

In September 2015, the Company entered into a Technology Investment Agreement (or, as amended, the 2015 TIA) with The Defense Advanced Research Projects Agency (or DARPA), under which the Company, with the assistance of five specialized subcontractors, will work to create new research and development tools and technologies for strain engineering and scale-up activities. The program that is the subject of the 2015 TIA will be performed and funded on a milestone basis, where DARPA, upon the Company’s successful completion of each milestone event in the 2015 TIA, will pay the Company the amount set forth in the 2015 TIA corresponding to such milestone event. Under the 2015 TIA, the Company and its subcontractors could collectively receive DARPA funding of up to $35.0 million over the program’s 4-year term if all of the program’s milestones are achieved. In conjunction with DARPA’s funding, the Company and its subcontractors are obligated to collectively contribute approximately $15.5 million toward the program over its four year term (primarily by providing specified labor and/or purchasing certain equipment). The Company can elect to retain title to the patentable inventions it produces under the program, but DARPA receives certain data rights as well as a government purposes license to certain of such inventions. Either party may, upon written notice and subject to certain consultation obligations, terminate the 2015 TIA upon a reasonable determination that the program will not produce beneficial results commensurate with the expenditure of resources.

The Company recognized collaboration revenues of $1.0 million and $0.4 million under this agreement for the three months ended March 31, 2017 and 2016, respectively.

Nenter Supply Agreement

In April 2016, the Company entered into a Renewable Farnesene Supply Agreement (or the Nenter Supply Agreement) with Nenter & Co., Inc. (or Nenter) to establish the terms of a supply and value-share arrangement between the Company and Nenter related to farnesene. Under the Nenter Supply Agreement and related agreements, the Company has agreed to supply Nenter with farnesene at prices and on delivery terms set forth in the Nenter Supply Agreement and to provide Nenter with certain exclusive purchase rights, and Nenter has agreed to annual minimum purchase volume requirements and to provide the Company with quarterly value-share payments representing a portion of Nenter’s profit on the sale of products produced using farnesene purchased under the Nenter Supply Agreement. Unless earlier terminated in accordance with its terms, the Nenter Supply Agreement will remain in effect until December 31, 2020 and will automatically renew at the end of such initial term for an additional 5-year term unless a party provides the other party written notice, no later than July 1, 2020, of its desire to terminate the agreement at the end of the initial term.

The Company recognized $2.3 million of revenues from product sales under the Nenter Supply Agreement for the three months ended March 31, 2017.

Givaudan Agreements

In February 2011, the Company entered into an Amended and Restated Research Agreement with Givaudan International, SA (or Givaudan), a global flavors and fragrances company, relating to the development of a fragrance ingredient. In October 2015, the Company and Givaudan entered into a Farnesene Supply Agreement (or the Givaudan Supply Agreement) related to the supply of farnesene by the Company to Givaudan for use in the production of such ingredient, on such terms and at such prices set forth in the Givaudan Supply Agreement. The Company recognized $0.6 million and zero of revenues from product sales under the Givaudan Supply Agreement for the three months ended March 31, 2017 and 2016, respectively. The Givaudan Supply Agreement has an initial term of 5 years, which term shall be automatically extended for additional periods of 2 years each, up to a maximum of three such extensions, unless sooner terminated in accordance with its terms.

In June 2016, the Company entered into a Collaboration Agreement with Givaudan to establish a collaboration for the development and commercialization of certain renewable compounds for use in the fields of active cosmetics and flavors (or the Givuadan Collaboration Agreement). Under the Givaudan Collaboration Agreement, the Company agreed to use its labor, intellectual property and technology infrastructure to develop and commercialize certain compounds for Givaudan. In exchange, Givaudan agreed to pay to the Company $12.0 million in semi-annual installments of $3.0 million each, beginning on June 30, 2016. The Company received installments of $3.0 million on June 30, 2016 and December 29, 2016, and these amounts were recognized in deferred revenue as of such dates.

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Pursuant to the Givaudan Collaboration Agreement, the Company agreed to grant to Givaudan an exclusive license to the intellectual property that the Company generates under the agreement. Such license will include the rights to make, use and sell compounds in the active cosmetics and flavors fields, and is subject to certain ‘claw back’ rights by the Company if a compound is not commercialized by Givaudan during the term of the agreement. The Company also agreed to grant Givaudan non-exclusive rights to certain portions of the Company’s existing intellectual property in order to facilitate activities under the Givaudan Collaboration Agreement. Givaudan, on the other hand, agreed to grant the Company a non-exclusive license to the intellectual property that is generated under the Givaudan Collaboration Agreement. Such non-exclusive license will include the rights to make, use and sell compounds in all fields except active cosmetics and flavors.

Subject to certain rights granted to a third party, Givaudan will have the exclusive right to commercialize the compounds in the active cosmetics and flavors markets during the term of the agreement. Further, the Company has agreed that it will not assist any third party in the development or commercialization of other compounds for sale or use in the active cosmetics or flavors markets during the term of the Givaudan Collaboration Agreement. In addition, the Givaudan Collaboration Agreement contemplates that the Company will be the primary supplier of commercial quantities of the compounds to Givaudan pursuant to supply agreements to be mutually negotiated by the parties. Unless sooner terminated in accordance with its terms, the Givaudan Collaboration Agreement has an initial term of 2 years and, prior to the expiration of the initial term, the parties will meet and discuss in good faith the extension of the agreement beyond the initial term.

The Company recognized collaboration revenues of $1.5 million under the Givaudan Collaboration Agreement for the three months ended March 31, 2017.

Ginkgo Initial Strategic Partnership Agreement and Collaboration Agreement

In June 2016, the Company entered into an Initial Strategic Partnership Agreement (Initial Ginkgo Agreement) with Ginkgo Bioworks, Inc. (or Ginkgo), pursuant to which the Company licensed certain intellectual property to Ginkgo in exchange for a fee of $20.0 million, to be paid by Ginkgo to the Company in two installments, and a ten percent royalty on net revenue, including without limitation net sales, royalties, fees and any other amounts received by Ginkgo related directly to such license. The first installment of $15.0 million was received on July 25, 2016. The second installment, in the amount of $5.0 million, has not been received as of March 31, 2017.

In addition, pursuant to the Initial Ginkgo Agreement, (i) the Company and Ginkgo agreed to pursue the negotiation and execution of a detailed definitive partnership and license agreement setting forth the terms of a commercial partnership and collaboration arrangement between the parties (Ginkgo Collaboration), (ii) the Company agreed to issue to Ginkgo an option to purchase five million shares of the Company’s common stock at an exercise price of $0.50, exercisable for one year from the date of issuance, in connection with the execution of such definitive agreement for the Ginkgo Collaboration, (iii) the Company received a deferment of all scheduled principal repayments under the Senior Secured Loan Facility, the lender and administrative agent under which is an affiliate of Ginkgo, as well as a waiver of the Minimum Cash Covenant, through October 31, 2016 and (iv) in connection with the execution of the definitive agreement for the Ginkgo Collaboration, the parties would effect an amendment of the LSA to (x) extend the maturity date of all outstanding loans under the Senior Secured Loan Facility, (y) waive any required amortization payments under the Senior Secured Loan Facility until maturity and (z) eliminate the Minimum Cash Covenant under the Senior Secured Loan Facility. See Note 5, “Debt and Mezzanine Equity” for details regarding the amendments to the LSA entered into in connection with the Initial Ginkgo Agreement and Ginkgo Collaboration Agreement (as defined below).

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On August 6, 2016, the Company issued to Ginkgo a warrant to purchase five million shares of the Company’s common stock at an exercise price of $0.50 per share, exercisable for one year from the date of issuance. The warrant was issued prior to the execution of the definitive agreement for the Ginkgo Collaboration in connection with the transfer of certain information technology from Ginkgo to the Company.

On September 30, 2016, the Company and Ginkgo entered into a Collaboration Agreement (Ginkgo Collaboration Agreement) setting forth the terms of the Ginkgo Collaboration, under which the parties will collaborate to develop, manufacture and sell commercial products and will share in the value created thereby. The Ginkgo Collaboration Agreement provides that, subject to certain exceptions, all third party contracts for the development of chemical small molecule compounds whose manufacture is enabled by the use of microbial strains and fermentation technologies that are entered into by the Company or Ginkgo during the term of the Ginkgo Collaboration Agreement will be subject to the Ginkgo Collaboration and the approval of the other party (not to be unreasonably withheld). Responsibility for the engineering and small-scale process development of the newly developed products will be allocated between the parties on a project-by-project basis, and the Company will be principally responsible for the commercial scale-up and production of such products, with each party generally bearing their own respective costs and expenses relating to the Ginkgo Collaboration, including capital expenditures. Notwithstanding the foregoing, subject to the Company sourcing funding and breaking ground on a new production facility by March 30, 2017, Ginkgo will pay the Company a fee of $5.0 million on or before March 31, 2017. The $5.0 million fee has not been received as of March 31, 2017.

Under the Ginkgo Collaboration Agreement, subject to certain exceptions, including excluded or refused products and cost savings initiatives, the profit on the sale of products subject to the Ginkgo Collaboration Agreement as well as cost-sharing, milestone and “value-creation” payments associated with the development and production of such products will be shared equally between the parties. The parties also agreed to provide each other with a license and other rights to certain intellectual property necessary to support the development and manufacture of the products under the Ginkgo Collaboration, and also to provide each other with access to certain other intellectual property useful in connection with the activities to be undertaken under the Ginkgo Collaboration Agreement, subject to certain carve-outs.

The initial term of the Ginkgo Collaboration Agreement is three years, and will automatically renew for successive one-year terms unless either party provides written notice of termination not less than 90 days prior to the expiration of the then-current term. In addition, the Ginkgo Collaboration Agreement provides that the parties will evaluate the performance of the Ginkgo Collaboration as of the 18-month anniversary of the Ginkgo Collaboration Agreement, and if either party has been repeatedly unable to perform or meet its commitments under the Ginkgo Collaboration Agreement, the other party will have the right to terminate the Ginkgo Collaboration Agreement on 30 days written notice.

The Company recognized zero of collaboration revenue under the Initial Ginkgo Agreement and the Ginkgo Collaboration Agreement for the three months ended March 31, 2017. As of March 31, 2017, $3.0 million is payable by the Company to Ginkgo under the Ginkgo Collaboration Agreement for its share of collaboration payments and license .fees (December 31, 2016, $1.6 million).

Intellectual Property License and Strain Access Agreement with Blue California

In December 2016, the Company entered into an Intellectual Property License and Strain Access Agreement with Phyto Tech Corp. (d/b/a Blue California), a food ingredients and nutraceuticals company. Pursuant to the agreement, the Company granted Blue California a royalty-free, non-exclusive, worldwide, license to access and use certain Company intellectual property for the purpose of research and development, scale-up, manufacturing and commercialization activities. In exchange for such license, Blue California agreed to pay the Company a fee of $10 million in cash. On March 31, 2017, the Company entered into a subsequent agreement with Blue California whereby, among other things, Blue California’s affiliates will provide the Company with access to their fermentation manufacturing capacity in China and the Company will transfer additional intellectual property to Blue California for use in collaboration activities between the parties. See Note 18 “Subsequent Events” for further details.

Financing Agreements

At Market Issuance Sales Agreement

On March 8, 2016, the Company entered into an At Market Issuance Sales Agreement (ATM Sales Agreement) with FBR Capital Markets & Co. and MLV & Co. LLC (Agents) under which the Company may issue and sell shares of its common stock having an aggregate offering price of up to $50.0 million (ATM Shares) from time to time through the Agents, acting as its sales agents, under the Company’s Registration Statement on Form S-3 (File No. 333-203216), effective April 15, 2015. Sales of the ATM Shares through the Agents, if any, will be made by any method that is deemed an “at the market offering” as defined in Rule 415 under the Securities Act, including by means of ordinary brokers’ transactions at market prices, in block transactions, or as otherwise agreed by the Company and the Agents. Each time that the Company wishes to issue and sell ATM Shares under the ATM Sales Agreement, the Company will notify one of the Agents of the number of ATM Shares to be issued, the dates on which such sales are anticipated to be made, any minimum price below which sales may not be made and other sales parameters as the Company deems appropriate. The Company will pay the designated Agent a commission rate of up to 3.0% of the gross proceeds from the sale of any ATM Shares sold through such Agent as agent under the ATM Sales Agreement. The ATM Sales Agreement contains customary terms, provisions, representations and warranties. The ATM Sales Agreement includes no commitment by other parties to purchase shares the Company offers for sale.

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During the three months ended March 31, 2017, the Company did not sell any shares of common stock under the ATM Sales Agreement. As of the date hereof, $50.0 million remained available for future sales under the ATM Sales Agreement.

LSA Amendment

See Note 5, “Debt and Mezzanine Equity” for details regarding the Fifth LSA Amendment.

Fidelity Notes Exchange

See Note 5, “Debt and Mezzanine Equity” for details regarding the Fidelity Exchange.

Amendment to March 2016 R&D Note

See Note 5, “Debt and Mezzanine Equity” for details regarding the March 2016 R&D Note Amendment.

9. Goodwill and Intangible Assets

The following table presents the components of the Company's intangible assets (in thousands):

		March 31, 2017							December 31, 2016
	Useful Life in Years	Gross Carrying Amount		Accumulated Amortization/ Impairment			Net Carrying Value		Gross Carrying Amount		Accumulated Amortization/ Impairment			Net Carrying Value
In-process research and development	Indefinite	$	8,560	$	(8,560	)	$	—	$	8,560	$	(8,560	)	$	—
Acquired licenses and permits	2		772		(772	)		—		772		(772	)		—
Goodwill	Indefinite		560		—			560		560		—			560
		$	9,892	$	(9,332	)	$	560	$	9,892	$	(9,332	)	$	560

The in-process research and development (IPR&D) of $8.6 million was acquired through the acquisition of Draths in October 2011 and was treated as indefinite lived intangible assets pending completion or abandonment of the projects to which the IPR&D related. The IPR&D was fully impaired in 2015.

The Company has a single reportable segment (see Note 15, “Reporting Segments” for further details). Consequently, all of the Company's goodwill is attributable to that single reportable segment.

10. Stockholders’ Deficit

Unexercised Common Stock Warrants

As of March 31, 2017 and 2016, the Company had 14,663,411 and 7,328,069, respectively, of unexercised common stock warrants with exercise prices ranging from $0.01 to $10.67 per warrant and a weighted average remaining maturity of 5.1 years.

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11. Stock-Based Compensation

The Company’s stock option activity and related information for the three months ended March 31, 2017 was as follows:

	Number Outstanding			Weighted- Average Exercise Price		Weighted- Average Remaining Contractual Life (Years)		Aggregate Intrinsic Value
								(in thousands)
Outstanding - December 31, 2016		13,487,685		$	3.63		6.70	$	443
Options granted		726,000		$	0.58		—		—
Options exercised		(500	)	$	0.28		—		—
Options cancelled		(695,912	)	$	1.82		—		—
Outstanding - March 31, 2017		13,517,273		$	3.55		6.83	$	44
Vested and expected to vest after March 31, 2017		12,347,493		$	3.79		6.63	$	38
Exercisable at March 31, 2017		7,478,686		$	5.42		5.28	$	1

The aggregate intrinsic value of options exercised under all option plans was zero for each of the three months ended March 31, 2017 and 2016, determined as of the date of option exercise.

The Company’s restricted stock units (or "RSUs") and restricted stock activity and related information for the three months ended March 31, 2017 was as follows:

	RSUs			Weighted- Average Grant- Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2016		6,997,084		$	1.18		1.44
Awarded		825,980		$	0.59		—
Vested		(348,699	)	$	1.28		—
Forfeited		(250,329	)	$	1.03		—
Outstanding - March 31, 2017		7,224,036		$	1.11		1.39
Expected to vest after March 31, 2017		5,735,089		$	1.15		1.17

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The following table summarizes information about stock options outstanding as of March 31, 2017:

			Options Outstanding						Options Exercisable
Exercise Price			Number of Options		Weighted- Average Remaining Contractual Life (Years)		Weighted-Average Exercise Price		Number of Options		Weighted-Average Exercise Price
$0.28	—	$0.58		795,734		9.48	$	0.49		2,234	$	0.28
$0.59	—	$0.59		2,224,375		9.13	$	0.59		—	$	—
$0.69	—	$1.63		1,491,082		8.67	$	1.30		361,067	$	1.60
$1.64	—	$1.96		2,192,975		7.51	$	1.84		1,026,492	$	1.83
$1.98	—	$2.87		1,780,408		6.07	$	2.69		1,579,154	$	2.73
$2.96	—	$3.44		688,795		6.40	$	3.15		597,154	$	3.13
$3.51	—	$3.51		1,447,979		6.90	$	3.51		1,057,049	$	3.51
$3.55	—	$4.31		1,723,976		3.31	$	3.97		1,683,443	$	3.98
$4.35	—	$26.84		1,111,949		3.52	$	17.71		1,111,949	$	17.71
$30.17	—	$30.17		60,000		3.96	$	30.17		60,000	$	30.17
$0.28	—	$30.17		13,517,273		6.83	$	3.55		7,478,686	$	5.42

Stock-Based Compensation Expense

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):

	Three Months Ended March 31,
	2017		2016
Research and development	$	484	$	491
Sales, general and administrative		1,162		1,560
Total stock-based compensation expense	$	1,646	$	2,051

As of March 31, 2017, there was unrecognized compensation expense of $3.7 million and $4.7 million related to stock options and RSUs, respectively, the Company expects to recognize this expense over a weighted average period of 2.71 years and 2.58 years, respectively.

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Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on their fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended March 31,
	2017			2016
Expected dividend yield		—	%		—	%
Risk-free interest rate		2.1	%		1.4	%
Expected term (in years)		6.15			6.23
Expected volatility		80	%		73	%

Expected Dividend Yield—The Company has never paid dividends and does not expect to pay dividends.

Risk-Free Interest Rate—The risk-free interest rate was based on the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

Expected Term—Expected term represents the period that the Company’s stock-based awards are expected to be outstanding. The Company’s assumptions about the expected term have been based on that of companies that have similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected Volatility—The expected volatility is based on a combination of historical volatility for the Company's stock and the historical stock volatilities of several of the Company’s publicly listed comparable companies over a period equal to the expected terms of the options, as the Company does not have a long trading history.

Forfeiture Rate—The Company estimates its forfeiture rate based on an analysis of its actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior, and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual number of future forfeitures differs from that estimated by the Company, the Company may be required to record adjustments to stock-based compensation expense in future periods.

Each of the inputs discussed above is subjective and generally requires significant management and director judgment.

12. Employee Benefit Plan

The Company established a 401(k) Plan to provide tax deferred salary deductions for all eligible employees. Participants may make voluntary contributions to the 401(k) Plan up to 90% of their eligible compensation, limited by certain Internal Revenue Service (or the "IRS") restrictions. Effective January 2014, the Company implemented a discretionary employer match plan whereby the Company will match employee contributions up to the IRS limit or 90% of compensation, with a minimum one year of service required for vesting. The total matching amount for each of the three months ended March 31, 2017 and 2016 was $0.1 million.

13. Related Party Transactions

Related Party Financings

See Note 5, “Debt and Mezzanine Equity” for a description of the February 2016 Private Placement transaction with Foris Ventures, LLC (or Foris), Naxyris S.A. and Biolding Investment SA, each a related party of the Company, the March 2016 R&D Note transaction with Total and the June 2016 and October 2016 Private Placement transactions with Foris. In addition, see Note 18, “Subsequent Events” for related party financings and related transactions subsequent to March 31, 2017.

As of March 31, 2017 and December 31, 2016, convertible notes and loan with related parties were outstanding in an aggregate amount of $73.9 million and $72.4 million, respectively, net of debt and issuance costs of $6.0 million and $6.7 million, respectively.

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The fair value of the derivative liability related to the related party convertible notes as of March 31, 2017 and December 31, 2016 was $1.4 million and $0.8 million, respectively. The Company recognized a gain from change in fair value of the derivative instruments of $1.1 million and $4.5 million for the three months ended March 31, 2017 and 2016, respectively, (see Note 3, "Fair Value of Financial Instruments" for further details).

Related Party Revenues

The Company recognized no related party revenues from product sales to Total for each of the three months ended March 31, 2017 and 2016. Related party accounts receivable from Total as of March 31, 2017 and December 31, 2016, were $0.3 million and $0.8 million, respectively. In addition, in October 2016 the Company entered into an assistance agreement with the United States Department of Energy, in which Total and Renmatix participate as subcontractors. There was no amount accrued by or due to Total or Renmatix for the three months ended March 31, 2017 and for the year ended December 31, 2016.

Loans to Related Parties

See Note 7, "Joint Ventures and Noncontrolling Interest" for details of the Company's transactions with its affiliate, Novvi LLC.

Joint Venture with Total

In November 2013, the Company and Total formed TAB as discussed above under Note 7, "Joint Ventures and Noncontrolling Interest."

Pilot Plant Agreements

In May 2014, the Company received the final consents necessary for the Pilot Plant Services Agreement (Pilot Plant Services Agreement) and a Sublease Agreement (Sublease Agreement), each dated as of April 4, 2014 (collectively the Pilot Plant Agreements), between the Company and Total. The Pilot Plant Agreements generally have a term of five years. Under the terms of the Pilot Plant Services Agreement, the Company agreed to provide certain fermentation and downstream separations scale-up services and training to Total and receives an aggregate annual fee payable by Total for all services in the amount of up to approximately $0.9 million per annum. In July 2015, Total and the Company entered into Amendment #1 (Pilot Plant Agreement Amendment) to the Pilot Plant Services Agreement whereby the Company agreed to waive a portion of these fees, up to approximately $2.0 million, over the term of the Pilot Plant Services Agreement in connection with the restructuring of TAB discussed above. Prior to February 28, 2017, Total charged its secondees to the Company for research and development services pursuant to an Amended and Restated Secondment Agreement, dated August 1, 2012, between the Company and Total. On February 28, 2017, the Company and Total entered into an amendment to the Amended and Restated Secondment Agreement, which provided that Total would not charge Amyris for the cost of Total’s secondees on or after May 1, 2016, other than overhead charges. Total charges its secondees to the Company for research and development services. The payable to Total under these arrangements was $1.7 million and $2.2 million as of March 31, 2017 and December 31, 2016, respectively.

As of March 31, 2017, the Company had received $1.7 million in cash under the Pilot Plant Agreements from Total. In connection with these arrangements, sublease payments and service fees of $0.0 million and $0.2 million was offset against cost and operating expenses for the three months ended March 31, 2017 and 2016, respectively.

14. Income Taxes

The Company recorded a benefit from income taxes of $0.04 million for the three months ended March 31, 2017 and a provision for income taxes of $0.1 million for the three months ended March 31, 2016. The provision for income taxes for the three months ended March 31, 2017 and 2016 consisted of an accrual of Brazilian withholding tax on intercompany interest on intercompany loans. Other than the above mentioned income tax amounts, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

On December 15, 2011, the IRS completed its audit of the Company for tax year 2008 which concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year 2008, the US federal tax carryforwards (net operating losses and tax credits) may be adjusted by the IRS in the year in which the carryforward is utilized.

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15. Reportable Segments

The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure.

Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

Revenues

	Three Months Ended March 31,
	2017		2016
Europe	$	5,376	$	4,372
United States		3,096		3,462
Asia		4,433		590
Brazil		19		375
Other		56		12
Total	$	12,980	$	8,811

Long-Lived Assets (Property, Plant and Equipment)

	March 31, 2017		December 31, 2016
Brazil	$	39,137	$	44,153
United States		13,683		9,342
Europe		225		240
Total	$	53,045	$	53,735

16. Comprehensive Loss

Comprehensive loss represents all changes in stockholders’ deficit except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive loss excluded from the Company’s net loss and have been disclosed in the condensed consolidated statements of comprehensive loss for the periods presented.

The components of accumulated other comprehensive loss are as follows (in thousands):

	March 31, 2017			December 31, 2016
Foreign currency translation adjustment, net of tax	$	(40,581	)	$	(40,904	)
Total accumulated other comprehensive loss	$	(40,581	)	$	(40,904	)

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17. Net Loss Attributable to Common Stockholders and Net Loss per Share

The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants and convertible promissory notes using the treasury stock method or the as converted method, as applicable. For the three months ended March 31, 2017, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss was the same for that period.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

	Three Months Ended March 31,
	2017			2016
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(37,371	)	$	(15,308	)
Interest on convertible debt		—			1,817
Accretion of debt discount		—			1,633
Gain from change in fair value of derivative instruments		—			(18,415	)
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$	(37,371	)	$	(30,273	)
Denominator:
Weighted average shares of common stock outstanding for basic EPS		290,039,216			207,199,563
Basic and diluted loss per share	$	(0.13	)	$	(0.07	)
Weighted average shares of common stock outstanding		290,039,216			207,199,563
Effect of dilutive securities:
Convertible promissory notes		—			53,732,522
Weighted common stock equivalents		—			53,732,522
Diluted weighted-average common shares		290,039,216			260,932,085
Diluted loss per share	$	(0.13	)	$	(0.12	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock because including them would have been anti-dilutive:

	Three Months Ended March 31,
	2017		2016
Period-end stock options to purchase common stock		13,517,273		12,159,154
Convertible promissory notes(1)		72,826,108		99,648,739
Period-end common stock warrants		5,021,087		5,885,762
Period-end restricted stock units		7,224,036		5,175,430
Total		98,588,504		122,869,085

______________

⁽¹⁾ The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

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18. Subsequent Events

Ginkgo Collaboration Note

On April 13, 2017, the Company issued a secured promissory note to Ginkgo, in the principal amount of $3 million dollars (or the Ginkgo Collaboration Note), in satisfaction of certain payments owed by the Company to Ginkgo under the Ginkgo Collaboration Agreement (see Note 8, “Significant Agreements” above for details regarding the Ginkgo Collaboration Agreement). The Ginkgo Collaboration Note is collateralized by a second priority lien on the assets securing the Company’s obligations under the Senior Secured Loan Facility, and is subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to a Subordination Agreement, dated as of October 27, 2016 and ratified on April 13, 2017, by and among the Company, Ginkgo and Stegodon. Interest will accrue on the Ginkgo Collaboration Note from and including April 13, 2017 at a rate of 13.50% per annum and is payable in full on May 15, 2017, the maturity date of the Ginkgo Collaboration Note, unless the Ginkgo Collaboration Note is prepaid in accordance with their terms prior to such date. The Ginkgo Collaboration Note contains customary terms, provisions, representations and warranties, including certain events of default after which the Ginkgo Collaboration Note may be due and payable immediately, as set forth in the Ginkgo Collaboration Note.

April 2017 Convertible Note Offering

On April 13, 2017, the Company entered into a securities purchase agreement (or the April 2017 Purchase Agreement) between the Company and a private investor (or the Purchaser) relating to the sale of up to $15.0 million aggregate principal amount of convertible notes (or the April 2017 Convertible Notes) that are convertible into shares of the Company’s common stock at an initial conversion price of $1.90 per share. The April 2017 Purchase Agreement includes customary representations, warranties and covenants by the Company. The April 2017 Purchase Agreement also provides the Purchaser with a right of first refusal with respect to any variable rate transaction, subject to certain exceptions, on the same terms and conditions as are offered to a third-party purchaser for as long as the Purchaser holds any April 2017 Convertible Notes or shares of common stock underlying the April 2017 Convertible Notes.

The April 2017 Convertible Notes will be issued and sold in two separate closings. The initial closing occurred on April 17, 2017. At the initial closing, the Company issued and sold an April 2017 Convertible Note in a principal amount of $7.0 million to the Purchaser. If the Purchaser so elects at its option and in its sole discretion, the second closing will occur on or prior to December 31, 2017, subject to the satisfaction of certain closing conditions, including certain equity conditions. At the second closing, the Company will issue and sell an April 2017 Convertible Note in a principal amount of $8.0 million to the Purchaser. 

The April 2017 Convertible Notes are general unsecured obligations of the Company. Unless earlier converted or redeemed, the April 2017 Convertible Notes will mature on or about the 18-month anniversary of their respective issuance, subject to the rights of the holders to extend the maturity date in certain circumstances.

The April 2017 Convertible Notes are payable in monthly installments, in either cash at 118% of such installment amount or, at the Company’s option, subject to the satisfaction of certain equity conditions, shares of common stock at a discount to the then-current market price, subject to a price floor. In addition, in the event that the Company elects to pay all or any portion of a monthly installment in common stock, the holders of the April 2017 Convertible Notes shall have the right to require that the Company repay in common stock an additional amount of the April 2017 Convertible Notes not to exceed 50% of the cumulative sum of the aggregate amounts by which the dollar-weighted trading volume of the common stock for all trading days during the applicable installment period exceeds $200,000.

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The April 2017 Convertible Notes contain customary terms and covenants, including certain events of default after which the holders may require the Company to redeem all or any portion of their April 2017 Convertible Notes in cash at a price equal to the greater of (i) 118% of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

In the event of a Fundamental Transaction (as defined in the April 2017 Convertible Notes), holders of the April 2017 Convertible Notes may require the Company to redeem all or any portion of their April 2017 Convertible Notes at a price equal to the greater of (i) 118% of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

The Company has the right to redeem the April 2017 Convertible Notes for cash, in whole, at any time, or in part, from time to time, at a redemption price equal to 118% of the principal amount of the April 2017 Convertible Notes to be redeemed.

The April 2017 Convertible Notes will be convertible from time to time, at the election of the holders, into shares of common stock at an initial conversion price of $1.90 per share. The conversion price will be subject to adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

Notwithstanding the foregoing, the holders will not have the right to convert any portion of an April 2017 Convertible Note, and the Company will not have the option to pay any amount in shares of common stock, if (a) the holder, together with its affiliates, would beneficially own in excess of 4.99% (or such other percentage as determined by the holder and notified to the Company in writing, not to exceed 9.99%, provided that any increase of such percentage will not be effective until 61 days after notice thereof) of the number of shares of common stock outstanding immediately after giving effect to such conversion or payment, as applicable, or (b) the aggregate number of shares issued with respect to the April 2017 Convertible Notes (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed 54,676,770 shares of common stock (or the Exchange Cap). In the event that the Company is prohibited from issuing any shares of common stock under the April 2017 Convertible Notes as a result of the Exchange Cap, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess of the Exchange Cap. In addition, pursuant to the April 2017 Purchase Agreement, in the event that the aggregate number of shares of common stock issuable with respect to the April 2017 Convertible Notes (and any other transaction aggregated for such purpose) would equal or exceed 49,233,710 of shares of common stock, the Company will be required to take all actions necessary for, and use its reasonable best efforts to solicit and obtain, stockholder approval for the issuance of shares of common stock in excess of the Exchange Cap.

For as long as they hold April 2017 Convertible Notes or shares of common stock issued under the April 2017 Convertible Notes, the holders may not sell any shares of common stock at a price less than $1.05 per share; provided, that with respect to any shares of Common Stock issued under the April 2017 Convertible Notes at a price less than $1.00, the holders may sell such shares at a price not less than the price floor applicable to the installment period with respect to which such shares were issued.

Amendment to Convertible Notes

On May 2, 2017, in connection with the Purchaser agreeing to extend the time period for certain obligations of the Company under the April 2017 Purchase Agreement, the Company and the Purchaser entered into an Amendment Agreement (or the Amendment Agreement) with respect to the December 2016 Purchase Agreement, the April 2017 Purchase Agreement, the December 2016 Convertible Note and the April 2017 Convertible Notes (or the Amended Notes). Pursuant to the Amendment Agreement, the Company and the Purchaser agreed, among other things, to amend the December 2016 Convertible Note and the April 2017 Convertible Notes to (i) reduce the price at which the Company may pay monthly installments under the Amended Notes in shares of common stock from a 10% discount to a market-based price to a 20% discount to a market-based price and (ii) reduce the price floor related to any such payment from 80% of, in the case of the December 2016 Convertible Note, the volume-weighted average price per share (VWAP) of the Company’s common stock on the trading day immediately preceding the applicable installment date and, in the case of the April 2017 Convertible Notes, the arithmetic average of the VWAP of the Company’s common stock for the five trading days immediately preceding the applicable installment date, to 70% of such amount. The closing of the Amendment Agreement and the issuance of the Amended Notes is subject to customary closing conditions.

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Blue California

In April 2017, the Company announced that it had amended the terms of its December 2016 Intellectual Property License and Strain Access Agreement with Blue California to take a minority equity stake in SweeGen, Inc. (or SweeGen), one of Blue California’s affiliates focused on the sweetener market, in lieu of a $10 million cash payment for intellectual property transferred to Blue California in December 2016. On April 21, 2017, Amyris received 850,115 shares of SweeGen common stock in satisfaction of Blue California’s payment obligation under the Intellectual Property License and Strain Access Agreement.

May 2017 Financing Transactions

On May 8, 2017, the Company entered into a Securities Purchase Agreement (or the May 2017 Purchase Agreement) with certain investors for the issuance and sale of 22,140 shares of the Company’s Series A 17.38% Convertible Preferred Stock, par value $0.0001 per share (or the Series A Preferred Stock), 65,203.8756 shares of the Company’s Series B 17.38% Convertible Preferred Stock, par value $0.0001 per share (or the Series A Preferred Stock and, together with the Series A Preferred Stock, the Preferred Stock), which Preferred Stock is convertible into the Company’s common stock, par value $0.0001 per share as described below, and Cash Warrants (as defined below) to purchase an aggregate of 207,954,414 shares of Common Stock and Dilution Warrants (as defined below) (or, collectively, the May 2017 Warrants, and the shares of common stock issuable upon exercise of the Warrants, the May 2017 Warrant Shares) (or the May 2017 Offering).

On May 11, 2017, the Company and the investors closed the issuance and sale of the Series A Preferred Stock, Series B Preferred Stock and May 2017 Warrants (or the May 2017 Offering Closing). The net proceeds to the Company from the May 2017 Offering were approximately $44.5 million after payment of the estimated offering expenses and placement agent fees. The Series A Preferred Stock and May 2017 Warrants relating thereto were sold to the purchasers thereof in exchange for aggregate cash consideration of $22,140,000, and the Series B Preferred Stock and May 2017 Warrants relating thereto were sold to the purchasers thereof in exchange for (i) aggregate cash consideration of $25,000,000 and (ii) the cancellation of approximately $40.2 million of outstanding indebtedness (including accrued interest thereon) owed by the Company to such purchasers, as further described below.

The May 2017 Purchase Agreement includes customary representations, warranties and covenants of the parties. In addition, pursuant to the May 2017 Purchase Agreement, the Company, subject to certain exceptions, including the issuance of the Second Tranche Securities (as defined below), (i) may not issue, enter into any agreement to issue or announce the issuance or proposed issuance of any shares of Common Stock or securities convertible into or exercisable or exchangeable for Common Stock until July 31, 2017 and (ii) may not enter into an agreement to effect any issuance by the Company involving a variable rate transaction until one year from the May 2017 Offering Closing (as defined below).

Series A Preferred Stock

Each share of Series A Preferred Stock has a stated value of $1,000 and is convertible at any time, at the option of the holder, into Common Stock at an initial conversion price of $1.15 per share (or the Preferred Stock Conversion Rate). The Preferred Stock Conversion Rate is subject to adjustment in the event of any dividends or distributions of common stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction. If not previously converted at the option of the holder, each share of Series A Preferred Stock will be automatically converted, without any further action by the holder, on the 90th day following the date that the Stockholder Approval (as defined below) has been obtained and effected.

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Dividends, at a rate per year equal to 17.38% of the stated value of the Series A Preferred Stock, will be payable semi-annually from the issuance of the Series A Preferred Stock until the tenth anniversary of the date of issuance, on each October 15 and April 15, beginning October 15, 2017, on a cumulative basis, at the Company’s option, in cash, out of any funds legally available for the payment of dividends, or, subject to the satisfaction of certain conditions, in Common Stock at the Preferred Stock Conversion Rate, or a combination thereof. In addition, upon the conversion of the Series A Preferred Stock prior to the tenth anniversary of the date of issuance, the holders of the Series Preferred A Stock shall be entitled to a payment equal to $1,738 per $1,000 of stated value of the Series A Preferred Stock, less the amount of all prior semi-annual dividends paid on such converted Series A Preferred Stock prior to the relevant conversion date (the Preferred Stock Make-Whole Payment), at the Company’s option, in cash, out of any funds legally available for the payment of dividends, or, subject to the satisfaction of certain conditions, in Common Stock at the Preferred Stock Conversion Rate, or a combination thereof. If the Company elects to pay any dividend in the form of cash, it shall provide each holder with notice of such election not later than the first day of the month of prior to the applicable dividend payment date.

Unless and until converted into common stock in accordance with its terms, the Series A Preferred Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the Series A Preferred Stock.

In the event of a fundamental transaction, the holders of the Series A Preferred Stock will have the right to receive the consideration receivable as a result of such fundamental transaction by a holder of the number of shares of Common Stock for which the Series A Preferred Stock is convertible immediately prior to such fundamental transaction (without regard to whether such Series A Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of Common Stock.

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series A Preferred Stock shall be entitled to receive out of the assets of the Company the same amount that a holder of Common Stock would receive if the Series A Preferred Stock were fully converted to Common Stock immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series A Preferred Stock is convertible at such time) , which amount shall be paid pari passu with all holders of Common Stock.

Notwithstanding the foregoing, the holders (other than the Designated Holder (as defined below)) will not have the right to convert any Series A Preferred Stock, and the Company shall not effect any conversion of the Series A Preferred Stock, if the holder, together with its affiliates, would beneficially own in excess of 4.99% (or such other percentage as determined by the holder and notified to the Company in writing, not to exceed 9.99%, provided that any increase of such percentage will not be effective until 61 days after notice thereof) of the number of shares of common stock outstanding immediately after giving effect to the issuance of shares of common stock issuable upon conversion of such Series A Preferred Stock.

On May 8, 2017, the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series A 17.38% Convertible Preferred Stock with the Secretary of State of Delaware.

Series B Preferred Stock

The Series B Preferred Stock will have substantially identical terms to the Series A Preferred Stock (as described above), except that the issuance of the shares of common stock issuable upon conversion of the Series B Preferred Stock or as payment of dividends or the Make-Whole Payment on the Series B Preferred Stock (or the Series B Conversion Shares) will be subject to the Stockholder Approval (as defined below).

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The investors that purchased shares of the Series B Preferred Stock included existing stockholders of the Company affiliated with certain members of our Board of Directors (or the Affiliated Investors): Foris Ventures, LLC (Foris, an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder), which purchased 30,728.589 shares of Series B Preferred Stock and May 2017 Warrants to purchase 73,160,764 shares of Common Stock; and Naxyris S.A. (or Naxyris, an investment vehicle owned by Naxos Capital Partners SCA Sicar; director Carole Piwnica is Director of NAXOS UK, which is affiliated with Naxos Capital Partners SCA Sicar), which purchased 2,333.216 shares of Series B Preferred Stock and May 2017 Warrants to purchase 5,556,038 shares of common stock. The Affiliated Investors purchased their respective shares of Series B Preferred Stock and Warrants in exchange for the cancellation of existing indebtedness of the Company held by such Affiliated Investors: Foris agreed to exchange an aggregate principal amount of $27.0 million of indebtedness, plus accrued interest thereon, issued to Foris by the Company on February 12, 2016, June 24, 2016 and October 21, 2016, as described above in Note 5, “Debt and Mezzanine Equity”; and Naxyris exchanged an aggregate principal amount of $2.0 million of indebtedness, plus accrued interest thereon, issued to Naxyris by the Company on February 12, 2016, as described above in Note 5, “Debt and Mezzanine Equity”.

In addition, the investors that purchased shares of the Series B Preferred Stock included holders of certain of the Company’s existing indebtedness, including the 2014 144A Notes and the 2015 144A Notes (see Note 5, “Debt and Mezzanine Equity” for details regarding the terms of the 2014 144A Notes and the 2015 144A Notes), which investors exchanged all or a portion of their holding of such indebtedness, including accrued interest thereon, representing an aggregate of $3.4 million of 2014 144A Notes and approximately $3.7 million of 2015 144A Notes, for Series B Preferred Stock and May 2017 Warrants in the May 2017 Offering. Upon the May 2017 Offering Closing, such indebtedness was cancelled and the agreements relating thereto, including any note purchase agreements or unsecured or secured promissory notes (including any security interest relating thereto), were terminated, except to the extent such investors or other investors retain a portion of such indebtedness.

The Series B Preferred Stock was issued in a private placement pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act.

On May 8, 2017, the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series B 17.38% Convertible Preferred Stock with the Secretary of State of Delaware.

May 2017 Warrants

Pursuant to the May 2017 Purchase Agreement, at the May 2017 Offering Closing the Company issued to each investor (i) a warrant, with an exercise price of $0.52 per share, to purchase a number of shares of Common Stock equal to 50% of the shares of common stock into which such investor’s shares of Preferred Stock were initially convertible (including shares of Common Stock issuable as payment of the Make-Whole Payment, assuming that the Make-Whole Payment is made in Common Stock), representing warrants to purchase 103,977,207 shares of common stock in the aggregate for all investors and (ii) a warrant, with an exercise price of $0.62 per share, to purchase a number of shares of Common Stock equal to 50% of the shares of common stock into which such investor’s shares of Preferred Stock were initially convertible (including shares of Common Stock issuable as payment of the Make-Whole Payment, assuming that the Make-Whole Payment is made in Common Stock), representing warrants to purchase 103,977,207 shares of common stock in the aggregate for all investors (or, collectively, the Cash Warrants). The exercise price of the Cash Warrants is subject to standard adjustments as well as full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the three-year period following the May 2017 Offering Closing at a per share price (including any conversion or exercise price, if applicable) less than the then-current exercise price of the Cash Warrants, subject to certain exceptions.

In addition, at the May 2017 Offering Closing, the Company issued to each investor a warrant, with an exercise price of $0.0001 per share (or, collectively, the Dilution Warrants), to purchase a number of shares of common stock sufficient to provide the investor with full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the three-year period following the May 2017 Offering Closing at a per share price (including any conversion or exercise price, if applicable) less than $0.42 per share, the effective per share price paid by the investors for the shares of common stock issuable upon conversion of the Preferred Stock purchased by the investors in the May 2017 Offering (including shares of common stock issuable as payment of dividends or the Make-Whole Payment, assuming that all such dividends and the Make-Whole Payment are made in common stock), subject to certain exceptions.

The exercise of the May 2017 Warrants will be subject to the Stockholder Approval (as defined below). The May 2017 Warrants each have a term of five years from the date the Warrants are initially exercisable following the Stockholder Approval.

The May 2017 Warrants were issued in a private placement pursuant to the exemption from registration under Section 4 (a)(2) of the Securities Act and Regulation D promulgated under the Securities Act.

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Stockholder Approval

Pursuant to the May 2017 Purchase Agreement, the Company has agreed to solicit from the Company’s stockholders (i) any approval for the transactions contemplated by the May 2017 Purchase Agreement required by the rules and regulations of the NASDAQ Stock Market, including without limitation the issuance of shares of common stock upon conversion of the Series B Preferred Stock and upon exercise of the May 2017 Warrants (or the NASDAQ Approval) and (ii) approval to effect a reverse stock split of the common stock (together with the NASDAQ Approval, collectively, the Stockholder Approval) at an annual or special meeting of stockholders to be held on or prior to July 10, 2017, and to use commercially reasonable efforts to secure the Stockholder Approval. As described in more detail below, the parties subject to the Voting Agreements (as defined below) have agreed to vote in favor of the Stockholder Approval. The Company has presented a 15-for-1 reverse stock split to its stockholders for approval at its 2017 Annual Meeting of Stockholders to be held on May 23, 2017 (or the Annual Meeting), and intends to solicit the NASDAQ Approval at a special meeting of stockholders to occur on or prior to July 10, 2017 (or the Special Meeting and, together with the Annual Meeting, the Stockholder Meetings) Pursuant to the May 2017 Purchase Agreement, if the Company does not obtain Stockholder Approval at the Stockholder Meetings, the Company will call a stockholder meeting every four months thereafter to seek the Stockholder Approval until the earlier of the date Stockholder Approval is obtained or the Preferred Stock and May 2017 Warrants are no longer outstanding.

Registration Rights

Pursuant to the May 2017 Purchase Agreement, within 30 calendar days of the date of the Stockholder Approval, the Company has agreed to file a registration statement on Form S-3 (or other appropriate form if the Company is not then S-3 eligible) providing for the resale by the Investors of the Series B Conversion Shares and May 2017 Warrant Shares. The Company shall use commercially reasonable efforts to cause such registration statement to become effective within 181 days following the Closing and commercially reasonable efforts to keep such registration statement effective at all times until (i) no Investor owns any Series B Conversion Shares or May 2017 Warrant Shares or (ii) the Series B Conversion Shares and May 2017 Warrant Shares are eligible for resale under Rule 144 without regard to volume limitations.

Stockholder Agreement

In connection with, and as a condition to, the May 2017 Offering Closing, on May 11, 2017, the Company and one of the investors, DSM International B.V. (or the Designated Holder), a subsidiary of Koninklijke DSM N.V., entered into a Stockholder Agreement (or the Stockholder Agreement) setting forth certain rights and obligations of the Designated Holder and the Company. The Designated Holder purchased 25,000 shares of Series B Preferred Stock, Cash Warrants for the purchase of 59,521,740 shares of Common Stock and Dilution Warrants in the May 2017 Offering in exchange for aggregate cash consideration of $25,000,000. Pursuant to the Stockholder Agreement, the Designated Holder will have the right to designate one director selected by the Designated Holder (a Designated Holder Director), subject to certain restrictions, to the Company’s Board of Directors (or the Board). The Company will agree to appoint the Designated Holder Director and to use reasonable efforts, consistent with the Board’s fiduciary duties, to cause the Designated Holder Director to be re-nominated in the future; provided, that the Designated Holder will no longer have the right to designate any Designated Holder Director at such time as the Designated Holder holds less than 4.5% of the Company’s outstanding common stock. In addition, for as long as there is a Designated Holder Director serving on the Board, the Company will agree not to engage in certain commercial or financial transactions or arrangements without the consent of any then-serving Designated Holder Director. The Company will also agree to provide the Designated Holder with certain exclusive negotiating rights in connection with certain future commercial projects and arrangements, whereby the Designated Holder will have a 60-day negotiation period with respect to any such projects, as well as a right to use a portion of the Company’s manufacturing capacity for toll manufacturing of the Designated Holder’s products, subject to certain conditions, including, with respect to the toll manufacturing option, that the Designated Holder provide the Company with a minimum annual level of cash funding in connection with commercial activity between the Company and the Designated Holder, beginning in 2018. The Designated Holder will also have the right to purchase additional shares of capital stock of the Company in connection with a sale of equity or equity-linked securities by the Company in a capital raising transaction for cash, subject to certain exceptions, to maintain its proportionate ownership percentage in the Company. At the May 2017 Offering Closing, the Company and the Designated Holder entered into licenses granted by the Company to the Designated Holder with respect to certain Company intellectual property useful in the Designated Holder’s business, which licenses will become effective upon the occurrence of certain events specified therein.

Pursuant to the Stockholder Agreement, the Designated Holder agreed not to sell or transfer any of the shares of Series B Preferred Stock or May 2017 Warrants purchased by the Designated Holder in the Offering, any Second Tranche Securities (as defined below), or any shares of Common Stock issuable upon conversion or exercise thereof (or the Transfer Restricted Shares), other than to its affiliates, without the consent of the Company during the one-year period following the May 2017 Closing. Thereafter, the Designated Holder will have the right to sell or transfer the Transfer Restricted Shares to any third party, other than a competitor of the Company or any controlled affiliate of a competitor of the Company; provided, that the Company will have a customary right of first offer with respect to any such sale or transfer other than to affiliates of the Designated Holder. In addition, the Designated Holder will agree that, other than in connection with the purchase, conversion or exercise of (i) the Series B Preferred Stock or May 2017 Warrants purchased by the Designated Holder pursuant to the May 2017 Purchase Agreement or (ii) the Second Tranche Securities (as defined below) in accordance with their terms or the exercise of its pre-emptive rights, until three months after there is no Designated Holder Director on the Board, the Designated Holder will not, without the prior consent of the Board, among other things, purchase any Common Stock, any options or other rights to acquire Common Stock or any indebtedness of the Company, or make any public offer to acquire common stock, options or other rights to acquire common stock or indebtedness of the Company, that would result in the Designated Holder and its affiliates beneficially owning more than 33% of the Company’s outstanding voting securities at the time of acquisition (assuming the exercise or conversion, whether then exercisable or convertible, of any shares of Series B Preferred Stock, May 2017 Warrants or Second Tranche Securities beneficially owned by the Designated Holder and/or its affiliates), join in any solicitation of proxies for any matter not previously approved by the Board, or join any “group” (as such term is defined in Section 13(d)(3) of the Securities Exchange Act of 1934) with respect to any of the foregoing.

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In addition, the Company has agreed to register, via one or more registration statements filed with the SEC under the Securities Act, the shares of common stock issuable upon conversion or exercise, as applicable, of the Series B Preferred Stock, May 2017 Warrants and Second Tranche Securities held by the Designated Holder. Under the terms of the Stockholder Agreement, the Company is required to file such registration statement within 180 days following the May 2017 Closing, and to use its commercially reasonable efforts to cause the Registration Statement to be declared effective by the SEC as soon as practicable and no later than the 225th day following the May 2017 Closing. In addition, the Designated Holder may request that up to three of such registrations provide for an underwritten offering of such shares. In addition, if the Company registers any of its securities for public sale under the Securities Act, the Designated Holder will have the right to include their shares in the registration statement, subject to certain exceptions. The managing underwriter of any underwritten offering will have the right to limit, due to marketing reasons, the number of shares registered by the Designated Holder to 25% of the total shares covered by the registration statement. The Company will agree to pay all expenses incurred in connection with the exercise of such demand and piggyback registration rights, except for legal costs of the Designated Holder, stock transfer taxes and underwriting discounts and commissions.

Pursuant to the Stockholder Agreement, the Company and the Designated Holder have agreed to negotiate in good faith during the 90-day period following the May 2017 Closing to mutually agree on certain terms and conditions upon which the Designated Holder shall purchase additional shares of Series B Preferred Stock and warrants (or the Second Tranche Securities), in an amount to be agreed by the Company and the Designated Holder, provided such amount is no less than $25 million and no more than $30 million (such amount, the Second Tranche Funding Amount) prior to the end of such 90-day period (or the Second Tranche Funding). The Second Tranche Funding is subject to approval of the Designated Holder’s managing board. In connection with the Second Tranche Funding, the Company and the Designated Holder shall enter into an amendment to the Stockholder Agreement providing for a second Designated Holder Director on terms to be agreed by the parties, and certain of the License Agreements will become effective. If the Second Tranche Funding occurs, the parties will thereafter negotiate in good faith regarding an agreement concerning the development of certain products in the health and nutrition field. In the event that the parties do not reach such agreement prior to the earlier of 90 days after the Second Tranche Funding or December 31, 2017, (a) the exclusive negotiating right granted to the Designated Holder in connection with certain future commercial projects and arrangements of the Company will expire, (b) on the first anniversary of the closing of the Second Tranche Funding and each subsequent anniversary thereof, the Company will make a $5 million cash payment to the Designated Holder, provided that the aggregate amount of such payments shall not exceed the Second Tranche Funding Amount, and (c) an intellectual property escrow agreement relating to the License Agreements, entered into by the Company and the Designated Holder at the Closing, will become effective.

Exchange

In connection with the transactions contemplated by the May 2017 Purchase Agreement, on May 8, 2017, the Company entered into a Security Holder Agreement with Foris and Naxyris. Pursuant to the Security Holder Agreement, Foris and Naxyris agreed to exchange (or the May 2017 Exchange) their outstanding shares of common stock, representing a total of 20,920,578 shares, for 20,920.578 shares of the Company’s Series C Convertible Preferred Stock, par value $0.0001 per share (or the Series C Preferred Stock). In addition, pursuant to the Security Holder Agreement, Foris and Naxyris agreed to not convert any of their outstanding convertible promissory notes, warrants and any other equity-linked securities of the Company until the Stockholder Approval, to not sell or otherwise transfer or assign any voting securities of the Company prior to the Stockholder Approval, and to vote any shares of Common Stock and Series C Preferred Stock beneficially owned by them in favor of the Stockholder Approval. The Exchange was consummated concurrently with the closing of the May 2017 Offering.

Series C Preferred Stock

Each share of Series C Preferred Stock has a stated value of $1,000 and will automatically convert into common stock upon the approval by the Company’s stockholders and implementation of the reverse stock split, on a 1:1 basis (i.e., each $1 of stated value of the Series C Preferred Stock will convert into 1 share of Common Stock) (or the Series C Conversion Rate). The Series C Conversion Rate is subject to adjustment in the event of any dividends or distributions of the common stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

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The Series C Preferred Stock will be entitled to participate with the common stock on an as-converted basis with respect to any dividends or other distributions to holders of common stock.

The Series C Preferred Stock shall vote together as one class with the Common Stock on an as-converted basis, and shall also vote with respect to matters specifically affecting the Series C Preferred Stock.

In the event of a fundamental transaction, the holders of the Series C Preferred Stock will have the right to receive the consideration receivable as a result of such fundamental transaction by a holder of the number of shares of common stock for which the Series C Preferred Stock is convertible immediately prior to such fundamental transaction (without regard to whether such Series C Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of common stock.

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series C Preferred stock shall be entitled to receive out of the assets of the Company an amount equal to the greater of (i) the par value of each share of Series C Preferred Stock, plus any accrued and unpaid dividends or other amounts due on such Series C Preferred Stock, prior to any distribution or payment to the holders of common stock or (ii) the amount that a holder would receive if the Series C Preferred Stock were fully converted to common stock immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series C Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of Common Stock.

On May 8, 2017, the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series C Convertible Preferred Stock with the Secretary of State of Delaware.

The Series C Preferred Stock will be issued in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the Securities Act.

Voting Agreements

In connection with the transactions contemplated by the May 2017 Purchase Agreement, the Company and certain stockholders of the Company, including Total, Temasek and Biolding Investment SA, entered into Voting Agreements, pursuant to which such existing stockholders agreed to vote their shares of common stock in favor of the Stockholder Approval. The stockholders who are party to the Voting Agreements held approximately 51.2% of the Company’s outstanding common stock as of April 30, 2017.

Nenter Termination Agreement

In connection with the transactions contemplated by the May 2017 Purchase Agreement and the Stockholder Agreement, on May 8, 2017, the Company and Nenter & Co., Inc. (or Nenter) entered into a letter agreement to terminate the Cooperation Agreement, dated as of October 26, 2016, between the Company and Nenter, pursuant to which the parties had agreed to collaborate to create and develop certain compounds and, in the event the parties achieved certain specified development targets, to establish and implement a worldwide manufacturing and commercialization plan relating thereto. In connection with the termination of the Cooperation Agreement, the Company agreed to pay Nenter a fee of $2.5 million on or before June 22, 2017.

Temasek Letter Agreement

On May 5, 2017, the Company entered into a letter agreement with Temasek, pursuant to which the Company and Temasek agreed that Temasek’s Remaining Notes under the Maturity Treatment Agreement ($10.0 million s of March 31, 2017) would no longer be subject to mandatory conversion by Temasek at or prior to the maturity of such Remaining Notes. Accordingly, the Company will be required to pay any portion of such Remaining Notes that remain outstanding at maturity in cash in accordance with the terms of such Remaining Notes. See Note 5, “Debt and Mezzanine Equity” for details regarding the Maturity Treatment Agreement and the Remaining Notes.

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ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Forward-Looking Statements

The following discussion and analysis should be read in conjunction with our condensed consolidated financial statements and the related notes that appear elsewhere in this Form 10-Q. These discussions contain forward-looking statements reflecting our current expectations that involve risks and uncertainties which are subject to safe harbors under the Securities Act of 1933, as amended, or the Securities Act, and the Securities Exchange Act of 1934, as amended, or the Exchange Act. These forward looking statements include, but are not limited to, statements concerning our strategy of achieving a significant reduction in net cash outflows in 2016, future production capacity and other aspects of our future operations, ability to improve our production efficiencies, future financial position, future revenues, projected costs, expectations regarding demand and acceptance for our technologies, growth opportunities and trends in the market in which we operate, prospects and plans and objectives of management. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements and you should not place undue reliance on our forward looking statements. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in Part II, Item 1A, “Risk Factors,” in this Quarterly Report on Form 10-Q and in our other filings with the Securities and Exchange Commission. We do not assume any obligation to update any forward-looking statements.

Trademarks

Amyris, the Amyris logo, Biofene, Biossance, Dial-A-Blend, Diesel de Cana, Evoshield, µPharm, Muck Daddy, Myralene, Neossance and No Compromise are trademarks or registered trademarks of Amyris, Inc. This report also contains trademarks and trade names of other businesses that are the property of their respective holders.

Overview

Amyris, Inc. (referred to as the “Company,” “Amyris,” “we,” “us,” or “our”) is a leading integrated industrial biotechnology company that is applying its technology platform to engineer, manufacture and sell high performance, low cost products into the Health and Nutrition, Personal Care and Performance Materials markets. Our proven technology platform allows us to rapidly engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. Our biotechnology platform and industrial fermentation process replaces existing complex and expensive chemical manufacturing processes. We believe industrial synthetic biology represents a third industrial revolution, bringing together biology and engineering to generate new, more sustainable materials to meet the growing global demand for bio-based replacements for petroleum, animal- or plant-derived ingredients. We continue to build demand for our current portfolio of products through a sales network comprised of direct sales and distributors, and are engaged in collaborations across each of our three market focus areas to drive additional product sales and partnership opportunities. Via our partnership model, we co-invest in the development of each molecule to bring it from the lab to commercial scale and then capture long term revenue either via the sale of the molecule to the partner and/or value sharing of end product sales.

Amyris was founded in 2003 in the San Francisco Bay Area by a group of scientists from the University of California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda Gates Foundation, we developed technology capable of creating microbial strains that produce artemisinic acid - a precursor of artemisinin, an effective anti-malarial drug. In 2008, we granted royalty-free licenses to allow Sanofi-Aventis (Sanofi) to produce artemisinic acid using our technology. Building on our success with artemisinic acid, in 2007 we began applying our technology platform to develop, manufacture and sell sustainable alternatives to a broad range of markets..

We focused our initial development efforts primarily on the production of Biofene^®, our brand of renewable farnesene, a long-chain, branched hydrocarbon molecule that we manufacture through fermentation using engineered microbes. Our farnesene derivatives are sold in hundreds of products as nutraceuticals, skin care, fragrances, solvents, polymers, and lubricants ingredients. The commercialization of farnesene pushed us to create a more cost efficient, faster and accurate development process in the lab and drive costs out of our Brotas, Brazil production facility. This investment has enabled our technology platform to rapidly develop microbial strains and commercialize target molecules. In 2014, we began manufacturing additional molecules for the flavors and fragrance (F&F) industry, in 2015 we began investing to expand our capabilities to other small molecule chemical classes beyond terpenes via our collaboration with the Defense Advanced Research Project Agency (DARPA), as discussed above, and in 2016 we expanded into proteins.

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We have invested over $500 million in infrastructure and technology to create microbes that produce chemicals from sugar or other feedstocks at commercial scale. This platform has been used to design, build, optimize, and upscale strains producing four distinct molecules, leading to more than 15 commercial products used in over 500 consumer products. Our time to market for molecules has decreased from seven years to less than a year for our most recent molecule, mainly due to our ability to leverage the technology platform we have built.

Our technology platform has been in active use since 2008, and has been integrated with our commercial production since 2011, creating a seamless organism development process that we believe makes Amyris an industry leader in the successful scale-up of small molecules. The key performance characteristics of our platform that we believe differentiate Amyris include our proprietary computational tools, strain construction tools, screening and analytics tools, and advanced lab automation and data integration. Our state-of-the-art infrastructure includes industry leading strain engineering and lab automation located in Emeryville, CA, pilot scale production facilities in Emeryville, CA and Campinas, Brazil, a demonstration scale facility in Campinas, Brazil and a commercial scale production facility in Brotas, Brazil.

We are able to use a wide variety of feedstocks for production, but have focused on accessing Brazilian sugarcane for our large-scale production because of its renewability, low cost and relative price stability. We have also successfully used other feedstocks such as sugar beets, corn dextrose, sweet sorghum and cellulosic sugars at various manufacturing facilities.

We are currently producing three molecules at our Brotas, Brazil plant: farnesene and two fragrance molecules.

Our mission is to apply innovative science to deliver sustainable solutions for a growing world. We seek to become the world's leading provider of renewable, high-performance alternatives to non-renewable and scarce products. In the past, choosing a renewable product often required producers to compromise on performance or price. With our technology, leading consumer brands can develop products made from renewable sources that offer equivalent or better performance and stable supply with competitive pricing. We call this our No Compromise® value proposition. We aim to improve the world one molecule at a time by providing the best alternatives to the products the world relies on every day.

We have developed and are operating our company under a business model that generates cash from collaborations, from product sales, and value share. We believe this combination will enable us to realize our vision of becoming the world’s leading renewable products company.

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Sales and Revenues

Our revenues are comprised of product revenues and grants and collaborations revenues. We generate the substantial majority of our product revenues from sales to distributors or collaborators and only a small portion from direct sales, although we have begun to market and sell some of our products directly to end-consumers, initially in the cosmetics and industrial cleaning markets. To commercialize our initial Biofene-derived product, squalane, in the cosmetics sector for use as an emollient, we have entered into certain marketing and distribution agreements in Europe, Asia, and North America. For the industrial lubricants market, we established a joint venture with Cosan U.S. for the worldwide development, production and commercialization of renewable base oils in the lubricant sector. We have also entered into certain supply agreements with customers in the F&F industry to commercialize products derived from our fragrance molecules. In addition, we have entered into research and development collaboration arrangements pursuant to which we receive payments from our collaborators, which include Total, Manufacture Francaise de Pnematiques Michelin, The Defense Advanced Research Projects Agency, Givaudan International, SA and Cosan US, Inc. Some of such collaboration arrangements include advance payments in consideration for grants of exclusivity or research efforts to be performed by us. Once a collaboration agreement has been signed, receipt of payments may depend on our achievement of milestones. See Note 8, “Significant Agreements” to our unaudited condensed consolidated financial statements included in this report for more details regarding these agreements and arrangements.

Financing

In February 2016, we issued to certain purchasers an aggregate of $20.0 million of unsecured promissory notes and warrants for the purchase, at an exercise price of $0.01 per share, of an aggregate of 2,857,142 shares of our common stock, as described in more detail in Note 5, “Debt and Mezzanine Equity” to our unaudited condensed consolidated financial statements included in this report. The exercisability of these warrants was subject to stockholder approval, which was obtained on May 17, 2016.

In March 2016, we sold to Total one half of our ownership stake in TAB in exchange for Total cancelling $1.3 million of R&D Notes and certain other indebtedness, as described in more detail under “Relationship with Total” above and in Note 5, “Debt and Mezzanine Equity” and Note 7, “Joint Ventures and Noncontrolling Interest” to our unaudited condensed consolidated financial statements included in this report.

In May 2016, we sold and issued 4,385,964 shares of common stock to the Bill & Melinda Gates Foundation at a purchase price per share of $1.14.

In May, September, October and December 2016, we sold and issued $25.0 million in aggregate principal amount of convertible promissory notes to a private investor, as described in more detail in Note 5, “Debt and Mezzanine” and Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report.

In June and October 2016, we sold and issued $19.5 million in aggregate principal amount of secured promissory notes to Foris Ventures, LLC, an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, and Ginkgo, as described in more detail in Note 5, “Debt and Mezzanine Equity” to our unaudited condensed consolidated financial statements included in this report.

In October 2016, we entered into a credit agreement with Guanfu Holding Co., Ltd. to make available to Amyris an unsecured credit facility with an aggregate principal amount of up to $25.0 million, which amount was fully drawn on December 31, 2016, as described in more detail in Note 5, “Debt and Mezzanine Equity” to our unaudited condensed consolidated financial statements included in this report.

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In December 2016, we sold and issued a purchase money promissory note in the principal amount of $3.5 million to Salisbury Partners, LLC in connection with our purchase of a production facility in Leland, North Carolina, as described in more detail in Note 5, “Debt and Mezzanine Equity” and Note 7, "Joint Ventures and Noncontrolling Interest" to our unaudited condensed consolidated financial statements included in this report.

In December 2016, we sold and issued a promissory note in the principal amount of $3.9 million to Nikko Chemicals Co., Ltd. in connection with the formation of our Aprinnova joint venture, as described in more detail in Note 5, “Debt and Mezzanine Equity” and Note 7, “Joint Ventures and Noncontrolling Interest” to our unaudited condensed consolidated financial statements included in this report.

In January 2017, we exchanged $15.3 million of our 3% Senior Unsecured Convertible Promissory Notes due 2017 for $19.1 million of our 9.50% Convertible Senior Notes due 2019, as described in more detail in Note 5, “Debt and Mezzanine Equity” to our unaudited condensed consolidated financial statements included in this report.

See Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report for details regarding financing transactions completed subsequent to March 31, 2017.

Exchange (debt conversion)

On July 29, 2015, we closed the "Exchange" pursuant to that certain Exchange Agreement, dated as of July 26, 2015 (or the “Exchange Agreement”), among us, Maxwell (Mauritius) Pte Ltd (or “Temasek”) and Total.

Under the Exchange Agreement, at the closing of the Exchange, Temasek exchanged approximately $71.0 million in principal of outstanding convertible promissory notes (including paid-in-kind and accrued interest through July 29, 2015) and Total exchanged $70.0 million in principal amount of outstanding convertible promissory notes for shares of the Company’s common stock. The exchange price was $2.30 per share (or the “Exchange Price”) and was paid by the exchange and cancellation of such outstanding convertible promissory notes, and Temasek and Total received 30,860,633 and 30,434,782 shares of the Company’s common stock, respectively, in the Exchange.

Under the Exchange Agreement, Total also received the following warrants, each with a five-year term, at the closing of the Exchange:

• A warrant to purchase 18,924,191 shares of our common stock (or the “Total Funding Warrant”).

• A warrant to purchase 2,000,000 shares of our common stock that would only be exercisable if we failed, as of March 1, 2017, to achieve a target cost per liter to manufacture farnesene (or the “Total R&D Warrant”). The Total Funding Warrant and the Total R&D Warrant are collectively referred to as the “Total Warrants.”

Additionally, under the Exchange Agreement, Temasek received the following warrants at the closing of the Exchange:

• A warrant to purchase 14,677,861 shares of our common stock (or the “Temasek Exchange Warrant”).

• A warrant exercisable for that number of shares of our common stock equal to (1) (A) the number of shares for which Total exercises the Total Funding Warrant plus (B) the number of additional shares for which the certain convertible notes remaining outstanding following the completion of the Exchange may become exercisable as a result of a reduction in the conversion price of such remaining notes as a result of and/or subsequent to the date of the Exchange plus (C) that number of additional shares in excess of 2,000,000, if any, for which the Total R&D Warrant becomes exercisable multiplied by a fraction equal to 30.6% divided by 69.4% plus (2) (A) the number of any additional shares for which certain other outstanding convertible promissory notes may become exercisable as a result of a reduction to the conversion price of such notes multiplied by (B) a fraction equal to 13.3% divided by 86.7% (or the “Temasek Funding Warrant”).

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• A warrant exercisable for that number of shares of our common stock equal to 880,339 multiplied by a fraction equal to the number of shares for which Total exercises the Total R&D Warrant divided by 2,000,000 (or the “Temasek R&D Warrant”). If Total is entitled to, and does, exercise the Total R&D Warrant in full, the Temasek R&D Warrant would be exercisable for 880,339 shares.

The Temasek Exchange Warrant, the Temasek Funding Warrant and the Temasek R&D Warrant each have ten-year terms and are referred to herein as the “Temasek Warrants” and, the Temasek Warrants and Total Warrants are hereinafter collectively referred to as the “Exchange Warrants.” All of the Exchange Warrants have an exercise price of $0.01 per share.

In addition to the grant of the Exchange Warrants, a warrant issued by the Company to Temasek in October 2013 in conjunction with a prior convertible debt financing (or the “2013 Warrant”) became exercisable in full upon the completion of the Exchange. There were 1,000,000 shares underlying the 2013 Warrant, which was exercised in full at the exercise price of $0.01 per share.

The exercisability of all of the Exchange Warrants was subject to stockholder approval, which was obtained on September 17, 2015.

In February and May 2016, as a result of adjustments to the conversion price of our senior convertible notes issued in October 2013 (or the “Tranche I Notes”) and January 2014 (or the “Tranche II Notes”) discussed in Note 5, “Debt and Mezzanine Equity” to our unaudited condensed consolidated financial statements included in this, the Temasek Funding Warrant became exercisable for an additional 127,194 and 2,335,342 shares of common stock, respectively. Following the issuance by the Company of shares of convertible preferred stock and warrants to purchase common stock in May 2017, as described in Note 18, “Subsequent Events,” to our unaudited condensed consolidated financial statements included in this report, and a corresponding adjustment to the conversion price of the Tranche I Notes and Tranche II Notes, as described in Note 5, “Debt and Mezzanine Equity” to our unaudited condensed consolidated financial statements included in this report, the Temasek Funding Warrant became exercisable for an additional 16,886,320 shares of common stock.

As of March 1, 2017, we had not achieved the target cost per liter to manufacture farnesene provided in the Total R&D Warrant, and as a result, on March 1, 2017 the Total R&D Warrant became exercisable in accordance with its terms. In addition, upon any exercise by Total of the Total R&D Warrant, the Temasek R&D Warrant will become exercisable for that number of shares of the Company's common stock equal to 880,339 multiplied by a fraction equal to the number of shares for which Total exercises the Total R&D Warrant divided by 2,000,000.

As of March 31, 2017, the Total Funding Warrant, the Temasek Exchange Warrant and the 2013 Warrant had been fully exercised, and Temasek had exercised the Temasek Funding Warrant with respect to 12,700,244 shares of our common stock. The Total R&D Warrant and the Temasek R&D Warrant had not been exercised as of March 31, 2017. Warrants to purchase 2,462,536 shares of common stock under the Temasek Funding Warrant were unexercised as of March 31, 2017.

Maturity Treatment Agreement

At the closing of the Exchange, we, Total and Temasek also entered into a Maturity Treatment Agreement, dated as of July 29, 2015, pursuant to which Total and Temasek agreed to convert any Tranche I Notes, Tranche II Notes or 2014 144A Notes held by them that were not cancelled in the Exchange (or the “Remaining Notes”) into shares of our common stock in accordance with the terms of such Remaining Notes upon maturity, provided that certain events of default had not occurred with respect to the applicable Remaining Notes prior to such maturity. As of immediately following the closing of the Exchange and December 31, 2016, Temasek held $10.0 million in aggregate principal amount of Remaining Notes and Total held approximately $27.0 million and $29.5 million, respectively, in aggregate principal amount of Remaining Notes. See Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report for additional details regarding the Remaining Notes.

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Liquidity

We have incurred significant losses since our inception and believe that we will continue to incur losses and negative cash flow from operations through at least 2017. As of March 31, 2017, we had an accumulated deficit of $1,171.8 million and had cash, cash equivalents and short term investments of $2.5 million. We have significant outstanding debt and contractual obligations related to capital and operating leases, as well as purchase commitments. Refer to "Liquidity and Capital Resources" for further details.

Results of Operations

Comparison of Three Months Ended March 31, 2017 and 2016

Revenues

	Three Months Ended March 31,				Period-to-period Change			Percentage Change
	2017		2016
	(Dollars in thousands)
Revenues
Renewable product sales	$	8,292	$	3,140	$	5,152			164	%
Grants and collaborations revenue		4,688		5,671		(983	)		(17	)%
Total revenues	$	12,980	$	8,811	$	4,169			47	%

Our total revenues increased by $4.2 million to $13.0 million for the three months ended March 31, 2017, as compared to the same period in the prior year, primarily due to a significant growth in product sales and our production facilities operating at higher capacity than the comparative period.

Product sales increased by $5.2 million to $8.3 million for the three months ended March 31, 2017, as compared to the same period in the prior year, primarily due to increases in sales of products in the personal care and health and nutrition markets.

Cost and Operating Expenses

	Three Months Ended March 31,				Period-to-period Change		Percentage Change
	2017		2016
	(Dollars in thousands)
Cost of products sold	$	12,768	$	11,178	$	1,590		14	%
Research and development		14,778		11,906		2,872		24	%
Sales, general and administrative		12,778		12,266		512		4	%
Total cost and operating expenses	$	40,324	$	35,350	$	4,974		14	%

Our cost of products sold includes the cost of raw materials, labor and overhead, amounts paid to contract manufacturers, period costs related to inventory write-downs resulting from applying lower of cost or market inventory valuations, and costs related to scale-up in production of such products. Our cost of products sold increased by $1.6 million to $12.8 million for the three months ended March 31, 2017, as compared to the same period in the prior year, primarily driven by higher volumes of products sold, production scale-up costs and product mix.

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Research and Development Expenses

Our research and development expenses increased by $2.9 million to $14.8 million for the three months ended March 31, 2017, as compared to the same period in the prior year, primarily as a result of increases of $0.8 million in salaries and benefits expense, $0.4 million in lab supplies and equipment and $1.6 million in consulting and outside services.

Sales, General and Administrative Expenses

Our sales, general and administrative expenses were $12.8 million for the three months ended March 31, 2017, representing a small increase from the $12.3 million in the same period in the prior year.

Other Income (Expense)

	Three Months Ended March 31,						Period-to-period Change			Percentage Change
	2017			2016
	(Dollars in thousands)
Other income (expense):
Interest income	$	61		$	57		$	4			7	%
Interest expense		(12,184	)		(8,359	)		(3,825	)		46	%
Gain from change in fair value of derivative instruments		2,339			21,678			(19,339	)		(89	)%
Loss upon extinguishment of debt		96			(216	)		312			nm
Other income (expense), net		(380	)		(1,814	)		1,434			(79	)%
Total other income (expense)	$	(10,068	)	$	11,346		$	(21,414	)		(189	)%

Total other expense increased by approximately $21.4 million to $10.1 million for the three months ended March 31, 2017, as compared to the same period in the prior year. The increase was primarily attributable to the decrease in the gain from change in fair value of derivative instruments of $19.3 million, attributed to the compound embedded derivative liabilities associated with our senior convertible promissory notes and the change in fair value of our interest rate swap derivative liability. The change was driven by fluctuation of various inputs used in the valuation models from one reporting period to another, such as stock price, credit risk rate and estimated stock volatility.

Liquidity and Capital Resources

	March 31,  2017			December 31, 2016
	(Dollars in thousands)
Working capital deficit, excluding cash and cash equivalents	$	(78,850	)	$	(77,895	)
Cash and cash equivalents and short-term investments	$	2,485		$	28,524
Debt and capital lease obligations	$	221,748		$	228,299
Accumulated deficit	$	(1,171,809	)	$	(1,134,438	)

	Three Months Ended March 31,
	2017			2016
	(Dollars in thousands)
Net cash used in operating activities	$	(25,393	)	$	(23,743	)
Net cash provided by/(used in) investing activities	$	3,896		$	(8	)
Net cash provided by/(used in) financing activities	$	(4,273	)	$	19,063

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Working Capital Deficit. Our working capital deficit, excluding cash and cash equivalents, was $78.9 million at March 31, 2017, which represents an increase of $1.0 million compared to a working capital deficit of $77.9 million at December 31, 2016. The increase of $1.0 million in working capital deficit during the three months ended March 31, 2017 is due to various items.

To support production of our products in contract manufacturing and dedicated production facilities, we have incurred, and we expect to continue to incur, capital expenditures as we invest in these facilities. We plan to continue to seek external debt and equity financing from U.S. and Brazilian sources to help fund our investment in these contract manufacturing and dedicated production facilities.

We expect to fund our operations for the foreseeable future with cash and investments currently on hand, cash inflows from collaboration and grant funding, cash contributions from product sales, and proceeds from new debt and equity financings as well as strategic asset divestments. Some of our anticipated financing sources, such as research and development collaborations and debt and equity financings, are subject to risk that we cannot meet milestones, are not yet subject to definitive agreements or mandatory funding commitments and, if needed, we may not be able to secure additional types of financing in a timely manner or on reasonable terms, if at all. Our planned 2017 and 2018 working capital needs and our planned operating and capital expenditures for 2017 are dependent on significant inflows of cash from renewable product sales and existing collaboration partners, as well as additional funding from new collaborations, new debt and equity financings and proceeds from strategic asset divestments. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of our business.

Liquidity. We have incurred significant losses since our inception and believe that we will continue to incur losses and may have negative cash flow from operations through at least 2018. As of March 31, 2017, we had an accumulated deficit of $1,171.8 million and had cash, cash equivalents and short term investments of $2.5 million. In March 2016, we entered into an At Market Issuance Sales Agreement with third party Agents under which we may issue and sell shares of our common stock through the Agents having an aggregate offering price of up to $50.0 million from time to time in “at the market” offerings under our Registration Statement on Form S-3 (File No. 333-203216). This agreement includes no commitment by other parties to purchase shares we offer for sale. See Note 8, “Significant Agreements” to our unaudited condensed consolidated financial statements included in this report. As of the date hereof, $50.0 million remained available for future issuance under this facility. We have significant outstanding debt and contractual obligations related to capital and operating leases, as well as purchase commitments.

As of March 31, 2017, our debt, net of discount and issuance costs of $42.0 million, totaled to $220.9 million, of which $49.5 million is classified as current. In addition to upcoming debt maturities, our debt service obligations over the next twelve months are significant, including $20.8 million of anticipated interest payments. Our debt agreements also contain various covenants, including restrictions on our business that could cause us to be at risk of defaults such as restrictions on additional indebtedness, material adverse effect and cross default clauses. A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make a payment when required would generally result in events of default under such instruments, which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under our other outstanding indebtedness, permitting acceleration of such other outstanding indebtedness. Any required repayment of our indebtedness as a result of acceleration or otherwise would lower our current cash on hand such that we would not have those funds available for use in our business or for payment of other outstanding indebtedness. Refer to Note 5, "Debt and Mezzanine Equity" and Note 6, “Commitments and Contingencies” for further details of our debt arrangements.

Our condensed consolidated financial statements as of and for the three months ended March 31, 2017 have been prepared on the basis that the Company will continue as a going concern, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business. Due to the factors described above, there is substantial doubt about the Company’s ability to continue as a going concern within one year after the date that the financial statements are issued. Our ability to continue as a going concern will depend, in large part, on our ability to obtain necessary financing, which is uncertain. The financial statements do not include any adjustments that might result from the outcome of this uncertainty, which could have a material adverse effect on our financial condition. In addition, if we are unable to continue as a going concern, we may be unable to meet our obligations under our existing debt facilities, which could result in an acceleration of our obligation to repay all amounts outstanding under those facilities, and we may be forced to liquidate our assets. In such a scenario, the values we receive for our assets in liquidation or dissolution could be significantly lower than the values reflected in our financial statements.

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Our operating plan for 2017 contemplates a significant reduction in our net cash outflows, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, (iii) cash inflows from collaborations, (iv) access to various financing commitments and (v) strategic asset divestments (see Note 5, “Debt and Mezzanine Equity” and Note 8, “Significant Agreements” for details of financing commitments, and Note 18 “Subsequent Events” for details of financing transactions subsequent to March 31, 2017).

If we are unable to generate sufficient cash contributions from product sales, payments from existing and new collaboration partners, and draw sufficient funds from certain financing commitments due to contractual restrictions and covenants, we will need to obtain additional funding from equity or debt financings, agree to burdensome covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights, or grant licenses on terms that are not favorable.

If we are unable to raise additional financing, or if other expected sources of funding are delayed or not received, our ability to continue as a going concern would be jeopardized and we would take the following actions to support our liquidity needs through the remainder of 2017 and into 2018:

• Effect significant headcount reductions, particularly with respect to employees not connected to critical or contracted activities across all functions of the Company, including employees involved in general and administrative, research and development, and production activities.

• Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.

• Reduce production activity at our Brotas manufacturing facility to levels only sufficient to satisfy volumes required for product revenues forecast from existing products and customers.

• Reduce expenditures for third party contractors, including consultants, professional advisors and other vendors.

• Reduce or delay uncommitted capital expenditures, including non-essential facility and lab equipment, and information technology projects.

• Closely monitor our working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in our ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have an adverse effect on our ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

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Collaboration Funding. For the three months ended March 31, 2017, we received $2.6 million in cash from collaborations, including $1.3 million under a collaboration agreement with a flavors and fragrances partner.

We depend on collaboration funding to support our research and development and operating expenses. While part of this funding is committed based on existing collaboration agreements, we will be required to identify and obtain funding from additional collaborations. In addition, some of our existing collaboration funding is subject to our achievement of milestones or other funding conditions.

If we cannot secure sufficient collaboration funding to support our operating expenses in excess of cash contributions from product sales and existing debt and equity financings, we may need to issue additional preferred and/or discounted equity, agree to onerous covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights or grant licenses on terms that are not favorable to us. If we fail to secure such funding, we could be forced to curtail our operations, which would have a material adverse effect on our ability to continue with our business plans.

Government Contracts. In September 2015, we entered into a Technology Investment Agreement (as amended, the “TIA”) with The Defense Advanced Research Project Agency (or “DARPA”) under which we, with the assistance of five specialized subcontractors, will work to create new research and development tools and technologies for strain engineering and scale-up activities. The program that is the subject of the TIA is being performed and funded on a milestone basis. Under the TIA, we and our subcontractors could collectively receive DARPA funding of up to $35.0 million over the program’s four year term if all of the program’s milestones are achieved. In conjunction with DARPA’s funding, we and our subcontractors are obligated to collectively contribute approximately $15.5 million toward the program over its four year term (primarily by providing specified labor and/or purchasing certain equipment). We can elect to retain title to the patentable inventions we produce in the program, but DARPA receives certain data rights as well as a government purposes license to certain of such inventions. Either party may, upon written notice and subject to certain consultation obligations, terminate the TIA upon a reasonable determination that the program will not produce beneficial results commensurate with the expenditure of resources. We recognized $1.0 million in revenue under this agreement for the three months ended March 31, 2017. Total cash received under this agreement for the three months ended March 31, 2017 was $2.6 million.

In October 2016, we entered into an assistance agreement with the United States Department of Energy (DOE) relating to a research grant award (Award) under which we, with the assistance of two specialized subcontractors, Total and Renmatix, which are related parties of the Company, will work to develop a manufacturing-ready process utilizing wood as the cellulosic feedstock to produce farnesene. The program that is the subject of the Award is being performed and funded on a milestone basis. Under the Award, we and our subcontractors could collectively receive reimbursement for up to $8.8 million in costs expended by us and our subcontractors over the program’s three year term if all of the program’s milestones are achieved. We can elect to retain title to the patentable inventions we produce in the program, but DOE receives certain data rights as well as a government purposes license to certain of such inventions. Either party may, upon written notice and subject to certain consultation obligations, terminate the Award upon a reasonable determination that the program will not produce beneficial results commensurate with the expenditure of resources. We recognized $0.3 million in revenue under this agreement for the three months ended March 31, 2017. Total cash received under this agreement as of March 31, 2017 was zero and no payments were due to Renmatix or Total as of March 31, 2017.

Convertible Note Offerings. In February 2012, we sold $25.0 million in principal amount of senior unsecured convertible promissory notes due March 1, 2017 as described in more detail in Note 5, "Debt and Mezzanine Equity."

In July and September 2012, we issued $53.3 million in aggregate principal amount of 1.5% Senior Unsecured Convertible Notes to Total under the Total Fuel Agreements for an aggregate of $30.0 million in cash proceeds and our repayment of $23.3 million in previously-provided research and development funds pursuant to the Total Fuel Agreements, as described in more detail under "Related Party Convertible Notes" in Note 5, "Debt and Mezzanine Equity" to our unaudited condensed consolidated financial statements included in this report. As part of our December 2012 private placement, we issued 1,677,852 shares of our common stock to Total in exchange for the cancellation of $5.0 million of an outstanding senior unsecured convertible promissory note held by Total.

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In June and July 2013, we sold and issued $30.0 million in aggregate principal amount of 1.5% Senior Unsecured Convertible Notes to Total with a March 1, 2017 maturity date pursuant to the Total Fuel Agreements.

In August 2013, we entered into an agreement with Total and Temasek to issue up to $73.0 million in convertible promissory notes in private placements over a period of up to 24 months from the date of signing as described in more detail in Note 5, "Debt and Mezzanine Equity" to our unaudited condensed consolidated financial statements included in this report (such agreement referred to as the “August 2013 SPA” and such financing referred to as the “August 2013 Financing”). The August 2013 Financing was divided into two tranches (one for $42.6 million and one for $30.4 million). Of the total possible purchase price in the financing, $25.0 million was to be paid in the form of cash by Temasek ($25.0 million in the second tranche), $35.0 million was to be paid by the exchange and cancellation of the Temasek Bridge Note, as described below, and $13.0 million was to be paid by the exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche).

On October 4, 2013, we issued a senior secured promissory note in the principal amount of $35.0 million (Temasek Bridge Note) to Temasek for cash proceeds of $35.0 million. The Temasek Bridge Note was due on February 2, 2014 and accrued interest at a rate of 5.5% per month from October 4, 2013. The Temasek Bridge Note was cancelled as payment for Temasek's purchase of a first tranche convertible note in the initial closing of the August 2013 Financing, as described below.

In October 2013, we amended the August 2013 SPA to include certain entities affiliated with FMR LLC (or the “Fidelity Entities”) in the first tranche closing (participating for a principal amount of $7.6 million), and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes by Total to $14.6 million ($9.2 million in the first tranche and up to $5.4 million in the second tranche). Also in October 2013, we completed the closing of the issuance and sale of senior convertible notes under the first tranche of the August 2013 Financing (or the “Tranche I Notes”) for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from the exchange and cancellation of the Temasek Bridge Note and the remaining $9.2 million from the exchange and cancellation of an outstanding convertible promissory notes held by Total. In December 2013, we further amended the August 2013 SPA to sell $3.0 million of senior convertible notes under the second tranche of the August 2013 Financing (or the “Tranche II Notes”) to funds affiliated with Wolverine Asset Management, LLC and we elected to call $25.0 million in additional funds from Temasek pursuant to its previous commitment to purchase such amount of Tranche II Notes. Additionally, pursuant to that amendment, we sold approximately $6.0 million of Tranche II Notes to Total through exchange and cancellation of the same amount of principal of previously outstanding convertible notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation of indebtedness). The closing of the issuance and sale of such Tranche II Notes under the December amendment to the August 2013 SPA occurred in January 2014. The August 2013 Financing is more fully described in Note 5, "Debt and Mezzanine Equity".

In December 2013, in connection with our entry into agreements establishing our joint venture with Total, we exchanged the $69.0 million of then-outstanding unsecured convertible notes issued to Total pursuant to the Total Fuel Agreements for replacement 1.5% Senior Secured Convertible Notes, in principal amounts equal to the principal amounts of the cancelled notes.

In May 2014, we issued and sold $75.0 million in aggregate principal amount of 6.50% Convertible Senior Notes due 2019 (or the “2014 144A Notes”) to Morgan Stanley & Co. LLC as the Initial Purchaser in a private placement, and for initial resale by the Initial Purchaser to qualified institutional buyers pursuant to Rule 144A of the Securities Act (or the “2014 144A Offering”). The 2014 144A Offering and the 2014 144A Notes are described in more detail in Note 5, "Debt and Mezzanine Equity" and Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report. In October 2015, we repurchased $22.9 million in aggregate principal amount of the 2014 144A Notes with a portion of the proceeds from our sale of the 2015 144A Notes (as defined below), as described in more detail in Note 5, "Debt and Mezzanine Equity" to our unaudited condensed consolidated financial statements included in this report.

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In July 2014 and January 2015, we issued and sold $21.7 million in aggregate principal amount of 1.5% Senior Secured Convertible Notes with a March 1, 2017 maturity date to Total pursuant to the Total Fuel Agreements.

In July 2015, Temasek exchanged approximately $71.0 million in principal amount of outstanding convertible promissory notes and Total exchanged $70.0 million in principal amount of outstanding convertible promissory notes for shares of our common stock, as described in more detail in Note 5, "Debt and Mezzanine Equity" to our unaudited condensed consolidated financial statements included in this report.

In October 2015, we issued and sold $57.6 million in aggregate principal amount of 9.50% Convertible Senior Notes due 2019 (2015 144A Notes), which were sold only to qualified institutional buyers and institutional accredited investors in a private placement (2015 144A Offering) under the Securities Act. The 2015 144A Offering and the 2015 144 Notes are described in more detail in Note 5, "Debt and Mezzanine Equity" and Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report. In January 2017, we issued an additional $19.1 million in aggregate principal amount of 2015 144A Notes in exchange for the cancellation of $15.3 million in aggregate principal amount of outstanding senior unsecured convertible promissory notes issued in February 2012, as described in more detail in Note 5, "Debt and Mezzanine Equity" to our unaudited condensed consolidated financial statements included in this report.

In March 2016, we sold to Total one half of our ownership stake in TAB in exchange for Total cancelling $3.7 million in aggregate principal amount of outstanding 1.5% Senior Secured Convertible Notes and certain other indebtedness, as described in more detail under “Relationship with Total” above and in Note 5, “Debt and Mezzanine Equity” and Note 7, “Joint Ventures and Noncontrolling Interest”. In February 2017, we and Total agreed to extend the maturity of the remaining outstanding indebtedness under the Total Fuel Agreements from March 1, 2017 to May 15, 2017.

In May, September, October and December 2016, we issued $25.0 million in aggregate principal amount of convertible promissory notes to a private investor in offerings registered under the Securities Act, as described in more detail in Note 5, “Debt and Mezzanine Equity” and Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report.

See Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report for details regarding convertible note offerings completed subsequent to March 31, 2017.

Export Financing with ABC Brasil. In March 2013, we entered into a one-year export financing agreement with Banco ABC Brasil S.A. (or “ABC Brasil”) for approximately $2.5 million to fund exports through March 2014. This loan was collateralized by future exports from our subsidiary in Brazil. As of March 31, 2017, the loan was fully paid.

In March 2014, we entered into an additional one-year-term export financing agreement with ABC Brasil for approximately $2.2 million to fund exports through March 2015. This loan is collateralized by future exports from our subsidiary in Brazil. As of March 31, 2017, the loan was fully paid.

In April 2015, we entered into an additional one-year-term export financing agreement with ABC Brasil for approximately $1.6 million to fund exports through April 2016. This loan is collateralized by future exports from our subsidiary in Brazil. As of March 31, 2017, the loan was fully paid.

Banco Pine/Nossa Caixa Financing. In July 2012, we entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods agreement with each of Nossa Caixa and Banco Pine. Under these instruments, we borrowed an aggregate of R$52.0 million (approximately US$16.4 million based on the exchange rate as of March 31, 2017) as financing for capital expenditures relating to our manufacturing facility in Brotas, Brazil. Under the loan agreements, Banco Pine agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at our manufacturing facility in Brotas, Brazil for more than 30 days, except during sugarcane off-season. The loans are secured by certain of our farnesene production assets at the manufacturing facility in Brotas, Brazil and we were required to provide parent guarantees to each of the lenders. As of March 31, 2017 and December 31, 2016, a principal amount of $10.9 million and $11.1 million, respectively, was outstanding under these loan agreements.

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BNDES Credit Facility. In December 2011, we entered into a credit facility with Banco Nacional de Desenvolvimento Econômico e Social (or BNDES), a government-owned bank headquartered in Brazil (or the "BNDES Credit Facility") to finance a production site in Brazil. The BNDES Credit Facility was for R$22.4 million (approximately US$7.1 million based on the exchange rate as of March 31, 2017). The credit line is divided into an initial tranche for up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. As of March 31, 2017 and December 31, 2016, we had R$2.9 million (approximately US$0.9 million based on the exchange rate as of March 31, 2017) and R$3.8 million (approximately US$1.2 million based on the exchange rate as of December 31, 2016), respectively, in outstanding advances under the BNDES Credit Facility.

The principal of loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment due in January 2013 and the last due in December 2017. Interest was initially due on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments are due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per year. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is collateralized by first priority security interest in certain of our equipment and other tangible assets totaling R$24.9 million (approximately US$7.7 million based on the exchange rate as of December 31, 2016). We are a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, we were required to provide a bank guarantee equal to 10% of the total approved amount (R$22.4 million in total debt) available under the BNDES Credit Facility. For advances in the second tranche (above R$19.1 million), we are required to provide additional bank guarantees equal to 90% of each such advance, plus additional Amyris guarantees equal to at least 130% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under the credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, BNDES may terminate its commitments and declare immediately due all borrowings under the facility.

FINEP Credit Facility. In November 2010, we entered into a credit facility with Financiadora de Estudos e Projetos (or "FINEP"), a state-owned company subordinated to the Brazilian Ministry of Science and Technology (or the “FINEP Credit Facility”) to finance a research and development project on sugarcane-based biodiesel (or the “FINEP Project”) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.0 million based on the exchange rate as of March 31, 2017) which are secured by a chattel mortgage on certain equipment of Amyris as well as by bank letters of guarantee. All available credit under this facility was fully drawn. As of March 31, 2017 and December 31, 2016, the total outstanding loan balance under this credit facility was R$2.0 million (approximately US$0.7 million based on the exchange rate as of March 31, 2017) and R$2.3 million (approximately US$0.7 million based on the exchange rate as of December 31, 2016).

Interest on loans drawn under the FINEP Credit Facility is fixed at 5.0% per annum. In case of default under, or non-compliance with, the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the “TJLP”). If the TJLP at the time of default is greater than 6%, then the interest will be 5.0% plus a TJLP adjustment factor, otherwise the interest will be at 11.0% per annum. In addition, a fine of up to 10.0% will apply to the amount of any obligation in default. Additional interest on late balances will be 1.0% per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011.

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Senior Secured Loan Facility. In March 2014, we entered into a Loan and Security Agreement (LSA) with Hercules Technology Growth Capital, Inc. (Hercules) to make available a collateralized loan facility (Senior Secured Loan Facility) in the aggregate principal amount of up to $25.0 million, which loan facility was fully drawn at the closing. The initial loan of $25.0 million under the Senior Secured Loan Facility accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 6.25% or 9.5%. We may repay the outstanding amounts under the Senior Secured Loan Facility before the maturity date (October 15, 2018) if we pay an additional fee of 1% of the outstanding amounts. We were also required to pay a 1% facility charge at the closing of the Senior Secured Loan Facility, and are required to pay a 10% end of term charge with respect to the initial loan of $25.0 million. In connection with the entry into the LSA, we agreed to certain customary representations and warranties and covenants, as well as certain covenants that were subsequently amended (as described below).

In June 2014, we entered into a first amendment of the LSA with Hercules. Pursuant to the first amendment, the parties agreed to extend the maturity date of the loans under the Senior Secured Loan Facility from May 31, 2015 to February 1, 2017 and remove (i) a requirement for us to pay a forbearance fee of $10.0 million in the event certain covenants were not satisfied, (ii) a covenant that we maintain positive cash flow commencing with the fiscal quarter beginning October 1, 2014, (iii) a covenant that, commencing with the fiscal quarter beginning July 1, 2014, we and our subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for us to file a registration statement on Form S-3 with the SEC by no later than June 30, 2014 and complete an equity financing of more than $50.0 million by no later than September 30, 2014. We further agreed to include a new covenant in the LSA requiring us to maintain unrestricted, unencumbered cash in an amount equal to at least 50% of the principal amount of the loans then outstanding under the Senior Secured Loan Facility (Minimum Cash Covenant) and borrow an additional $5.0 million under the Senior Secured Loan Facility. The additional $5.0 million borrowing was completed in June 2014, and accrues interest at a rate per annum equal to the greater of (i) the prime rate reported in the Wall Street Journal plus 5.25% and (ii) 8.5%.

In March 2015, we entered into a second amendment of the LSA with Hercules. Pursuant to the second amendment, the parties agreed to, among other things, establish an additional credit facility in the principal amount of up to $15.0 million, which would be available to be drawn by us through the earlier of March 31, 2016 or such time as we raised an aggregate of at least $20.0 million through the sale of new equity securities. The additional facility was cancelled undrawn upon the completion of our private stock and warrant offering in July 2015.

In November 2015, we entered into a third amendment of the LSA with Hercules. Pursuant to the third amendment, we borrowed an additional $10,960,000 (Third Amendment Borrowed Amount) from Hercules on November 30, 2015. As of December 1, 2015, after the funding of the Third Amendment Borrowed Amount (and including repayment of $9.1 million of principal that had occurred prior to the third amendment), the aggregate principal amount outstanding under the Senior Secured Loan Facility was approximately $31.7 million. The Third Amendment Borrowed Amount accrues interest at a rate per annum equal to the greater of (i) 9.5% and (ii) the prime rate reported in the Wall Street Journal plus 6.25%, and, like the previous loans under the Senior Secured Loan Facility, has a maturity date of October 15, 2018. Upon the earlier of the maturity date, prepayment in full or such obligations otherwise becoming due and payable, in addition to repaying the outstanding Third Amendment Borrowed Amount (and all other amounts owed under the Senior Secured Loan Facility, as amended), we are also required to pay an end-of-term charge of $767,200. Pursuant to the third amendment, we also paid Hercules fees of $1.0 million, $750,000 of which was owed in connection with the expired $15.0 million facility under the second amendment and $250,000 of which was related to the Third Amendment Borrowed Amount. Under the third amendment, the parties agreed that we would, commencing on December 1, 2015, be required to pay only the interest accruing on all outstanding loans under the Senior Secured Loan Facility until February 29, 2016. Commencing on March 1, 2016, we would have been required to begin repaying principal of all loans under the Senior Secured Loan Facility, in addition to the applicable interest. However, pursuant to the third amendment, we could, by achieving certain cash inflow targets in 2016, extend the interest-only period to December 1, 2016. Upon our issuance and sale of $20.0 million of unsecured promissory notes and warrants in a private placement in February 2016 for aggregate cash proceeds of $20.0 million, we satisfied the conditions for extending the interest-only period to May 31, 2016. On June 1, 2016, we commenced the repayment of outstanding principal under the Senior Secured Loan Facility. In June 2016, we were notified by Hercules that it had transferred and assigned its rights and obligations under the Senior Secured Loan Facility to Stegodon Corporation (Stegodon), an affiliate of Ginkgo Bioworks, Inc. (Ginkgo). On June 29, 2016, in connection with the execution by us and Ginkgo of an initial strategic partnership agreement, we received a deferment of all scheduled principal repayments under the Senior Secured Loan Facility, as well as a waiver of the Minimum Cash Covenant, through October 31, 2016. Refer to Note 8, “Significant Agreements” to our unaudited condensed consolidated financial statements included in this report for additional details. On October 6, 2016, in connection with the execution by us and Ginkgo of a definitive collaboration agreement (or the “Ginkgo Collaboration Agreement”), we entered into a fourth amendment of the LSA with Stegodon, pursuant to which the parties agreed to (i) subject to extending the maturity of certain of our other outstanding indebtedness (or the “Extension Condition”), extend the maturity date of the Senior Secured Loan Facility, (ii) make the Senior Secured Loan Facility interest-only until maturity, subject to the requirement that we apply certain monies received by it under the Ginkgo Collaboration Agreement to repay the amounts outstanding under the Senior Secured Loan Facility, up to a maximum amount of $1 million per month and (iii) waive the Minimum Cash Covenant until the maturity date of the Senior Secured Loan Facility. On January 11, 2017, the maturity date of the Senior Secured Loan Facility was extended to October 15, 2018 due to the Extension Condition being met as a result of the Fidelity Exchange (as defined below). Refer to Note 5, “Debt and Mezzanine Equity” to our unaudited condensed consolidated financial statements included in this report for additional details. In December 2016, in connection with Stegodon granting certain waivers and releases under the LSA in connection with our formation of its Neossance joint venture with Nikko, as described in more detail in Note 7, "Joint Ventures and Noncontrolling Interest" to our unaudited condensed consolidated financial statements included in this report, we agreed to pay to Stegodon (i) a fee of $425,000 on or prior to December 31, 2017 and (ii) a fee of $450,000 on or prior to the maturity date of the loans under the Senior Secured Loan Facility. Subsequently, in January 2017, in connection with Stegodon granting certain waivers of the debt and transfer covenants under the LSA, we entered into a fifth amendment of the LSA with Stegodon. Pursuant to the fifth amendment, we agreed to apply additional monies we receive under the Ginkgo Collaboration Agreement towards repayment of the outstanding loans under the Senior Secured Loan Facility, up to a maximum amount of $3 million, to the extent we receive any such monies. Refer to Note 5, “Debt and Mezzanine Equity” and Note 8, “Significant Agreements” to our unaudited condensed consolidated financial statements included in this report for additional details regarding the LSA and Senior Secured Loan Facility.

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As of March 31, 2017, $27.7 million was outstanding under the Senior Secured Loan Facility, net of discount and issuance cost of $0.9 million. The Senior Secured Loan Facility is secured by liens on our assets, including on certain of our intellectual property. The Senior Secured Loan Facility includes customary events of default, including failure to pay amounts due, breaches of covenants and warranties, material adverse effect events, certain cross defaults and judgments, and insolvency. If an event of default occurs, Stegodon may require immediate repayment of all amounts outstanding under the Senior Secured Loan Facility.

February 2016 Private Placement. In February 2016, we sold and issued to certain purchasers affiliated with members of our board of directors an aggregate of $20.0 million of unsecured promissory notes and warrants for the purchase, at an exercise price of $0.01 per share, of an aggregate of 2,857,142 shares of our common stock, as described in more detail in in Note 5, “Debt and Mezzanine Equity” and Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report. The exercisability of these warrants was subject to stockholder approval, which was obtained on May 17, 2016.

June 2016 Private Placement. In June 2016, we sold and issued $5.0 million in aggregate principal amount of secured promissory notes to Foris Ventures, LLC (or “Foris”), an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, as described in more detail in Note 5, “Debt and Mezzanine Equity” and Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report.

October 2016 Private Placements. In October 2016, we sold and issued to Foris and Ginkgo, respectively, $6.0 million and $8.5 million in principal amount of secured promissory notes, as described in more detail in Note 5, “Debt and Mezzanine Equity” and Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report.

Guanfu Credit Facility. In October 2016, we entered into a credit agreement with Guanfu Holding Co., Ltd. to make available to the Company an unsecured credit facility with an aggregate principal amount of up to $25.0 million, which amount was fully drawn on March 31, 2017, as described in more detail in Note 5, “Debt and Mezzanine Equity” to our unaudited condensed consolidated financial statements included in this report.

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Salisbury Purchase Money Promissory Note. In December 2016, we sold and issued a purchase money promissory note in the principal amount of $3.5 million to Salisbury Partners, LLC in connection with our purchase of a production facility in Leland, North Carolina, as described in more detail in Note 5, “Debt and Mezzanine Equity” and Note 7, "Joint Ventures and Noncontrolling Interest" to our unaudited condensed consolidated financial statements included in this report. The loan was repaid in January 2017 using the proceeds of the Nikko Promissory Note.

Nikko Promissory Note. In December 2016, we sold and issued a promissory note in the principal amount of $3.9 million to Nikko Chemicals Co., Ltd. in connection with the formation of our Aprinnova joint venture, as described in more detail in Note 5, “Debt and Mezzanine Equity” and Note 7, “Joint Ventures and Noncontrolling Interest” to our unaudited condensed consolidated financial statements included in this report.

Common Stock Offerings. In December 2012, we completed a private placement of 14,177,849 shares of our common stock for aggregate cash proceeds of $37.2 million, of which $22.2 million was received in December 2012 and $15.0 million was received in January 2013. Of the 14,177,849 shares issued in the private placement, 1,677,852 of such shares were issued to Total in exchange for cancellation of $5.0 million of an outstanding convertible promissory note we previously issued to Total.

In March 2013, we completed a private placement of 1,533,742 of our common stock to Biolding SA (Biolding), which is affiliated with one of our directors, for aggregate proceeds of $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by us of certain criteria associated with the commissioning of our production plant in Brotas, Brazil.

In March 2014, we completed a private placement of 943,396 shares of our common stock to Kuraray for aggregate proceeds of $4.0 million.

In July 2015, we entered into a Securities Purchase Agreement with certain purchasers, including entities affiliated with members of our board of directors, under which we agreed to sell 16,025,642 shares of our common stock at a price of $1.56 per share, for aggregate proceeds to the Company of $25 million. The sale of common stock under the Securities Purchase Agreement was completed on July 29, 2015. Pursuant to the Securities Purchase Agreement, the Company granted to each of the purchasers a warrant exercisable at an exercise price of $0.01 per share for the purchase of a number of shares of the Company’s common stock equal to 10% of the shares purchased by such investor. The exercisability of the warrants was subject to stockholder approval, which was obtained on September 17, 2015. As of March 31, 2017, 160,255 of such warrants had been exercised.

In May 2016, we sold and issued 4,385,964 shares of our common stock to the Bill & Melinda Gates Foundation in a private placement at a purchase price per share equal to $1.14, for aggregate proceeds to the Company of approximately $5.0 million.

See Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report for details regarding equity offerings completed subsequent to March 31, 2017.

Cash Flows during the Three Months Ended March 31, 2017 and 2016

Cash Flows from Operating Activities

Our primary uses of cash from operating activities are costs related to production and sales of our products and personnel-related expenditures, offset by cash received from product sales, grants and collaborations. Cash used in operating activities was $25.4 million and $23.7 million for the three months ended March 31, 2017 and 2016, respectively.

Net cash used in operating activities of $25.4 million for the three months ended March 31, 2017 was attributable to our net loss of $37.4 million, offset by net non-cash charges of $6.0 million and net change in our operating assets and liabilities of $5.9 million. Net non-cash charges of $6.0 million for the three months ended March 31, 2017 consisted primarily of $4.5 million of debt discount and issuance costs and $1.6 million of stock-based compensation, offset by $0.1 million of gain upon extinguishment of debt. Net change in operating assets and liabilities of $5.9 million for the three months ended March 31, 2017 primarily consisted of decreases of $5.4 million in account receivable, and offset by an increase of $0.5 million in accounts payable.

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Net cash used in operating activities of $23.7 million for the three months ended March 31, 2016 was attributable to our net loss of $15.3 million, offset by net non-cash charges of $12.4 million and net change in our operating assets and liabilities of $4.0 million. Net non-cash charges of $12.5 million for the three months ended March 31, 2016 consisted primarily of a $21.7 million change in the fair value of derivative instruments related to the embedded derivative liabilities associated with our senior convertible promissory notes and currency interest rate swap derivative liability, offset by $2.9 million of depreciation and amortization expenses, $3.0 million of amortization of debt discount and issuance costs, $2.1 million of stock-based compensation, $1.1 million on loss on foreign currency exchange rates and $0.2 million on loss from extinguishment of debt. Net change in operating assets and liabilities of $4.0 million for the three months ended March 31, 2016 primarily consisted of $2.9 million increase in accrued other liabilities and $3.9 million decrease in inventory, offset by $1.8 million increase in account receivable and $1.0 million decrease in accounts payable and deferred rent.

Cash Flows from Investing Activities

Our investing activities consist primarily of capital expenditures and other investment activities. Net cash provided by investing activities of $3.9 million for the three months ended March 31, 2017, resulted from $4.0 million of change in restricted cash and $2.1 million of maturities of short-term investments, offset by $1.8 million of purchase of short-term investments and $0.4 million of purchase of property, plant and equipment.

Our investing activities consist primarily of capital expenditures and other investment activities. Net cash used in investing activities of $0.0 million for the three months ended March 31, 2016, resulted from $1.3 million of short-term investments and $0.3 million of purchases of property, plant and equipment, offset by $1.6 million of maturities of short-term investments.

Cash Flows from Financing Activities

Net cash used in financing activities of $4.3 million for the three months ended March 31, 2017, was a result of the receipt of $1.5 million of proceeds from debt issued, offset by $5.1 million of principal payments on debt and $0.7 million of principal payments on capital leases.

Net cash provided by financing activities of $19.1 million for the three months ended March 31, 2016, was a result of the receipt of $20.0 million of proceeds from debt issued to related parties, offset by $0.7 million of principal payments on debt, $0.2 million of principal payments on capital leases and 0.1 million of employee's taxes paid upon vesting of restricted stock units.

Off-Balance Sheet Arrangements

We did not have during the periods presented, and we do not currently have, any material off-balance sheet arrangements, as defined under SEC rules, such as relationships with unconsolidated entities or financial partnerships, which are often referred to as structured finance or special purpose entities, established for the purpose of facilitating financing transactions that are not required to be reflected on our condensed consolidated financial statements.

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Contractual Obligations

The following is a summary of our contractual obligations as of March 31, 2017 (in thousands):

	Total		2017		2018		2019		2020		2021		Thereafter
Principal payments on debt(1)	$	260,363	$	50,363	$	53,784	$	125,286	$	2,282	$	27,294	$	1,354
Interest payments on debt, fixed rate(2)		50,296		15,532		20,897		8,260		2,874		2,645		88
Operating leases		44,138		5,194		6,909		6,782		7,012		7,248		10,993
Principal payments on capital leases		810		702		100		8		—		—		—
Interest payments on capital leases		39		32		7		—		—		—		—
Purchase obligations(3)		3,701		1,606		2,026		69		—		—		—
Total	$	359,347	$	73,429	$	83,723	$	140,405	$	12,168	$	37,187	$	12,435

____________________

⁽¹⁾ The forecast payments assume no proceeds to be received by the Company under the Ginkgo Collaboration Agreement, which, if received, would need to be applied by the Company up to $1 million per month towards repayment of the debt due to Stegodon. Also including $3.9 million in 2017 related to Nomis Bay convertible note which, at the Company’s election, may be settled in shares or cash, and $46.8 million between 2018 and 2019 subject to Maturity Treatment Agreement, which will be converted to common stock at maturity, subject to there being no default under the terms of the debt. See Note 18, “Subsequent Events” to our unaudited condensed consolidated financial statements included in this report for additional details regarding the notes subject to the Maturity Treatment Agreement.

⁽²⁾ Does not include any obligations related to make-whole interest or downround provisions. The fixed interest rates are more fully described in Note 5, "Debt” of our condensed consolidated financial statements.

⁽³⁾ Purchase obligations include noncancellable contractual obligations and construction commitments of zero, of which zero have been accrued as loss on purchase commitments.

Recent Accounting Pronouncements

The information contained in Note 2 to the Unaudited Condensed Consolidated Financial Statements under the heading "Recent Accounting Pronouncements" is hereby incorporated by reference into this Part I, Item 2.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

The market risk inherent in our market risk sensitive instruments and positions is the potential loss arising from adverse changes in: commodity market prices, foreign currency exchange rates, and interest rates as described below.

Interest Rate Risk

Our exposure to market risk for changes in interest rates relates primarily to our investment portfolio and our outstanding debt obligations (including embedded derivatives therein). We generally invest our cash in investments with short maturities or with frequent interest reset terms. Accordingly, our interest income fluctuates with short-term market conditions. As of March 31, 2017, our investment portfolio consisted primarily of money market funds and certificates of deposit, all of which are highly liquid investments. Due to the short-term nature of our investment portfolio, we do not believe that an immediate 10% increase in interest rates would have a material effect on the fair value of our portfolio. Since we believe we have the ability to liquidate this portfolio, we do not expect our operating results or cash flows to be materially affected to any significant degree by a sudden change in market interest rates on our investment portfolio. Additionally, as of March 31, 2017, 100% of our outstanding debt is in fixed rate instruments or instruments which have capped rates. Therefore, our exposure to the impact of variable interest rates is limited. Changes in interest rates may significantly change the fair value of our embedded derivative liabilities.

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Foreign Currency Risk

Most of our sales contracts are principally denominated in U.S. dollars and, therefore, our revenues are currently not subject to significant foreign currency risk. The functional currency of our wholly-owned consolidated subsidiary in Brazil is the local currency (Brazilian real) in which recurring business transactions occur. We do not use currency exchange contracts as hedges against amounts permanently invested in our foreign subsidiary. The amount we consider permanently invested in our foreign subsidiary and translated into U.S. dollars using the March 31, 2017 exchange rate is $122.8 million as of March 31, 2017 and $119.4 million at December 31, 2016. The increase in the permanent investments in our foreign subsidiary between December 31, 2016 and March 31, 2017 is due to the depreciation of the U.S. dollar versus the Brazilian real. The potential loss in value, which would be principally recognized in Other Comprehensive Loss, resulting from a hypothetical 10% adverse change in quoted Brazilian real exchange rates, is $1.8 million and $2.7 million as of March 31, 2017 and December 31, 2016, respectively. Actual results may differ.

We make limited use of derivative instruments, which include currency interest rate swap agreements, to manage the Company's exposure to foreign currency exchange rate and interest rate related to the Company's Banco Pine loan. In June 2012, we entered into a currency interest rate swap arrangement with Banco Pine for R$22.0 million (approximately US$6.9 million based on the exchange rate as of March 31, 2017). The swap arrangement exchanges the principal and interest payments under the Banco Pine loan entered into in July 2012 for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. This arrangement hedges the fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real.

We analyzed our foreign currency exposure to identify assets and liabilities denominated in other currencies. For those assets and liabilities, we evaluated the effects of a 10% shift in exchange rates between those currencies and the U.S. dollar. We have determined that there would be an immaterial effect on our results of operations from such a shift.

Commodity Price Risk

Our primary exposure to market risk for changes in commodity prices currently relates to our purchases of sugar feedstocks. When possible, we manage our exposure to this risk primarily through the use of supplier pricing agreements.

ITEM 4. CONTROLS AND PROCEDURES

Disclosure Controls and Procedures

Our management, with the participation of our chief executive officer (or “CEO”) and chief financial officer (or “CFO”), evaluated the effectiveness of our disclosure controls and procedures pursuant to Rules 13a-15 and 15d-15(e) under the Securities Exchange Act of 1934, as amended (or the “Exchange Act”), as of the end of the period covered by this Quarterly Report on Form 10-Q.  Based on this evaluation, our CEO and CFO concluded that, as of March 31, 2017, our disclosure controls and procedures are designed and are effective to provide reasonable assurance that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in the SEC's rules and forms, and that such information is accumulated and communicated to our management, including our CEO and CFO, as appropriate, to allow timely decisions regarding required disclosure.

Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

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Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting identified in management’s evaluation pursuant to Rules 13a-15(d) or 15d-15(d) of the Exchange Act during our first fiscal quarter ended March 31, 2017 that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Inherent Limitations on the Effectiveness of Internal Controls

The effectiveness of any system of internal control over financial reporting, including ours, is subject to inherent limitations, including the exercise of judgment in designing, implementing, operating, and evaluating the controls and procedures, and the inability to eliminate misconduct completely. Accordingly, any system of internal control over financial reporting, including ours, no matter how well designed and operated, can only provide reasonable, not absolute assurances. In addition, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. We intend to continue to monitor and upgrade our internal controls as necessary or appropriate for our business, but cannot assure you that such improvements will be sufficient to provide us with effective internal control over financial reporting.

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PART II

ITEM 1. LEGAL PROCEEDINGS

In April 2017, a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and CFO, Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all individuals who acquired our common stock between March 2, 2017 and April 17, 2017. The complaint alleges securities law violations based on statements made by the Company in its earnings press release issued on March 2, 2017 and Form 12b-25 filed with the SEC on April 3, 2017. We believe the complaint lacks merit, and intend to defend ourselves vigorously.

We may be involved, from time to time, in legal proceedings and claims arising in the ordinary course of our business. Such matters are subject to many uncertainties and there can be no assurance that legal proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on our business, results of operations, financial position or cash flows.

ITEM 1A. RISK FACTORS

Investing in our common stock involves a high degree of risk. You should carefully consider the risks and uncertainties described below, together with all of the other information set forth in this Quarterly Report on Form 10-Q, which could materially affect our business, financial condition or future results. If any of the following risks actually occurs, our business, financial condition, results of operations and future prospects could be materially and adversely harmed. The trading price of our common stock could decline due to any of these risks, and, as a result, you may lose all or part of your investment.

Risks Related to Our Business

We have incurred losses to date, anticipate continuing to incur losses in the future, and may never achieve or sustain profitability.

We have incurred significant losses in each year since our inception and believe that we will continue to incur losses and negative cash flow from operations into at least 2018. As of March 31, 2017, we had an accumulated deficit of $1,171.8 million and had cash, cash equivalents and short term investments of $2.5 million. We have significant outstanding debt, a significant working capital deficit and contractual obligations related to capital and operating leases, as well as purchase commitments of $3.7 million. As of March 31, 2017, our debt totaled $220.9 million, net of discount and issuance cost of $42.0 million, of which $49.5 million is classified as current. Our debt service obligations over the next twelve months are significant, including approximately $18.3 million of anticipated interest payments (excluding interest paid in kind by adding to outstanding principal) and may include potential early conversion payments of up to approximately $15.8 million (assuming all note holders convert) under our outstanding 9.50% Convertible Senior Notes due 2019 (or the “2015 144A Notes”). Furthermore, our debt agreements contain various financial and operating covenants, including restrictions on business that could cause us to be at risk of defaults. We expect to incur additional costs and expenses related to the continued development and expansion of our business, including construction and operation of our manufacturing facilities, contract manufacturing, research and development operations, and operation of our pilot plants and demonstration facility. There can be no assurance that we will ever achieve or sustain profitability on a quarterly or annual basis.

Our unaudited condensed consolidated financial statements as of and for the three months ended March 31, 2017 have been prepared on the basis that we will continue as a going concern, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business. We have incurred significant losses since our inception and we expect that we will continue to incur losses as we aim to successfully execute our business plan and will be dependent on additional public or private financings, collaborations or licensing arrangements with strategic partners, or additional credit lines or other debt financing sources to fund continuing operations. Based on our cash balances, recurring losses since inception and our existing capital resources to fund our planned operations for a twelve month period, there is substantial doubt about our ability to continue as a going concern within one year after the date that the financial statements are issued. Our operating plans for 2017 and 2018 contemplate a significant reduction in our net cash outflows resulting from (i) growth of sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, (iii) cash inflows from collaborations, (iv) access to various financing commitments and (v) strategic asset divestments. In addition, as noted below, for our 2017 and 2018 operating plans, we are dependent on funding from sources that are not subject to existing commitments. We will need to obtain additional funding from equity or debt financings, which may require us to agree to burdensome covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements that require us to relinquish commercial rights, or grant licenses on terms that are not favorable. No assurance can be given at this time as to whether we will be able to achieve our expense reduction or fundraising objectives, regardless of the terms. If we are unable to raise additional financing, or if other expected sources of funding are delayed or not received, our ability to continue as a going concern would be jeopardized and we may be forced to delay, scale back or eliminate some of our general and administrative, research and development, or production activities or other operations and reduce investment in new product and commercial development efforts in an effort to provide sufficient funds to continue our operations. If any of these events occurs, our ability to achieve our development and commercialization goals would be adversely affected. In addition, if we are unable to continue as a going concern, we may be unable to meet our obligations under our existing debt facilities, which could result in an acceleration of our obligation to repay all amounts outstanding under those facilities, and we may be forced to liquidate our assets. In such a scenario, the value we receive for our assets in liquidation or dissolution could be significantly lower than the value reflected in our financial statements.

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Our unaudited condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty, which could have a material adverse effect on our financial condition and cause investors to suffer the loss of all or a substantial portion of their investment.

We have limited experience producing our products at commercial scale and may not be able to commercialize our products to the extent necessary to sustain and grow our current business.

To commercialize our products, we must be successful in using our yeast strains to produce target molecules at commercial scale and at a commercially viable cost. If we cannot achieve commercially-viable production economics for enough products to support our business plan, including through establishing and maintaining sufficient production scale and volume, we will be unable to achieve a sustainable integrated renewable products business. Virtually all of our production capacity is through a purpose-built, large-scale production plant in Brotas, Brazil. This plant commenced operations in 2013, and scaling and running the plant has been, and continues to be, a time-consuming, costly, uncertain and expensive process. Given our limited experience commissioning and operating our own manufacturing facilities and our limited financial resources, we cannot be sure that we will be successful in achieving production economics that allow us to meet our plans for commercialization of various products we intend to offer. In addition, our attempts to scale production of new molecules at the plant are subject to uncertainty and risk. For example, even to the extent we successfully complete product development in our laboratories and pilot and demonstration facilities, and at contract manufacturing facilities, we may be unable to translate such success to large-scale, purpose-built plants. If this occurs, our ability to commercialize our technology will be adversely affected and we may be unable to produce and sell any significant volumes of our products. Also, with respect to products that we are able to bring to market, we may not be able to lower the cost of production, which would adversely affect our ability to sell such products profitably. In addition, we will likely need to identify and secure access to additional production capacity to satisfy anticipated volume requirements in 2017. There can be no assurance that we will be able obtain such capacity on favorable or acceptable terms, if at all, and even if we are successful in obtaining such capacity, there can be no assurance that we will be able to scale and operate any additional plants to allow us to meet our operational goals, which could harm our ability to grow our business.

We will require significant inflows of cash from financings, product sales and collaborations to fund our anticipated operations and to service our debt obligations and may not be able to obtain such funding on favorable terms, if at all.

Our planned 2017 and 2018 working capital needs, our planned operating and capital expenditures for 2017 and 2018, and our ability to service our outstanding debt obligations are dependent on significant inflows of cash from financings, existing and new collaboration partners and renewable product sales. We will continue to need to fund our research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of our business. Some of our anticipated funding sources, such as research and development collaborations, are subject to the risk that we cannot meet milestones, that the collaborations may end prematurely for reasons that may be outside of our control (including technical infeasibility of the project or a collaborator’s right to terminate without cause), or the collaborations are not yet subject to definitive agreements or mandatory funding commitments and, if needed, we may not be able to secure additional types of funding in a timely manner or on reasonable terms, if at all. The inability to generate sufficient cash flow, as described above, could have an adverse effect on our ability to continue with our business plans and our status as a going concern.

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If we are unable to raise additional funding, or if other expected sources of funding are delayed or not received, our ability to continue as a going concern would be jeopardized and we would take the following actions as early as the second quarter of 2017 to support our liquidity needs in 2017 and 2018:

• Effect significant headcount reductions, particularly with respect to employees not connected to critical or contracted activities across all functions of the Company, including employees involved in general and administrative, research and development, and production activities.

• Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.

• Reduce production activity at our Brotas manufacturing facility to levels only sufficient to satisfy volumes required for product revenues forecast from existing products and customers.

• Reduce expenditures for third party contractors, including consultants, professional advisors and other vendors.

• Reduce or delay uncommitted capital expenditures, including non-essential facility and lab equipment, and information technology projects.

• Closely monitor the Company's working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on our ability to continue our business as currently contemplated, including, without limitation, delays or failures in our ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have an adverse effect on our ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

Future revenues are difficult to predict, and our failure to predict revenue accurately may cause our results to be below our expectations or those of analysts or investors and could result in our stock price declining.

Our revenues are comprised of product revenues and grants and collaborations revenues. We generate the substantial majority of our product revenues from sales to collaborators and distributors and only a small portion from direct sales. Our collaboration, supply and distribution agreements do not usually include any specific purchase obligations. The sales volume of our products in any given period has been difficult to predict. A significant portion of our product sales is dependent upon the interest and ability of third party distributors to create demand for, and generate sales of, such products to end-users. For example, if such distributors are unsuccessful in creating pull-through demand for our products with their customers, such distributors may purchase less of our products from us than we expect. In addition, many of our new and novel products are intended to be a component of other companies’ products; therefore, sales of our products may be contingent on our collaborators’ and/or customers’ timely and successful development and commercialization of end-use products that incorporate our products, and price volatility in the markets for such end-use products, which may include commodities, could adversely affect the demand for our products and the margin we receive for our product sales, which could harm our financial results. Furthermore, we have begun to market and sell some of our products directly to end-consumers, initially in the cosmetics market. Because we have little experience in marketing and selling directly to consumers, it is difficult to predict how successful our efforts will be and we may not achieve the product sales we expect to achieve on the timeline we anticipate, if at all.

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In addition, we have in the past entered into, and expect in the future to enter into, research and development collaboration arrangements pursuant to which we receive payments from our collaborators. Some of such collaboration arrangements include advance payments in consideration for grants of exclusivity or research and development activities to be performed by us. It has in the past been difficult for us to know with certainty when we will sign a new collaboration arrangement and receive payments thereunder. As a result, achievement of our quarterly and annual financial goals has been difficult to predict with certainty. Once a collaboration agreement has been signed, receipt of cash payments and/or recognition of related revenues may depend on our achievement of research, development, production or cost milestones, which may be difficult to predict. In addition, a portion of the advance payments we receive under our collaboration agreements is typically classified as deferred revenue and recognized over multiple quarters or years. Since our business model depends in part on collaboration agreements with advance payments that we recognize over time, it may also be difficult for us to rapidly increase our revenues through additional collaborations in any period, as revenue from such new collaborations will often be recognized over multiple quarters or years.

These factors have made it difficult to predict future revenues and have resulted in our revenues being below our previously announced guidance or analysts’ estimates. We continue to face these risks in the future, which may cause our stock price to decline.

A limited number of customers, collaboration partners and distributors account for a significant portion of our revenue, and the loss of major customers, collaboration partners or distributors could harm our operating results.

Our revenues have varied significantly from quarter to quarter and are dependent on sales to, and collaborations with, a limited number of customers, collaboration partners and/or distributors. We cannot be certain that customers, collaboration partners and/or distributors that have accounted for significant revenue in past periods, individually or as a group, will continue to generate similar revenue in any future period. If we fail to renew with, or if we lose a major customer, collaborator or distributor or group of customers, collaborators or distributors, our revenue could decline if we are unable to replace the lost revenue with revenue from other sources.

Our existing financing arrangements may cause significant risks to our stockholders and may impact our ability to pursue certain transactions and operate our business.

As of March 31, 2017, our debt totaled $220.9 million, net of discount and issuance costs of $42.0 million, of which $49.5 million is classified as current. Our cash balance is substantially less than the principal amount of our outstanding debt, and we will be required to generate cash from operations or raise additional working capital through future financings or sales of assets to enable us to repay this indebtedness as it becomes due. There can be no assurance that we will be able to do so.

In addition, we have agreed to significant covenants in connection with our debt financing transactions, including restrictions on our ability to incur future indebtedness, and customary events of default, including failure to pay amounts due, breaches of covenants and warranties, material adverse effect events, certain cross defaults and judgments, and insolvency. A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make a payment when required would generally result in events of default under such instruments, which could permit acceleration of such indebtedness and could result in a material adverse effect on us. If such indebtedness is accelerated, it would generally also constitute an event of default under our other outstanding indebtedness, permitting acceleration of such other outstanding indebtedness. Any required repayment of our indebtedness as a result of acceleration or otherwise would lower our current cash on hand such that we would not have those funds available for use in our business or for payment of other outstanding indebtedness.

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If we are at any time unable to generate sufficient cash flow from operations to service our indebtedness when payment is due, we may be required to attempt to renegotiate the terms of the instruments relating to the indebtedness, seek to refinance all or a portion of the indebtedness or obtain additional financing. There can be no assurance that we would be able to successfully renegotiate such terms, that any such refinancing would be possible or that any additional financing could be obtained on terms that are favorable or acceptable to us. Any debt financing that is available could cause us to incur substantial costs and subject us to covenants that significantly restrict our ability to conduct our business. If we seek to complete additional equity financings, the interests of existing equity holders may be diluted.

In addition, the covenants in our debt agreements materially limit our ability to take certain actions, including our ability to pay dividends, make certain investments and other payments, undertake certain mergers and consolidations, and encumber and dispose of assets. For example, the purchase agreement for convertible notes that we sold in separate closings in October 2013 and January 2014, which we refer to as the Tranche Notes, requires us to obtain the consent of the holders of a majority of these notes before completing any change of control transaction or purchasing assets in one transaction or a series of related transactions in an amount greater than $20.0 million, in each case while the Tranche Notes are outstanding. The holders of the Tranche Notes also have pro rata rights to invest in, and under which they could cancel up to the full amount of their outstanding Tranche Notes to pay for, equity securities that we issue in certain financings, which could delay or prevent us from completing such financings.

Furthermore, certain of our existing convertible notes, including the Tranche Notes, contain anti-dilution conversion price adjustment provisions, which may be triggered by future issuances of equity or equity-linked instruments in financing transactions. If such adjustment provisions are triggered, the conversion price of such convertible notes will decrease and the number of shares issuable upon conversion of such convertible notes will correspondingly increase. In such event, existing stockholders will be further diluted and the effective issuance price of such equity or equity-linked instruments will be reduced, which may harm our ability to engage in future financing transactions to fund our business.

Our substantial leverage could adversely affect our ability to fulfill our obligations under our existing indebtedness and may place us at a competitive disadvantage in our industry.

We continue to have substantial debt outstanding and we may incur additional indebtedness from time to time to finance working capital, product development efforts, strategic acquisitions, investments and partnerships, or capital expenditures, or for other general corporate purposes, subject to the restrictions contained in our debt agreements. Our significant indebtedness and debt service requirements could adversely affect our ability to operate our business and may limit our ability to take advantage of potential business opportunities. For example, our high level of indebtedness presents the following risks:

• we will be required to use a substantial portion of our cash flow from operations to pay principal and interest on our indebtedness, thereby reducing the availability of our cash flow to fund working capital, capital expenditures, product development efforts, acquisitions, investments and strategic alliances and other general corporate requirements;

• our substantial leverage increases our vulnerability to economic downturns and adverse competitive and industry conditions and could place us at a competitive disadvantage compared to those of our competitors that are less leveraged;

• our debt service obligations could limit our flexibility in planning for, or reacting to, changes in our business and our industry and could limit our ability to pursue other business opportunities, borrow more money for operations or capital in the future and implement our business strategies;

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• our level of indebtedness and the covenants within our debt instruments may restrict us from raising additional financing on satisfactory terms to fund working capital, capital expenditures, product development efforts, strategic acquisitions, investments and alliances, and other general corporate requirements; and

• our substantial leverage may make it difficult for us to attract additional financing when needed.

If we are at any time unable to generate sufficient cash flow from operations to service our indebtedness when payment is due, we may be required to attempt to renegotiate the terms of the instruments relating to the indebtedness, seek to refinance all or a portion of the indebtedness or obtain additional financing. There can be no assurance that we will be able to successfully renegotiate such terms, that any such refinancing would be possible or that any additional financing could be obtained on terms that are favorable or acceptable to us, if at all.

A failure to comply with the covenants and other provisions of our debt instruments, including any failure to make a payment when required, could result in events of default under such instruments, which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it could also constitute an event of default under our other outstanding indebtedness, permitting acceleration of such other outstanding indebtedness. Any required repayment of our indebtedness as a result of acceleration or otherwise would lower our current cash on hand such that we would not have those funds available for use in our business or for payment of other outstanding indebtedness.

Our GAAP operating results could fluctuate substantially due to the accounting for the early conversion payment features of outstanding convertible promissory notes.

Several of our outstanding convertible debt instruments are accounted for under Accounting Standards Codification 815, Derivatives and Hedging, or ASC 815, as an embedded derivative. For instance, with respect to the 2015 144A Notes, if the holders elect convert their 2015 144A Notes, such converting holders will receive an early conversion payment equal to the present value of the remaining scheduled payments of interest that would have been made on the 2015 144A Notes being converted through April 15, 2019, the maturity date of the 2015 144A Notes. Our 6.50% Convertible Senior Notes due 2019, or the 2014 144A Notes, contain a similar early conversion payment feature, provided that the last reported sale price of our common stock for 20 or more trading days (whether or not consecutive) in a period of 30 consecutive trading days ending within five trading days immediately prior to the date we receive a notice of such election to convert exceeds the conversion price in effect on each such trading day. The early conversion payment features of the 2014 144A Notes and the 2015 144A Notes are accounted for under ASC 815 as embedded derivatives. ASC 815 requires companies to bifurcate conversion options from their host instruments and account for them as free standing derivative financial instruments according to certain criteria. The fair value of the derivative is remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss related to the change in the fair value of the derivative being charged to earnings (loss). We have determined that we must bifurcate and account for the early conversion payment features of the 2014 144A Notes and the 2015 144A Notes, as well as certain other features of our other convertible debt instruments, as embedded derivatives in accordance with ASC 815. We have recorded these embedded derivative liabilities as non-current liabilities on our consolidated balance sheet with a corresponding debt discount at the date of issuance that is netted against the principal amount of the 2014 144A Notes, the 2015 144A Notes or other convertible debt instrument, as applicable. The derivative liabilities are remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss related to the change in the fair value of the derivative liabilities being recorded in other income or loss. There is no current observable market for this type of derivative and, as such, we determine the fair value of the embedded derivatives using the binomial lattice model. The valuation model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. Changes in the inputs for these valuation models may have a significant impact on the estimated fair value of the embedded derivative liabilities. For example, an increase in our stock price results in an increase in the estimated fair value of the embedded derivative liabilities. The embedded derivative liabilities may have, on a GAAP basis, a substantial effect on our balance sheet from quarter to quarter and it is difficult to predict the effect on our future GAAP financial results, since valuation of these embedded derivative liabilities are based on factors largely outside of our control and may have a negative impact on our earnings and balance sheet. The effects of these embedded derivatives may cause our GAAP operating results to be below expectations, which may cause our stock price to decline.

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If we are not able to successfully commence, scale up or sustain operations at our existing and planned manufacturing facilities, our customer relationships, business and results of operations may be adversely affected.

A substantial component of our planned production capacity in the near and long term depends on successful operations at our existing and potential large-scale production plants. We are currently operating our first purpose-built, large-scale production plant in Brotas, Brazil and may complete construction of certain other facilities in the coming years. Delays or problems in the construction, start-up or operation of these facilities will cause delays in our ramp-up of production and hamper our ability to reduce our production costs. Delays in construction can occur due to a variety of factors, including regulatory requirements and our ability to fund construction and commissioning costs. For example, in 2012 we determined it was necessary to delay further construction of our large-scale manufacturing facility with São Martinho in order to focus on the construction and commissioning of our Brotas facility. We have since permanently ceased construction of the São Martinho facility. In 2016 we produced at capacity at our Brotas facility and will likely need to identify and secure access to additional production capacity in 2017 based on anticipated volume requirements, either by constructing a new custom-built facility, acquiring an existing facility from a third party, retrofitting an existing facility operated by a current or potential partner or increasing our use of contract manufacturing facilities. In December 2016, we acquired a production facility in Leland, North Carolina, which facility had been previously operated by our partner Glycotech to perform chemical conversion and production of our end-products, and which facility was subsequently transferred to our newly-formed joint venture with Nikko Chemicals Co., Ltd. and Nippon Surfactant Industries Co., Ltd. (or collectively “Nikko”), as further described in Note 7, “Joint Ventures and Noncontrolling Interest” to our unaudited condensed consolidated financial statements included in this report. In addition, in February 2017 we broke ground on a second custom-built production facility adjacent to our existing Brotas facility. However, there can be no assurance that we will be able to complete such facility on our expected timeline, if at all.

Once our large-scale production facilities are built, acquired or retrofitted, we must successfully commission them, if necessary, and they must perform as we expect. If we encounter significant delays, cost overruns, engineering issues, contamination problems, equipment or raw material supply constraints, unexpected equipment maintenance requirements, safety issues, work stoppages or other serious challenges in bringing these facilities online and operating them at commercial scale, we may be unable to produce our renewable products in the time frame and at the cost we have planned. Industrial scale fermentation is an emerging field and it is difficult to predict the effects of scaling up production to commercial scale, which involves various risks to the quality and consistency of our molecules. In addition, in order to produce molecules at our existing and potential future plants, we have been and may in the future be required to perform thorough transition activities, and modify the design of the plant. Any modifications to the production plant could cause complications in the operations of the plant, which could result in delays or failures in production. If any of these risks occur, or if we are unable to create or obtain additional manufacturing capacity necessary to meet existing and potential customer demand, we may need to continue to use, or increase our use of, contract manufacturing sources, which generally entail greater cost to us to produce our products and would therefore reduce our anticipated gross margins and may also prevent us from accessing certain markets for our products. Further, if our efforts to increase (or commence, as the case may be) production at these facilities are not successful, our partners may decide not to work with us to develop additional production facilities, demand more favorable terms or delay their commitment to invest capital in our production. If we are unable to create and sustain manufacturing capacity and operations sufficient to satisfy the existing and potential demand of our customers and partners, our business and results of operations may be adversely affected.

Our reliance on the large-scale production plant in Brotas, Brazil subjects us to execution and economic risks.

Our decision to focus our efforts for production capacity on our manufacturing facility in Brotas, Brazil means that we have limited manufacturing sources for our products in 2017 and beyond. While we have undertaken efforts to identify and obtain additional manufacturing capacity for 2017 and beyond, including the manufacturing facility in Leland, North Carolina and the proposed second manufacturing facility at the Brotas site discussed above, there can be no assurance that such efforts will be successful on the timelines or at the cost we require, if at all. Any production delays could have a significant negative impact on our business, including our ability to achieve commercial viability for our products and meeting existing and potential customer demand. With the facility in Brotas, Brazil, we are, for the first time, operating a commercial fermentation and separation facility ourselves. We have in the past faced, and may in the future face, unexpected difficulties associated with the operation of our plants. For example, we have in the past, at certain contract manufacturing facilities and at the Brotas facility, encountered delays and difficulties in ramping up production based on contamination in the production process, problems with plant utilities, lack of automation and related human error, issues arising from process modifications to reduce costs and adjust product specifications or transition to producing new molecules, and other similar challenges. We cannot be certain that we will be able to remedy all of such challenges quickly or effectively enough to achieve commercially viable near-term production costs and volumes.

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To the extent we secure collaboration arrangements with new or existing partners, we may be required to make significant capital investments at our existing or new facilities in order to produce molecules or other products for such collaborations. Any failure or difficulties in establishing, building up or retooling our operations for these new collaboration arrangements could have a significant negative impact on our business, including our ability to achieve commercial viability for our products, lead to the inability to meet our contractual obligations and could cause us to allocate capital, personnel and other resources from our organization which could adversely affect our business and reputation.

As part of our arrangement to build the plant in Brotas, Brazil we have an agreement with Tonon Bioenergia S.A., or Tonon, to purchase from Tonon sugarcane juice and syrup corresponding to a certain number of tons of sugarcane per year, along with specified water and vapor volumes. Until this annual volume is reached, we are restricted from purchasing sugarcane juice or syrup for processing in the facility from any third party, subject to limited exceptions, unless we pay the premium to Tonon that we would have paid if we bought the sugarcane juice from them. As such, we will be relying on Tonon to supply such juice and syrup and utilities on a timely basis, in the volumes we need, and at competitive prices. If a third party can offer superior prices and Tonon does not consent to our purchasing from such third party, we would be required to pay Tonon the applicable premium, which would have a negative impact on our production cost. Furthermore, we agreed to pay a price for the juice or syrup that is based on the lower of the cost of two other products produced by Tonon using such juice, plus a premium. Tonon may not want to sell sugarcane juice or syrup to us if the price of one of the other products is substantially higher than the one setting the price for the juice or syrup we purchase. While the agreement provides that Tonon would have to pay a penalty to us if it fails to supply the agreed-upon volume of syrup or juice for a given month, the penalty may not be enough to compensate us for the increased cost if third-party suppliers do not offer competitive prices. Also, if the prices of the other products produced by Tonon increase, we could be forced to pay those increased prices for production without a related increase in the price at which we can sell our products, reducing or eliminating any margins we can otherwise achieve. If in the future these supply terms no longer provide a viable economic structure for the operation in Brotas, Brazil we may be required to renegotiate our agreement, which could result in manufacturing disruptions and delays. In December 2015, Tonon filed for bankruptcy protection in Brazil. If Tonon is unable to supply sugarcane juice or syrup, water and steam in accordance with our agreement, we may not be able to obtain substitute supplies from third parties in necessary quantities or at favorable prices, or at all. In such event, our ability to manufacture our products in a timely or cost-effective manner, or at all, would be negatively affected, which would have a material adverse effect on our business.

Furthermore, as we continue to scale up production of our products, through contract manufacturers, at our existing and planned production plants in Brotas, Brazil and Leland, North Carolina and at any future manufacturing facility, we may be required to store increasing amounts of our products for varying periods of time and under differing temperatures or other conditions that cannot be easily controlled, which may lead to a decrease in the quality of our products and their utility profiles and could adversely affect their value. If our stored products degrade in quality, we may suffer losses in inventory and incur additional costs in order to further refine our stored products or we may need to make new capital investments in shipping, improved storage or sales channels and related logistics.

Loss or termination of contract manufacturing relationships could harm our ability to meet our production goals.

As we have focused on building and commissioning, acquiring or retrofitting our own plants or the plants of existing or potential partners, respectively, and improving our production economics, we have reduced our use of contract manufacturing and have terminated relationships with some of our contract manufacturing partners. The failure to have multiple available supply options for farnesene or other target molecules could create a risk for us if a single source or a limited number of sources of manufacturing runs into operational issues. In addition, if we are unable to secure the services of contract manufacturers when and as needed, we may lose customer opportunities and the growth of our business may be impaired. We cannot be sure that contract manufacturers will be available when we need their services, that they will be willing to dedicate a portion of their capacity to our projects, or that we will be able to reach acceptable price and other terms with them for the provision of their production services. If we shift priorities and adjust anticipated production levels (or cease production altogether) at contract manufacturing facilities, such adjustments or cessations could also result in disputes or otherwise harm our business relationships with contract manufacturers. In addition, reducing or stopping production at one facility while increasing or starting up production at another facility generally results in significant losses of production efficiency, which can persist for significant periods of time. Also, in order for production to commence under our contract manufacturing arrangements, we generally must provide equipment for such operations, and we cannot be assured that such equipment can be ordered or installed on a timely basis, at acceptable costs, or at all. Further, in order to establish new manufacturing facilities, we need to transfer our yeast strains and production processes from our labs to commercial plants controlled by third parties, which may pose technical or operational challenges that delay production or increase our costs.

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Our use of contract manufacturers exposes us to risks relating to costs, contractual terms and logistics.

While we have commenced commercial production at our Brotas, Brazil and Leland, North Carolina plants, we continue to commercially produce, process and manufacture some specialty molecules through the use of contract manufacturers, and we anticipate that we will continue to use contract manufacturers for the foreseeable future for chemical conversion and production of end-products and, to mitigate cost and volume risks at our large-scale production facilities, for production of Biofene and other fermentation target compounds. Establishing and operating contract manufacturing facilities requires us to make significant capital expenditures, which reduces our cash and places such capital at risk. Also, contract manufacturing agreements may contain terms that commit us to pay for capital expenditures and other costs incurred or expected to be earned by the plant operators and owners, which can result in contractual liability and losses for us even if we terminate a particular contract manufacturing arrangement or decide to reduce or stop production under such an arrangement.

The locations of contract manufacturers can pose additional cost, logistics and feedstock challenges. If production capacity is available at a plant that is remote from usable chemical finishing or distribution facilities, or from customers, we will be required to incur additional expenses in shipping products to other locations. Such costs could include shipping costs, compliance with export and import controls, tariffs and additional taxes, among others. In addition, we may be required to use feedstock from a particular region for a given production facility. The feedstock available in such region may not be the least expensive or most effective feedstock for production, which could significantly raise our overall production cost or reduce our product’s quality until we are able to optimize the supply chain.

Our operations rely on sophisticated information technology and equipment systems and infrastructure, a disruption of which could harm our operations.

We rely on various information technology and equipment systems, some of which are dependent on services provided by third parties, to manage our technology platform and operations. These systems provide critical data and services for internal and external users, including procurement and inventory management, transaction processing, financial, commercial and operational data, human resources management, legal and tax compliance information and other information and processes necessary to operate and manage our business. These systems are complex and are frequently updated as technology improves, and include software and hardware that is licensed, leased or purchased from third parties. If our information technology and equipment systems experience breaches or other failures or disruptions, our systems and the information could be compromised. While we have implemented security measures and disaster recovery plans designed to mitigate the effects of any failures or disruption of these systems, such measures may not adequately prevent adverse events such as breaches or failures from occurring or mitigate their severity if they do occur. If our information technology or equipment systems are breached, damaged or fail to function properly due to internal errors or defects, implementation or integration issues, catastrophic events or power outages, we may experience a material disruption in our ability to manage our business operations. Failure or disruption of these systems could have an adverse effect on our operating results and financial condition.

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If we are unable to reduce our production costs, we may not be able to produce our products at competitive prices and our ability to grow our business will be limited.

In order to be competitive in the markets we are targeting, our products must have superior qualities or be competitively priced relative to alternatives available in the market. Currently, our costs of production are not low enough to allow us to offer some of our planned products at competitive prices relative to alternatives available in the market. Our production costs depend on many factors that could have a negative effect on our ability to offer our planned products at competitive prices, including, in particular, our ability to establish and maintain sufficient production scale and volume, and feedstock cost. For example, see “We have limited experience producing our products at commercial scale and may not be able to commercialize our products to the extent necessary to sustain and grow our current business,” “Our manufacturing operations require sugar feedstock, energy and steam, and the inability to obtain such feedstock, energy and steam in sufficient quantities or in a timely manner, or at reasonable prices, may limit our ability to produce products profitably or at all,” and “The price of sugarcane and other feedstocks can be volatile as a result of changes in industry policy and may increase the cost of production of our products.”

We face financial risk associated with scaling up production to reduce our production costs. To reduce per-unit production costs, we must increase production to achieve economies of scale and to be able to sell our products with positive margins. However, if we do not sell production output in a timely manner or in sufficient volumes, our investment in production will harm our cash position and generate losses. Additionally, we may incur added costs in storage and we may face issues related to the decrease in quality of our stored products, which could adversely affect the value of such products. Since achieving competitive product prices generally requires increased production volumes and our manufacturing operations and cash flows from sales are in their early stages, we have had to produce and sell products at a loss in the past, and may continue to do so as we build our business. If we are unable to achieve adequate revenues from a combination of product sales and other sources, we may not be able to invest in production and we may not be able to pursue our business plans. In addition, in order to attract potential collaboration or joint venture partners, or to meet payment milestones under existing or future collaboration agreements, we have in the past and may in the future be required to guarantee or meet certain levels of production costs. If we are unable to reduce our production costs to meet such guarantees or milestones, our net cash flow will be further reduced.

Key factors beyond production scale and feedstock cost that impact our production costs include yield, productivity, separation efficiency and chemical process efficiency. Yield refers to the amount of the desired molecule that can be produced from a fixed amount of feedstock. Productivity represents the rate at which our product is produced by a given yeast strain. Separation efficiency refers to the amount of desired product produced in the fermentation process that we are able to extract and the time that it takes to do so. Chemical process efficiency refers to the cost and yield for the chemical finishing steps that convert our target molecule into a desired product. In order to compete successfully in our target markets, we must produce our products at significantly lower costs, which will require both substantially higher yields than we have achieved to date and other significant improvements in production efficiency, including in productivity and in separation and chemical process efficiencies. There can be no assurance that we will be able to make these improvements or reduce our production costs sufficiently to offer our planned products at competitive prices or to attract and maintain collaboration partners, and any such failure could have a material adverse impact on our business and prospects.

Our ability to establish substantial commercial sales of our products is subject to many risks, any of which could prevent or delay revenue growth and adversely impact our customer relationships, business and results of operations.

There can be no assurance that our products will be approved or accepted by customers, that customers will choose our products over competing products, or that we will be able to sell our products profitably at prices and with features sufficient to establish demand. The markets we have entered first are primarily those for specialty chemical products used by large consumer products or specialty chemical companies. In entering these markets, we have sold and we intend to sell our products as alternatives to chemicals currently in use, and in some cases the chemicals that we seek to replace have been used for many years. The potential customers for our molecules generally have well developed manufacturing processes and arrangements with suppliers of the chemical components of their products and may have a resistance to changing these processes and components. These potential customers frequently impose lengthy and complex product qualification procedures on their suppliers, influenced by consumer preference, manufacturing considerations such as process changes and capital and other costs associated with transitioning to alternative components, supplier operating history, established business relationships and agreements, regulatory issues, product liability and other factors, many of which are unknown to, or not well understood by, us. Satisfying these processes may take many months or years. Additionally, we may be subject to product safety testing and may be required to meet certain regulatory and/or product safety standards. Meeting these standards can be a time consuming and expensive process, and we may invest substantial time and resources into such qualification efforts without ultimately securing approval. If we are unable to convince these potential customers (and the consumers who purchase products containing such chemicals) that our products are comparable to the chemicals that they currently use or that the use of our products is otherwise to their benefit, we will not be successful in entering these markets and our business will be adversely affected.

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We expect to face competition for our products from providers of petroleum-based products and from other companies seeking to provide alternatives to these products, and if we cannot compete effectively against these companies or products we may not be successful in bringing our products to market or further growing our business after we do so.

We expect that our renewable products will compete with both the traditional, largely petroleum-based products that are currently being used in our target markets and with the alternatives to these existing products that established enterprises and new companies are seeking to produce.

In the markets that we are initially entering, and in other markets that we may seek to enter in the future, we will compete primarily with the established providers of ingredients currently used in products in these markets. Producers of these incumbent products include global oil companies, large international chemical companies and companies specializing in specific products, such as squalane or essential oils. We may also compete in one or more of these markets with products that are offered as alternatives to the traditional petroleum-based or other traditional products being offered in these markets.

With the emergence of many new companies seeking to produce products from alternative sources, we may face increasing competition from such companies. As they emerge, some of these companies may be able to establish production capacity and commercial partnerships to compete with us. If we are unable to establish production and sales channels that allow us to offer comparable products at attractive prices, we may not be able to compete effectively with these companies.

We believe the primary competitive factors in our target markets are:

• product price;

• product performance and other measures of quality;

• infrastructure compatibility of products;

• sustainability; and

• dependability of supply.

The oil companies, large chemical companies and well-established agricultural products companies with whom we compete are much larger than us, have, in many cases, well developed distribution systems and networks for their products, have valuable historical relationships with the potential customers we are seeking to serve and have much more extensive sales and marketing programs in place to promote their products. In order to be successful, we must convince customers that our products are at least as effective as the traditional products they are seeking to replace and we must provide our products on a cost basis that does not greatly exceed these traditional products and other available alternatives. Some of our competitors may use their influence to impede the development and acceptance of renewable products of the type that we are seeking to produce.

We believe that for our chemical products to succeed in the market, we must demonstrate that our products are comparable alternatives to existing products and to any alternative products that are being developed for the same markets based on some combination of product cost, availability, performance, and consumer preference characteristics. With respect to our diesel and other transportation fuels products, we believe that our product must perform as effectively as petroleum-based fuel, or alternative fuels, and be available on a cost basis that does not greatly exceed these traditional products and other available alternatives. In addition, with the wide range of renewable fuels products under development, we must be successful in reaching potential customers and convincing them that ours are effective and reliable alternatives.

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Certain rights we have granted to Total and other existing stockholders, including in relation to our future securities offerings, could have substantial impacts on our company.

Under certain agreements between us and Total related to Total’s original investment in our capital stock, for as long as Total owns 10% of our voting securities, it has rights to an exclusive negotiation period if our Board of Directors decides to sell our company. Total also has the right to designate one director to serve on our Board of Directors. In addition, in connection with Total’s investments in Amyris, our certificate of incorporation includes a provision that excludes Total from prohibitions on business combinations between Amyris and an “interested stockholder.” These provisions could have the effect of discouraging potential acquirers from making offers to acquire us, and give Total more access to Amyris than other stockholders if Total decides to pursue an acquisition.

Additionally, in connection with subsequent investments by Total in Amyris, we granted Total, among other investors, a right of first investment if we propose to sell securities in a private placement financing transaction. With these rights, Total and other investors may subscribe for a portion of any new private placement financing and require us to comply with certain notice periods, which could discourage other investors from participating in, or cause delays in our ability to close, such a financing. Further, Total and such other investors have the right to pay for any securities purchased in connection with an exercise of their right of first investment by cancelling all or a portion of our debt held by them. To the extent Total or such other investors exercise these rights, it will reduce the cash proceeds we may realize from the relevant financing.

Our relationship with Ginkgo Bioworks, Inc. exposes us to financial and commercial risks.

In June 2016, we entered into an initial strategic partnership agreement with Ginkgo Bioworks, Inc., or Ginkgo, pursuant to which we licensed certain intellectual property to Ginkgo in exchange for a license fee and royalty, and agreed to pursue the negotiation and execution of a definitive partnership agreement setting forth the terms of a long-term commercial partnership and collaboration arrangement between us and Ginkgo, and in September 2016 we executed a definitive collaboration agreement with Ginkgo setting forth the terms of a commercial partnership under which the parties would collaborate to develop, manufacture and sell commercial products and would share in the value of such products. In connection with the entry into such commercial agreements, we received a waiver under, and subsequently entered into an amendment of, our senior secured credit facility, the agent and lender under which is an affiliate of Ginkgo, which amendment extended, subject to certain conditions which were satisfied in January 2017, the maturity of the loans under the senior secured credit facility, eliminated principal repayments under the facility prior to maturity, subject to the requirement that we apply certain monies received by us under the collaboration agreement with Ginkgo to repay the outstanding loans under the facility, and waived the covenant in the senior secured loan facility requiring the Company to maintain unrestricted, unencumbered cash in defined U.S. bank accounts in an amount equal to at least 50% of the principal amount outstanding under the facility until the maturity date. For more details on our transactions with Ginkgo, please see Note 5, “Debt and Mezzanine Equity” and Note 8, “Significant Agreements” to our unaudited condensed consolidated financial statements included in this report.

There can be no assurance that our partnership with Ginkgo will be successful, and the partnership may prevent us from pursuing other business opportunities in the future. If the partnership is unsuccessful, our ability to continue with our business plans would be adversely affected. In addition, negative developments in our commercial partnership with Ginkgo could negatively affect our relationship with the agent and lender under our senior secured credit facility, an affiliate of Ginkgo, which could adversely impact our ability to incur additional indebtedness in the future or take other actions the consent for which would be required from the agent and lender under the facility. In such event, our financial condition and business operations could be adversely affected.

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If we do not meet technical, development and commercial milestones in our collaboration agreements, our future revenue and financial results will be adversely impacted.

We have entered into a number of agreements regarding the further development of certain of our products and, in some cases, for ultimate sale of certain products to the customer under the agreement. None of these agreements affirmatively obligates the other party to purchase specific quantities of any products at this time, and most contain important conditions that must be satisfied before additional research and development funding or product purchases would occur. These conditions include research and development milestones and technical specifications that must be achieved to the satisfaction of our collaborators, which we cannot be certain we will achieve. If we do not achieve these contractual milestones, our revenues and financial results will be adversely affected.

We are subject to risks related to our reliance on collaboration arrangements to fund development and commercialization of our products and the success of such products is uncertain.

For most product markets we are seeking to enter, we either have or are seeking collaboration partners to fund the research and development, commercialization and production efforts required for the target products. Typically we provide limited exclusive rights and revenue sharing with respect to the production and sale of particular types of products in specific markets in exchange for such up-front funding. These exclusivity, revenue-sharing and other similar terms limit our ability to commercialize our products and technology, and may impact the size of our business or our profitability in ways that we do not currently envision. In addition, revenues from these types of relationships are a key part of our cash plan for 2017 and beyond. If we fail to collect expected collaboration revenues, or to identify and add sufficient additional collaborations to fund our planned operations, we may be unable to fund our operations or pursue development and commercialization of our planned products. To achieve our collaboration revenue targets from year to year, we may be forced to enter into agreements that contain less favorable terms. As part of our current and future collaboration arrangements, we may be required to make significant capital investments at our existing or new facilities in order to produce molecules or other products for such collaborations. Any failure or difficulties in establishing, building up or retooling our operations for these collaboration arrangements could have a significant negative impact on our business, including our ability to achieve commercial viability for our products, lead to the inability to meet our contractual obligations and could cause us to allocate capital, personnel and other resources from our organization which could adversely affect our business and reputation.

With respect to pharmaceutical collaborations, our experience in this industry is limited, so we may have difficulty identifying and securing collaboration partners and customers for pharmaceutical applications of our products and services. Furthermore, our success in the pharmaceutical market depends primarily upon our ability to identify and validate new small molecule compounds of pharmaceutical interest (including through the use of our discovery platform), and identify, test, develop and commercialize such compounds. Our research efforts may initially show promise in discovering potential new therapeutic candidates, yet fail to yield viable product candidates for clinical development for a number of reasons, including:

• because our research methodology, including our screening technology, may not successfully identify medically relevant product candidates;

• we may identify and select from our discovery platform novel untested classes of product candidates for the particular disease indication we are pursuing, which may be challenging to validate because of the novelty of the product candidates or we may fail to validate at all after further research work;

• our product candidates may cause adverse effects in patients or subjects, even after successful initial toxicology studies, which may make the product candidates unmarketable;

• our product candidates may not demonstrate a meaningful benefit to patients or subjects; and

• collaboration partners may change their development profiles or plans for potential product candidates or abandon a therapeutic area or the development of a partnered product.

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Research programs to identify new product targets and candidates require substantial technical, financial and human resources. We may focus our efforts and resources on potential discovery efforts, programs or product candidates that ultimately prove to be unsuccessful.

Our collaboration arrangements may restrict or prevent our future business activity in certain markets or industries, which could harm our ability to grow our business.

As part of our collaboration arrangements in the ordinary course of business, we may grant to our partners exclusive rights with respect to the development, production and/or commercialization of particular products or types of products in specific markets in exchange for up-front funding and/or downstream value sharing arrangements. These rights might inhibit potential collaboration or strategic partners or potential customers from entering into negotiations with us about further business opportunities, and we may be restricted or prevented from engaging with other partners or customers in those markets, which may limit our ability to grow our business.

For example, under our Amended and Restated Jet Fuel Agreement with TAB and our License Agreement regarding Diesel Fuel in the European Union with Total described above, we granted TAB and Total, respectively, certain exclusive rights to produce and commercialize farnesene- or farnesane-based jet and diesel fuel in certain jurisdictions, as well as certain purchase rights. As a result of these agreements, we generally no longer have an independent right to make or sell farnesene- or farnesane-based jet or diesel fuels in such jurisdictions without the approval of TAB or Total, as applicable. If, for any reason, we would like to pursue farnesene- or farnesane-based jet or diesel fuels in such jurisdictions independently or with a third party, these arrangements could impair our ability to develop, produce or commercialize such jet or diesel fuels, which could have a material adverse effect on our business and long term prospects.

In the past, we have had to grant concessions to existing partners in exchange for such partners waiving or modifying their exclusive rights with respect to a particular product, type of product or market so that we could engage with a third party with respect to such product, product type or market. There can be no assurance that existing partners will be willing to grant waivers or modify their exclusive rights in the future on favorable terms, if at all. If we are unable to engage other potential partners with respect to particular products, products types or markets for which we have previously granted exclusive rights, our ability to grow our business would be harmed and our results of operations may be adversely effected.

If our collaboration partners are not successful in commercializing products that incorporate our technology, our business and results of operations may be adversely affected.

We rely on our collaboration partners to create demand with end-users for products that incorporate our products and technologies. If such collaboration partners are unable to create such demand, we may not be able to successfully market or sell our products. In addition, while we maintain certain clawback rights to our technology in the event our collaboration partners are unable or unwilling to commercialize the products we create for them under the applicable collaboration arrangement, if our collaboration partners do not commercialize the products covered by our collaboration or supply arrangements, we may be restricted from or unable to market or sell such products or technologies to other potential collaboration partners, which could hinder the growth of our business. If we allocate resources to collaborations that do not lead to products that are commercially viable, our revenues, financial condition and results of operations could be adversely affected.

In addition, certain of our collaboration partners have the right to terminate their agreements with us if we undergo a change of control or a sale of our business, which could discourage a potential acquirer from making an offer to acquire us.

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We have limited control over our joint ventures.

As a result of the restructuring of our joint ventures TAB and Novvi during 2016, as discussed above, we do not have the right or power to control the management of such entities, and our joint venture partners may take action with respect to such joint ventures which is contrary to our interests or objectives. In addition, with respect to the joint venture we formed in December 2016 with Nikko relating to our Neossance cosmetic ingredients business, while we hold a 50% equity interest in such joint venture and have a right to appoint one half of its board of directors, our joint venture partners acting together will have the right to designate the Chief Executive Officer and certain other officers, which would restrict our ability to control the operations of such joint venture. If our joint venture partners act contrary to our interest, it could harm our brand, business, results of operations and financial condition. In addition, operating a joint venture often requires additional organizational formalities as well as time-consuming procedures for sharing information and making decisions, which can divert management resources, and if a joint venture partner changes or relationships deteriorate, our success in the joint venture may be materially adversely affected, which could harm our business. Furthermore, with respect to TAB, if we were to experience a change of control or fail to make any required capital contribution to TAB, Total has a right to buy out our interest in TAB at fair market value. If Total were to exercise these rights, we would, in effect, relinquish our economic rights to the intellectual property we have exclusively licensed to TAB, and our ability to seek future revenue from farnesene-based jet fuel outside of Brazil would be adversely affected (or completely prevented). This could significantly reduce the value of our product offerings and have a material adverse effect on our ability to grow our business in the future.

Our manufacturing operations require sugar feedstock, energy and steam, and the inability to obtain such feedstock, energy and steam in sufficient quantities or in a timely manner, or at reasonable prices, may limit our ability to produce our products profitably, or at all.

We anticipate that the production of our products will require large volumes of feedstock. We have relied on a mixture of feedstock sources for use at our contract manufacturing operations, including cane sugar, corn-based dextrose and beet molasses. For our large-scale production facility in Brazil, we are relying primarily on Brazilian sugarcane. We cannot predict the future availability or price of these various feedstocks, nor can we be sure that our mill partners, which we expect to supply the sugarcane feedstock necessary to produce our products in Brazil, will be able to supply it in sufficient quantities or in a timely manner. For example, in December 2015, Tonon, one of our suppliers of sugarcane juice and syrup, filed for bankruptcy protection in Brazil, which may adversely affect its ability to supply us with sugarcane juice and syrup in the future. Furthermore, to the extent we are required to rely on sugar feedstock other than Brazilian sugarcane, the cost of such feedstock may be higher than we expect, increasing our anticipated production costs. Feedstock crop yields and sugar content depend on weather conditions, such as rainfall and temperature. Weather conditions have historically caused volatility in the ethanol and sugar industries by causing crop failures or reduced harvests. Excessive rainfall can adversely affect the supply of sugarcane and other sugar feedstock available for the production of our products by reducing the sucrose content and limiting growers' ability to harvest. Crop disease and pestilence can also occur from time to time and can adversely affect feedstock growth, potentially rendering useless or unusable all or a substantial portion of affected harvests. With respect to sugarcane, our initial primary feedstock, seasonal availability and price, the limited amount of time during which it keeps its sugar content after harvest, and the fact that sugarcane is not itself a traded commodity, increases these risks and limits our ability to substitute supply in the event of such an occurrence. If production of sugarcane or any other feedstock we may use to produce our products is adversely affected by these or other conditions, our production will be impaired, and our business will be adversely affected.

Additionally, our facility in Brotas, Brazil depends on large quantities of energy and steam to operate. We have a supply agreement with Cogeração de Energia Elétrica Rhodia Brotas S.A. pursuant to which we receive energy and steam in sufficient amounts to meet our current needs. However, we cannot predict the future availability or price of energy and steam. If, for whatever reason, we must purchase energy or steam from a different supplier, the cost of such energy and steam may be higher than we expect, increasing our anticipated production costs. Droughts or other weather conditions or natural disasters in Brazil may also affect energy and steam production, cost and availability and, therefore, may adversely affect our production. If our supply and access to energy or steam is adversely affected by these or other conditions, our production will be impaired, and our business will be adversely affected.

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The price of sugarcane and other feedstocks can be volatile as a result of changes in industry policy and may increase the cost of production of our products.

In Brazil, Conselho dos Produtores de Cana, Açúcar e Álcool (Council of Sugarcane, Sugar and Ethanol Producers or Consecana), an industry association of producers of sugarcane, sugar and ethanol, sets market terms and prices for general supply, lease and partnership agreements for sugarcane. If Consecana makes changes to such terms and prices, it could result in higher sugarcane prices and/or a significant decrease in the volume of sugarcane available for the production of our products. Furthermore, if Consecana were to cease to be involved in this process, such prices and terms could become more volatile. Similar principles apply to the pricing of other feedstocks as well. Any of these events could adversely affect our business and results of operations.

Our large-scale commercial production capacity is centered in Brazil, and our business will be adversely affected if we do not operate effectively in that country.

For the foreseeable future, we will be subject to risks associated with the concentration of essential product sourcing and operations in Brazil. The Brazilian government has changed in the past, and may change in the future, monetary, taxation, credit, tariff, labor and other policies to influence the course of Brazil's economy. For example, the government's actions to control inflation have at times involved setting wage and price controls, adjusting interest rates, imposing taxes and exchange controls and limiting imports into Brazil. We have no control over, and cannot predict what policies or actions the Brazilian government may take in the future. Our business, financial performance and prospects may be adversely affected by, among others, the following factors:

• delays or failures in securing licenses, permits or other governmental approvals necessary to build and operate facilities and use our yeast strains to produce products;

• rapid consolidation in the sugar and ethanol industries in Brazil, which could result in a decrease in competition;

• political, economic, diplomatic or social instability in or affecting Brazil;

• changing interest rates;

• tax burden and policies;

• effects of changes in currency exchange rates;

• any changes in currency exchange policy that lead to the imposition of exchange controls or restrictions on remittances abroad;

• inflation;

• land reform or nationalization movements;

• changes in labor related policies;

• export or import restrictions that limit our ability to move our products out of Brazil or interfere with the import of essential materials into Brazil;

• changes in, or interpretations of foreign regulations that may adversely affect our ability to sell our products or repatriate profits to the United States;

• tariffs, trade protection measures and other regulatory requirements;

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• compliance with United States and foreign laws that regulate the conduct of business abroad;

• compliance with anti-corruption laws recently enacted in Brazil;

• an inability, or reduced ability, to protect our intellectual property in Brazil including any effect of compulsory licensing imposed by government action; and

• difficulties and costs of staffing and managing foreign operations. 

We cannot predict whether the current or future Brazilian government will implement changes to existing policies on taxation, exchange controls, monetary strategy, labor relations, social security and the like, nor can we estimate the impact of any such changes on the Brazilian economy or our operations.

Brazil’s economy has recently experienced quarters of slow or negative gross domestic product growth and has experienced high inflation and a growing fiscal deficit of its federal government accounts. In addition, major corruption scandals involving members of the executive, state-controlled enterprises and large private sector companies have been disclosed and are the subject of ongoing investigation by federal authorities. The final outcome of these investigations and their impact on the Brazilian economy is not yet known and cannot be predicted with certainty.

In addition, during the 2016 U.S. presidential election campaign, President Trump made comments suggesting that he was not supportive of certain existing international trade agreements as well as that he might take action to restrict or tax products imported into the U.S. from foreign jurisdictions. At this time, it remains unclear what President Trump will or will not do with respect to these international trade agreements or U.S. trade policy. If President Trump takes action to withdraw from or materially modify international trade agreements or place restrictions or tariffs on products imported from Brazil, our business, financial condition and results of operations could be adversely affected.

We maintain operations in foreign jurisdictions other than Brazil, and may in the future expand our operations to additional foreign jurisdictions. Many, if not all of the above-mentioned risks also apply to our operations in such jurisdictions. If any of these risks were to occur, our operations and business would be adversely affected.

Our international operations expose us to the risk of fluctuation in currency exchange rates and rates of foreign inflation, which could adversely affect our results of operations.

We currently incur significant costs and expenses in Brazilian real and may in the future incur additional expenses in foreign currencies and derive a portion of our revenues in the local currencies of customers throughout the world. As a result, our revenues and results of operations are subject to foreign exchange fluctuations, which we may not be able to manage successfully. During the past few decades, the Brazilian currency in particular has faced frequent and substantial exchange rate fluctuations in relation to the United States dollar and other foreign currencies. There can be no assurance that the Brazilian real will not significantly appreciate or depreciate against the United States dollar in the future. We also bear the risk that the rate of inflation in the foreign countries where we incur costs and expenses or the decline in value of the United States dollar compared to those foreign currencies will increase our costs as expressed in United States dollars. For example, future measures by the Central Bank of Brazil to control inflation, including interest rate adjustments, intervention in the foreign exchange market and actions to fix the value of the real, may weaken the United States dollar in Brazil. Whether in Brazil or elsewhere, we may not be able to adjust the prices of our products to offset the effects of inflation or foreign currency appreciation on our cost structure, which could increase our costs and reduce our net operating margins. If we do not successfully manage these risks through hedging or other mechanisms, our revenues and results of operations could be adversely affected.

Ethical, legal and social concerns about products using genetically modified microorganisms could limit or prevent the use of our products and technologies and could harm our business.

Our technologies and products involve the use of genetically modified microorganisms, or GMMs. Public perception about the safety of, and ethical, legal or social concerns over, genetically engineered products, including GMMs, could affect public acceptance of our products. If we are not able to overcome any such concerns relating to our products, our technologies may not be accepted by our customers or end-users. In addition, the use of GMMs has in the past received negative publicity, which could lead to greater regulation or restrictions on imports of our products. Further, there is a risk that products produced using our technologies could cause adverse health effects or other adverse events, which could also lead to negative publicity. If our technologies and products are not accepted by our customers or their end-users due to negative publicity or lack of public acceptance, our business could be significantly harmed.

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Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of regulatory limitations and rejection of our products.

The use of GMMs, such as our yeast strains, is subject to laws and regulations in many countries, some of which are new and some of which are still evolving. In the United States, the Environmental Protection Agency (EPA), regulates the commercial use of GMMs as well as potential products produced from GMMs. Various states or local governments within the United States could choose to regulate products made with GMMs as well. While the strain of genetically modified yeast that we currently use for the development and commercial production of our target molecules, S. cerevisiae, is eligible for exemption from EPA review because it is generally recognized as safe, we must satisfy certain criteria to achieve this exemption, including but not limited to use of compliant containment structures and safety procedures, and we cannot be sure that we will meet such criteria in a timely manner, or at all. If exemption of S. cerevisiae is not obtained, our business may be substantially harmed. In addition to S. cerevisiae, we may seek to use different GMMs in the future that will require EPA approval. If approval of different GMMs is not secured, our ability to grow our business could be adversely affected.

In Brazil, GMMs are regulated by the National Biosafety Technical Commission, or CTNBio. We have obtained approvals from CTNBio to use GMMs in a contained environment in our Brazil facilities for research and development purposes as well as at contract manufacturing facilities in Brazil. In addition, we have obtained initial commercial approvals from CTNBio for two of our yeast strains. As we continue to develop new yeast strains and deploy our technology at new production facilities in Brazil, we will be required to obtain further approvals from CTNBio in order to use these strains in commercial production in Brazil. We may not be able to obtain approvals from relevant Brazilian authorities on a timely basis, or at all, and if we do not, our ability to produce our products in Brazil would be impaired, which would adversely affect our results of operations and financial condition.

In addition to our production operations in the United States and Brazil, we have been party to contract manufacturing agreements with parties in other production locations around the world, including Europe. The use of GMM technology is strictly regulated in the European Union, which has established various directives for member states regarding regulation of the use of such technology, including notification processes for contained use of such technology. We expect to encounter GMM regulations in most, if not all, of the countries in which we may seek to establish production capabilities and/or conduct sales to customers or end-use consumers, and the scope and nature of these regulations will likely be different from country to country. If we cannot meet the applicable requirements in other countries in which we intend to produce or sell products using our yeast strains, or if it takes longer than anticipated to obtain such approvals, our business could be adversely affected. Furthermore, there are various non-governmental and quasi-governmental organizations that review and certify products with respect to the determination of whether products can be classified as “natural” or other similar classifications. While the certification from such non-governmental and quasi-governmental organizations is generally not mandatory, some of our current or prospective customers, collaborators or distributors may require that we meet the standards set by such organizations as a condition precedent to purchasing or distributing our products. We cannot be certain that we will be able to satisfy the standards of such organizations, and any delay or failure to do so could harm our ability to sell or distribute some or all of our products to certain customers and prospective customers, which could have a negative impact on our business.

We may not be able to obtain regulatory approval for the sale of our renewable products.

Our renewable chemical products may be subject to government regulation in our target markets. In the United States, the EPA administers the Toxic Substances Control Act, or the TSCA, which regulates the commercial registration, distribution, and use of many chemicals. Before an entity can manufacture or distribute a new chemical subject to the TSCA, it must file a Pre-Manufacture Notice, or PMN, to add the chemical to a product. The EPA has 90 days to review the filing but may request additional data, which could significantly extend the timeline for approval. As a result, we may not receive EPA approval to list future molecules on the TSCA registry as expeditiously as we would like, resulting in delays or significant increases in testing requirements. A similar program exists in the European Union, called REACH. Under this program, chemicals imported or manufactured in the European Union in certain quantities must be registered with the European Chemicals Agency, and this process could cause delays or entail significant costs. To the extent that other countries in which we are producing or selling (or seeking to produce or sell) our products, such as Brazil and various countries in Asia, rely on TSCA or REACH (or similar laws and programs) for chemical registration or regulation in their jurisdictions, delays with the United States or European authorities, or any relevant authorities in such other countries, may delay entry into these markets as well. In addition, some of our Biofene-derived products are sold for the cosmetics market, and some countries may impose additional regulatory requirements or permits for such uses, which could impair, delay or prevent sales of our products in those markets.

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We expect to encounter regulations in most, if not all, of the countries in which we may seek to produce, import or sell our products (and our customers may encounter similar regulations in selling end-use products to consumers), and we cannot assure you that we (or our customers) will be able to obtain necessary approvals in a timely manner or at all. If our products do not meet applicable regulatory requirements in a particular country, then we (or our customers) may not be able to commercialize our products in such country and our business will be adversely affected.

In addition, many of our products are intended to be a component of our collaborators’ and/or customers’ (or their customers’) end-use products. Such end-use products may be subject to various regulations, including regulations promulgated by the EPA or the United States Food and Drug Administration. If our collaborators and customers (or their customers) are not successful in obtaining any required regulatory approval for their end-use products that incorporate our products, or fail to comply with any applicable regulations for such end-use products, whether due to our products or otherwise, demand for our products may decline and our revenues will be adversely affected.

Changes in government regulations, including subsidies and economic incentives, could have a material adverse effect on our business.

The market for renewable chemical products is heavily influenced by foreign, federal, state and local government regulations and policies. Changes to existing or adoption of new domestic or foreign federal, state and local legislative initiatives that impact the production, distribution or sale of renewable chemical products may harm our business. The uncertainty regarding future standards and policies may also affect our ability to develop new renewable products or to license our technologies to third parties and to sell products to our end customers. Any inability to address these requirements and any regulatory or policy changes could have a material adverse effect on our business, financial condition and results of operations.

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Furthermore, the production of our products will depend on the availability of feedstock, especially sugarcane. Agricultural production and trade flows are subject to government policies and regulations. Governmental policies affecting the agricultural industry, such as taxes, tariffs, duties, subsidies, incentives and import and export restrictions on agricultural commodities and commodity products can influence the planting of certain crops, the location and size of crop production, whether unprocessed or processed commodity products are traded, the volume and types of imports and exports, and the availability and competitiveness of feedstocks as raw materials. Future government policies may adversely affect the supply of feedstocks, restrict our ability to use sugarcane or other feedstocks to produce our products, or encourage the use of feedstocks more advantageous to our competitors, which would put us at a commercial disadvantage and could negatively impact our future revenues and results of operations.

We may incur significant costs to comply with environmental laws and regulations, and failure to comply with these laws and regulations could expose us to significant liabilities.

We use hazardous chemicals and radioactive and biological materials in our business, and such materials are subject to a variety of federal, state and local laws and regulations governing the use, generation, manufacture, storage, handling and disposal of these materials in the United States and in Brazil. Although we have implemented safety procedures for handling and disposing of these materials and related waste products in an effort to comply with these laws and regulations, we cannot be sure that our safety measures will prevent accidental injury or contamination from the use, storage, handling or disposal of hazardous materials. In the event of contamination or injury, we could be held liable for any resulting damages, and any liability could exceed our insurance coverage. There can be no assurance that violations of environmental, health and safety laws will not occur in the future as a result of human error, accident, equipment failure or other causes. Compliance with applicable environmental laws and regulations may be expensive, and the failure to comply with past, present, or future laws could result in the imposition of fines, third party property damage, product liability and personal injury claims, investigation and remediation costs, the suspension of production, or a cessation of operations, and our liability may exceed our total assets. Liability under environmental laws can be joint and several, without regard to comparative fault, and may be punitive in nature. Furthermore, environmental laws could become more stringent over time, imposing greater compliance costs and increasing risks and penalties associated with violations, which could impair our research, development or production efforts and otherwise harm our business.

A decline in the price of petroleum and petroleum-based products has in the past and may in the future reduce demand for some of our renewable products and may otherwise adversely affect our business.

While many of our products do not compete with, and do not serve as alternatives to, petroleum-based products, we anticipate that some of our renewable products, and in particular our fuels, will be marketed as alternatives to corresponding petroleum-based products. The price of oil has fallen significantly in recent years, and accordingly, we may be unable to produce certain of our products as cost-effective alternatives to petroleum-based products. Declining oil prices, or the perception of a sustained or future decline in oil prices, has adversely affected the prices or demand for such products in the past and may do so in the future. During sustained periods of lower oil prices we may be unable to sell such products at anticipated levels, which could negatively impact our operating results.

Our financial results could vary significantly from quarter to quarter and are difficult to predict.

Our revenues and results of operations could vary significantly from quarter to quarter because of a variety of factors, many of which are outside of our control. As a result, comparing our results of operations on a period-to-period basis may not be meaningful. Factors that could cause our quarterly results of operations to fluctuate include:

• achievement, or failure, with respect to technology, product development or manufacturing milestones needed to allow us to enter identified markets on a cost effective basis;

• delays or greater than anticipated expenses associated with the completion, commissioning, acquisition or retrofittting of new production facilities, or the time to ramp up and stabilize production following completion, acquisition or retrofittting of a new production facility or the transition to, and ramp up of, producing new molecules at our existing facilities;

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• impairment of assets based on shifting business priorities and working capital limitations;

• disruptions in the production process at any manufacturing facility, including disruptions due to seasonal or unexpected downtime at our facilities as a result of feedstock availability, contamination, safety or other issues or other technical difficulties or the scheduled downtime at our facilities as a result of transitioning our equipment to the production of different molecules;

• losses of, or the inability to secure new, major customers, collaboration partners, suppliers or distributors;

• losses associated with producing our products as we ramp to commercial production levels;

• failure to recover value added tax (VAT) that we currently reflect as recoverable in our financial statements (e.g., due to failure to meet conditions for reimbursement of VAT under local law);

• the timing, size and mix of product sales to customers;

• increases in price or decreases in availability of feedstock;

• the unavailability of contract manufacturing capacity altogether or at reasonable cost;

• exit costs associated with terminating contract manufacturing relationships;

• fluctuations in foreign currency exchange rates;

• gains or losses associated with our hedging activities;

• change in the fair value of derivative instruments;

• fluctuations in the price of and demand for sugar, ethanol, and petroleum-based and other products for which our products are alternatives;

• seasonal variability in production and sales of our products;

• competitive pricing pressures, including decreases in average selling prices of our products;

• unanticipated expenses or delays associated with changes in governmental regulations and environmental, health, labor and safety requirements;

• reductions or changes to existing fuel and chemical regulations and policies;

• departure of executives or other key management employees resulting in transition and severance costs;

• our ability to use our net operating loss carryforwards to offset future taxable income;

• business interruptions such as earthquakes, tsunamis and other natural disasters;

• our ability to integrate businesses that we may acquire;

• our ability to successfully collaborate with business venture partners;

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• risks associated with the international aspects of our business; and

• changes in general economic, industry and market conditions, both domestically and in our foreign markets.

Due to the factors described above, among others, the results of any quarterly or annual period may not meet our expectations or the expectations of our investors and may not be meaningful indications of our future performance.

Loss of key personnel, including key management personnel, and/or failure to attract and retain additional personnel could delay our product development programs and harm our research and development efforts and our ability to meet our business objectives.

Our business involves complex, global operations across a variety of markets and requires a management team and employee workforce that is knowledgeable in the many areas in which we operate. As we continue to build our business, we will need to hire and retain qualified research and development, management and other personnel to succeed. The process of hiring, training and successfully integrating qualified personnel into our operations, in the United States, Brazil and other countries in which we may seek to operate, is a lengthy and expensive one. The market for qualified personnel is very competitive because of the limited number of people available who have the necessary technical skills and understanding of our technology and products, particularly in Brazil. Our failure to hire and retain qualified personnel could impair our ability to meet our research and development and business objectives and adversely affect our results of operations and financial condition.

The loss of any key member of our management or key technical and operational employees, or the failure to attract or retain such employees, could prevent us from developing and commercializing our products for our target markets and executing our business strategy. In addition, we may not be able to attract or retain qualified employees in the future due to the intense competition for qualified personnel among biotechnology and other technology-based businesses, particularly in the renewable chemicals and fuels area. Furthermore, reductions to our workforce as part of cost-saving measures, such as those discussed above with respect to our 2017 operating plan, may make it more difficult for us to attract and retain key employees. If we do not maintain the necessary personnel to accomplish our business objectives, we may experience staffing constraints that will adversely affect our ability to meet the demands of our collaborators and customers in a timely fashion or to support our internal research and development programs and operations. In particular, our product and process development programs depend on our ability to attract and retain highly skilled technical and operational personnel. Competition for such personnel from numerous companies and academic and other research institutions may limit our ability to do so on acceptable terms. All of our employees are “at-will” employees, which means that either the employee or we may terminate their employment at any time.

Growth may place significant demands on our management and our infrastructure.

We have experienced, and expect to continue to experience, expansion of our business as we continue to make efforts to develop and bring our products to market. We have grown from 18 employees at the end of 2005 to 456 full-time employees at March 31, 2017. Our growth and diversified operations have placed, and may continue to place, significant demands on our management and our operational and financial infrastructure. In particular, continued growth could strain our ability to:

• manage multiple research and development programs;

• operate multiple manufacturing facilities around the world;

• develop and improve our operational, financial and management controls;

• enhance our reporting systems and procedures;

• recruit, train and retain highly skilled personnel;

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• develop and maintain our relationships with existing and potential business partners;

• maintain our quality standards; and

• maintain customer satisfaction.

Managing our growth will require significant expenditures and allocation of valuable management resources. If we fail to achieve the necessary level of efficiency in our organization as it grows, our business, results of operations and financial condition would be adversely impacted.

Our proprietary rights may not adequately protect our technologies and product candidates.

Our commercial success will depend substantially on our ability to obtain patents and maintain adequate legal protection for our technologies and product candidates in the United States and other countries. As of March 31, 2017, we had approximately 510 issued United States and foreign patents and approximately 340 pending United States and foreign patent applications that were owned or co-owned by or licensed to us. We will be able to protect our proprietary rights from unauthorized use by third parties only to the extent that our proprietary technologies and future products are covered by valid and enforceable patents or are effectively maintained as trade secrets.

We apply for patents covering both our technologies and product candidates, as we deem appropriate. However, filing, prosecuting, maintaining and defending patents on product candidates in all countries throughout the world would be prohibitively expensive, and our intellectual property rights in some countries outside the United States are less extensive than those in the United States. We may also fail to apply for patents on important technologies or product candidates in a timely fashion, or at all. Our existing and future patents may not be sufficiently broad to prevent others from practicing our technologies or from designing products around our patents or otherwise developing competing products or technologies. In addition, the patent positions of companies like ours are highly uncertain and involve complex legal and factual questions for which important legal principles remain unresolved. No consistent policy regarding the breadth of patent claims has emerged to date in the United States and the landscape is expected to become even more uncertain in view of recent rule changes by the United States Patent Office, or USPTO. Additional uncertainty may result from legal decisions by the United States Federal Circuit and Supreme Court as they determine legal issues concerning the scope and construction of patent claims and inconsistent interpretation of patent laws or from legislation enacted by the U.S. Congress. The patent situation outside of the United States is even less predictable. As a result, the validity and enforceability of patents cannot be predicted with certainty. Moreover, we cannot be certain whether:

• we (or our licensors) were the first to make the inventions covered by each of our issued patents and pending patent applications;

• we (or our licensors) were the first to file patent applications for these inventions;

• others will independently develop similar or alternative technologies or duplicate any of our technologies;

• any of our or our licensors' patents will be valid or enforceable;

• any patents issued to us (or our licensors) will provide us with any competitive advantages, or will be challenged by third parties;

• we will develop additional proprietary products or technologies that are patentable; or

• the patents of others will have an adverse effect on our business.

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We do not know whether any of our pending patent applications or those pending patent applications that we license will result in the issuance of any patents. Even if patents are issued, they may not be sufficient to protect our technology or product candidates. The patents we own or license and those that may be issued in the future may be challenged, invalidated, rendered unenforceable, or circumvented, and the rights granted under any issued patents may not provide us with proprietary protection or competitive advantages. Moreover, third parties could practice our inventions in territories where we do not have patent protection or in territories where they could obtain a compulsory license to our technology where patented. Such third parties may then try to import products made using our inventions into the United States or other territories. Accordingly, we cannot ensure that any of our pending patent applications will result in issued patents, or even if issued, predict the breadth, validity and enforceability of the claims upheld in our and other companies' patents.

Many companies have encountered significant problems in protecting and defending intellectual property rights in foreign jurisdictions. The legal systems of certain countries do not favor the enforcement of patents or other intellectual property rights, which could hinder us from preventing the infringement of our patents or other intellectual property rights. Proceedings to enforce our patent rights in the United States or foreign jurisdictions could result in substantial costs and divert our efforts and attention from other aspects of our business, could put our patents at risk of being invalidated or interpreted narrowly and our patent applications at risk of not issuing and could provoke third parties to assert patent infringement or other claims against us. We may not prevail in any lawsuits that we initiate and the damages or other remedies awarded, if any, may not be commercially meaningful. Accordingly, our efforts to enforce our intellectual property rights around the world may be inadequate to obtain a significant commercial advantage from the intellectual property that we develop or license from third parties.

Unauthorized parties may attempt to copy or otherwise obtain and use our products or technology. Monitoring unauthorized use of our intellectual property is difficult, and we cannot be certain that the steps we have taken will prevent unauthorized use of our technology, particularly in certain foreign countries where the local laws may not protect our proprietary rights as fully as in the United States or may provide, today or in the future, for compulsory licenses. If competitors are able to use our technology, our ability to compete effectively could be harmed. Moreover, others may independently develop and obtain patents for technologies that are similar to, or superior to, our technologies. If that happens, we may need to license these technologies, and we may not be able to obtain licenses on reasonable terms, if at all, which could cause harm to our business.

We rely in part on trade secrets to protect our technology, and our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

We rely on trade secrets to protect some of our technology, particularly where we do not believe patent protection is appropriate or obtainable. However, trade secrets are difficult to maintain and protect. Our strategy for contract manufacturing and scale-up of commercial production requires us to share confidential information with our international business partners and other parties. Our product development collaborations with third parties, including with Total and Ginkgo, require us to share confidential information, including with employees of Total and Ginkgo who are seconded to Amyris during the term of the collaboration. While we use reasonable efforts to protect our trade secrets, our or our business partners' employees, consultants, contractors or scientific and other advisors may unintentionally or willfully disclose our proprietary information to competitors. Enforcement of claims that a third party has illegally obtained and is using trade secrets is expensive, time consuming and uncertain. In addition, foreign courts are sometimes less willing than United States courts to protect trade secrets. If our competitors independently develop equivalent knowledge, methods and know-how, we would not be able to assert our trade secrets against them.

We require new employees and consultants to execute confidentiality agreements upon the commencement of an employment or consulting arrangement with us. We additionally require consultants, contractors, advisors, corporate collaborators, outside scientific collaborators and other third parties that may receive trade secret information to execute confidentiality agreements. These agreements generally require that all confidential information developed by the individual or made known to the individual by us during the course of the individual's relationship with us be kept confidential and not disclosed to third parties. These agreements also generally provide that inventions conceived by the individual in the course of rendering services to us shall be our exclusive property. Nevertheless, our proprietary information may be disclosed, or these agreements may be unenforceable or difficult to enforce. If any of our trade secrets were to be lawfully obtained or independently developed by a competitor, we would have no right to prevent such third party, or those to whom they communicate such technology or information, from using that technology or information to compete with us. Additionally, trade secret law in Brazil differs from that in the United States, which requires us to take a different approach to protecting our trade secrets in Brazil. Some of these approaches to trade secret protection may be novel and untested under Brazilian law and we cannot guarantee that we would prevail if our trade secrets are contested in Brazil. If any of the above risks materializes, our failure to obtain or maintain trade secret protection could adversely affect our competitive business position.

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We may not be able to fully enforce covenants not to compete with and not to solicit our employees, and therefore we may be unable to prevent our competitors from benefiting from the expertise of such employees.

Our proprietary information and inventions agreements with our employees contain non-compete and non-solicitation provisions. These provisions prohibit our employees from competing directly with our business or proposed business or working for our competitors during their term of employment, and from directly and indirectly soliciting our employees and consultants to leave our company for any purpose. Under applicable U.S. and Brazilian law, we may be unable to enforce these provisions. If we cannot enforce these provisions with our employees, we may be unable to prevent our competitors from benefiting from the expertise of such employees. Even if these provisions are enforceable, they may not adequately protect our interests. The defection of one or more of our employees to a competitor could materially adversely affect our business, results of operations and ability to capitalize on our proprietary information.

Third parties may misappropriate our yeast strains.

Third parties, including collaborators, contract manufacturers, sugar and ethanol mill owners, other contractors and shipping agents, often have custody or control of our yeast strains. If our yeast strains were stolen, misappropriated or reverse engineered, they could be used by other parties who may be able to reproduce the yeast strains for their own commercial gain. If this were to occur, it would be difficult for us to challenge and prevent this type of use, especially in countries where we have limited intellectual property protection or that do not have robust intellectual property law regimes.

If we or one of our collaborators are sued for infringing intellectual property rights or other proprietary rights of third parties, litigation could be costly and time consuming and could prevent us from developing or commercializing our future products.

Our commercial success depends on our and our collaborators’ ability to operate without infringing the patents and proprietary rights of other parties and without breaching any agreements we have entered into with regard to our technologies and product candidates. We cannot determine with certainty whether patents or patent applications of other parties may materially affect our ability to conduct our business. Our industry spans several sectors, including biotechnology, renewable fuels, renewable specialty chemicals and other renewable compounds, and is characterized by the existence of a significant number of patents and disputes regarding patent and other intellectual property rights. Because patent applications can take several years to issue, there may currently be pending applications, unknown to us, that may result in issued patents that cover our technologies or product candidates. We are aware of a significant number of patents and patent applications relating to aspects of our technologies filed by, and issued to, third parties. The existence of third-party patent applications and patents could significantly reduce the coverage of patents owned by or licensed to us and our collaborators and limit our ability to obtain meaningful patent protection. If we wish to make, use, sell, offer to sell, or import the technology or compound claimed in issued and unexpired patents owned by others, we will need to obtain a license from the owner, enter into litigation to challenge the validity of the patents or incur the risk of litigation in the event that the owner asserts that we infringe its patents. If patents containing competitive or conflicting claims are issued to third parties and these claims are ultimately determined to be valid, we and our collaborators may be enjoined from pursing research, development, or commercialization of products, or be required to obtain licenses to these patents, or to develop or obtain alternative technologies.

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If a third party asserts that we infringe upon its patents or other proprietary rights, we could face a number of issues that could seriously harm our competitive position, including:

• infringement and other intellectual property claims, which could be costly and time consuming to litigate, whether or not the claims have merit, and which could delay getting our products to market and divert management attention from our business;

• substantial damages for past infringement, which we may have to pay if a court determines that our product candidates or technologies infringe a third party's patent or other proprietary rights;

• a court prohibiting us from selling or licensing our technologies or future products unless the holder licenses the patent or other proprietary rights to us, which it is not required to do; and

• if a license is available from a third party, such third party may require us to pay substantial royalties or grant cross licenses to our patents or proprietary rights.

The industries in which we operate, and the biotechnology industry in particular, are characterized by frequent and extensive litigation regarding patents and other intellectual property rights. Many biotechnology companies have employed intellectual property litigation as a way to gain a competitive advantage. If any of our competitors have filed patent applications or obtained patents that claim inventions also claimed by us, we may have to participate in interference proceedings declared by the relevant patent regulatory agency to determine priority of invention and, thus, the right to the patents for these inventions in the United States. These proceedings could result in substantial cost to us even if the outcome is favorable. Even if successful, an interference proceeding may result in loss of certain claims. Our involvement in litigation, interferences, opposition proceedings or other intellectual property proceedings inside and outside of the United States, to defend our intellectual property rights, or as a result of alleged infringement of the rights of others, may divert management time from focusing on business operations and could cause us to spend significant resources, all of which could harm our business and results of operations.

Many of our employees were previously employed at universities, biotechnology, specialty chemical or oil companies, including our competitors or potential competitors. We may be subject to claims that these employees or we have inadvertently or otherwise used or disclosed trade secrets or other proprietary information of their former employers. Litigation may be necessary to defend against these claims. If we fail in defending such claims, in addition to paying monetary damages, we may lose valuable intellectual property rights or personnel and be enjoined from certain activities. A loss of key research personnel or their work product could hamper or prevent our ability to commercialize our product candidates, which could severely harm our business. Even if we are successful in defending against these claims, litigation could result in substantial costs and demand on management resources.

We may need to commence litigation to enforce our intellectual property rights, which would divert resources and management's time and attention and the results of which would be uncertain.

Enforcement of claims that a third party is using our proprietary rights without permission is expensive, time consuming and uncertain. Significant litigation would result in substantial costs, even if the eventual outcome is favorable to us and would divert management's attention from our business objectives. In addition, an adverse outcome in litigation could result in a substantial loss of our proprietary rights and we may lose our ability to exclude others from practicing our technology or producing our product candidates.

The laws of some foreign countries do not protect intellectual property rights to the same extent as do the laws of the United States. Many companies have encountered significant problems in protecting and defending intellectual property rights in certain foreign jurisdictions. The legal systems of certain countries, particularly certain developing countries, do not favor the enforcement of patents and other intellectual property protection, particularly those relating to biotechnology and/or bioindustrial technologies. This could make it difficult for us to stop the infringement of our patents or misappropriation of our other intellectual property rights. Proceedings to enforce our patent rights in foreign jurisdictions could result in substantial costs and divert our efforts and attention from other aspects of our business. Moreover, our efforts to protect our intellectual property rights in such countries may be inadequate.

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We do not have exclusive rights to intellectual property we develop under U.S. federally funded research grants and contracts, including with DARPA and DOE, and we could ultimately share or lose the rights we do have under certain circumstances.

Some of our intellectual property rights have been or may be developed in the course of research funded by the U.S. government, including under our agreements with DARPA and DOE. As a result, the U.S. government may have certain rights to intellectual property embodied in our current or future products pursuant to the Bayh-Dole Act of 1980. Government rights in certain inventions developed under a government-funded program include a non-exclusive, non-transferable, irrevocable worldwide license to use inventions for any governmental purpose. In addition, the U.S. government has the right to require us, or an assignee or exclusive licensee to such inventions, to grant licenses to any of these inventions to a third party if they determine that: (i) adequate steps have not been taken to commercialize the invention; (ii) government action is necessary to meet public health or safety needs; (iii) government action is necessary to meet requirements for public use under federal regulations; or (iv) the right to use or sell such inventions is exclusively licensed to an entity within the U.S. and substantially manufactured outside the U.S. without the U.S. government’s prior approval. Additionally, we may be restricted from granting exclusive licenses for the right to use or sell our inventions created pursuant to such agreements unless the licensee agrees to additional restrictions (e.g., manufacturing substantially all of the invention in the U.S.). The U.S. government also has the right to take title to these inventions if we fail to disclose the invention to the government and fail to file an application to register the intellectual property within specified time limits. In addition, the U.S. government may acquire title in any country in which a patent application is not filed within specified time limits. Additionally, certain inventions are subject to transfer restrictions during the term of these agreements and for a period thereafter, including sales of products or components, transfers to foreign subsidiaries for the purpose of the relevant agreements, and transfers to certain foreign third parties. If any of our intellectual property becomes subject to any of the rights or remedies available to the U.S. government or third parties pursuant to the Bayh-Dole Act of 1980, this could impair the value of our intellectual property and could adversely affect our business.

Our products subject us to product-safety risks, and we may be sued for product liability.

The design, development, production and sale of our products involve an inherent risk of product liability claims and the associated adverse publicity. Our potential products could be used by a wide variety of consumers with varying levels of sophistication. Although safety is a priority for us, we are not always in control of the final uses and formulations of the products we supply or their use as ingredients. Our products could have detrimental impacts or adverse impacts we cannot anticipate. Despite our efforts, negative publicity about Amyris, including product safety or similar concerns, whether real or perceived, could occur, and our products could face withdrawal, recall or other quality issues. In addition, we may be named directly in product liability suits relating to our products, even for defects resulting from errors of our commercial partners, contract manufacturers, chemical finishers or customers or end users of our products. These claims could be brought by various parties, including customers who are purchasing products directly from us or other users who purchase products from our customers. We could also be named as co-parties in product liability suits that are brought against the contract manufacturers or Brazilian sugar and ethanol mills with whom we partner to produce our products. Insurance coverage is expensive, may be difficult to obtain and may not be available in the future on acceptable terms. We cannot be certain that our contract manufacturers or the sugar and ethanol producers who partner with us to produce our products will have adequate insurance coverage to cover against potential claims. Any insurance we do maintain may not provide adequate coverage against potential losses, and if claims or losses exceed our liability insurance coverage, our business would be adversely impacted. In addition, insurance coverage may become more expensive, which would harm our results of operations.

We may become subject to lawsuits or indemnity claims in the ordinary course of business, which could materially and adversely affect our business and results of operations.

From time to time, we may in the ordinary course of business be named as a defendant in lawsuits, indemnity claims and other legal proceedings. These actions may seek, among other things, compensation for alleged personal injury, employment discrimination, breach of contract, property damage and other losses or injunctive or declaratory relief. In the event that such actions, claims or proceedings are ultimately resolved unfavorably to us at amounts exceeding our accrued liability, or at material amounts, the outcome could materially and adversely affect our reputation, business and results of operations. In addition, payments of significant amounts, even if reserved, could adversely affect our liquidity position.

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If we fail to maintain an effective system of internal controls, we may not be able to report our financial results accurately or in a timely manner or prevent fraud; in that case, our stockholders could lose confidence in our financial reporting, which would harm our business and could negatively impact the price of our stock.

Effective internal controls are necessary for us to provide reliable financial reports and prevent fraud. In addition, Section 404 of the Sarbanes-Oxley Act of 2002, or Section 404, requires us to evaluate and report on our internal control over financial reporting. The process of implementing our internal controls and complying with Section 404 is expensive and time consuming, and requires significant attention of management. We cannot be certain that these measures will ensure that we maintain adequate controls over our financial processes and reporting in the future. In addition, to the extent we create joint ventures or have any variable interest entities and the financial statements of such entities are not prepared by us, we will not have direct control over their financial statement preparation. As a result, we will, for our financial reporting, depend on what these entities report to us, which could result in us adding monitoring and audit processes and increase the difficulty of implementing and maintaining adequate controls over our financial processes and reporting in the future and could lead to delays in our external reporting. In particular, this may occur where we are establishing such entities with commercial partners that do not have sophisticated financial accounting processes in place, or where we are entering into new relationships at a rapid pace, straining our integration capacity. Additionally, if we do not receive the information from the joint venture or variable interest entity on a timely basis, it could cause delays in our external reporting. Even if we conclude that our internal control over financial reporting provides reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles, because of its inherent limitations, internal control over financial reporting may not prevent or detect fraud or misstatements. Failure to implement required new or improved controls, or difficulties encountered in their implementation, could harm our results of operations or cause us to fail to meet our reporting obligations. If we or our independent registered public accounting firm discover a material weakness in our internal control over financial reporting, the disclosure of that fact, even if quickly remedied, could reduce the market’s confidence in our financial statements and harm our stock price. In addition, failure to comply with Section 404 could subject us to a variety of administrative sanctions, including SEC action, ineligibility for short form resale registration, the suspension or delisting of our common stock from the stock exchange on which it is listed, and the inability of registered broker-dealers to make a market in our common stock, which would further reduce our stock price and could harm our business.

If we fail to comply with our obligations as a public company, our business may be adversely affected.

As a public company, we incur significant legal, accounting and other expenses in connection with our obligations under applicable securities laws, including the internal and external costs of maintaining the system of internal controls discussed above as well as the costs of preparing and distributing periodic public reports, including financial statements and footnotes. In addition, changing laws, rules and regulations relating to corporate governance and public disclosure, including regulations implemented by the SEC and NASDAQ, increase our legal and financial costs, including costs relating to monitoring, evaluating and complying with such laws, rules and regulations. These laws, rules and regulations are subject to varying interpretations and may evolve over time as new guidance is provided by regulatory and governing bodies, which may result in increased compliance and governance costs and the diversion of management resources. If our efforts to comply with such laws, rules and regulations are not successful, we could be subject to fines, penalties or regulatory proceedings, which can be time consuming and costly to litigate and could lead to negative publicity about our company. These events could also make it more difficult for us to attract and retain qualified members of our board of directors, executive officers and other employees. If any of these risks occur, or if these requirements divert our management’s attention from other business concerns, they could have a material adverse effect on our business, financial condition and results of operations.

Our ability to use our net operating loss carryforwards to offset future taxable income may be subject to certain limitations.

In general, under Section 382 of the Internal Revenue Code, or the Code, a corporation that undergoes an “ownership change” is subject to limitations on its ability to utilize its pre-change net operating loss carryforwards, or NOLs, to offset future taxable income. If the Internal Revenue Service challenges our analysis that our existing NOLs are not subject to limitations arising from previous ownership changes, or if we undergo an ownership change in the future, our ability to utilize NOLs could be limited by Section 382 of the Code. Future changes in our stock ownership, some of which are outside of our control, could result in an ownership change under Section 382 of the Code. Furthermore, our ability to utilize NOLs of companies that we may acquire in the future may be subject to limitations under Section 382 of the Code. For these reasons, we may not be able to utilize a material portion of our NOLs as of March 31, 2017, even if we attain profitability, which could adversely affect our results of operations.

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Loss of, or inability to secure government contract revenues could impair our business.

We have contracts or subcontracts with certain governmental agencies or their contractors. Generally, these agreements, as they may be amended or modified from time to time, have fixed terms and may be terminated, modified or be subject to recovery of payments by the government agency under certain conditions (such as failure to comply with detailed reporting and governance processes or failure to achieve milestones). Under these agreements, we are also subject to audits, which can result in corrective action plans and penalties up to and including termination. If these governmental agencies terminate these agreements with us, it could reduce our revenues which could harm our business. Additionally, we anticipate securing additional government contracts as part of our business plan for 2017 and beyond. If we are unable to secure such government contracts, it could harm our business.

Our headquarters and other facilities are located in an active earthquake and tsunami zone, and an earthquake or other type of natural disaster affecting us or our suppliers could cause resource shortages, disrupt our business and harm our results of operations.

We conduct our primary research and development operations in the San Francisco Bay Area in an active earthquake and tsunami zone, and certain of our suppliers conduct their operations in the same region or in other locations that are susceptible to natural disasters. In addition, California and some of the locations where certain of our suppliers are located have experienced shortages of water, electric power and natural gas from time to time. The occurrence of a natural disaster, such as an earthquake, drought or flood, or localized extended outages of critical utilities or transportation systems, or any critical resource shortages, affecting us or our suppliers could cause a significant interruption in our business, damage or destroy our facilities, production equipment or inventory or those of our suppliers and cause us to incur significant costs or result in limitations on the availability of our raw materials, any of which could harm our business, financial condition and results of operations. The insurance we maintain against fires, earthquakes and other natural disasters may not be adequate to cover our losses in any particular case.

Risks Related to Ownership of Our Common Stock

Our stock price may be volatile.

The market price of our common stock has been, and we expect it to continue to be, subject to significant volatility, and it has declined significantly from our initial public offering price. As of March 31, 2017, the reported closing price of our common stock on The NASDAQ Stock Market was $0.53 per share. Market prices for securities of early stage companies have historically been particularly volatile. Such fluctuations could be in response to, among other things, the factors described in this “Risk Factors” section, or other factors, some of which are beyond our control, such as:

• fluctuations in our financial results or outlook or those of companies perceived to be similar to us;

• changes in estimates of our financial results or recommendations by securities analysts;

• changes in market valuations of similar companies;

• changes in the prices of commodities associated with our business such as sugar, ethanol and petroleum or changes in the prices of commodities that some of our products may replace, such as oil and other petroleum sourced products;

• changes in our capital structure, such as future issuances of securities or the incurrence of debt;

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• announcements by us or our competitors of significant contracts, acquisitions or strategic alliances;

• regulatory developments in the United States, Brazil, and/or other foreign countries;

• litigation involving us, our general industry or both;

• additions or departures of key personnel;

• investors' general perception of us; and

• changes in general economic, industry and market conditions.

Furthermore, stock markets have experienced price and volume fluctuations that have affected, and continue to affect, the market prices of equity securities of many companies. These fluctuations often have been unrelated or disproportionate to the operating performance of those companies. These broad market fluctuations, as well as general economic, political and market conditions, such as recessions, interest rate changes and international currency fluctuations, may negatively affect the market price of our common stock.

In the past, many companies that have experienced volatility and sustained declines in the market price of their stock have become subject to securities class action and derivative action litigation. We were involved in two such lawsuits which were dismissed in 2014, are currently involved in one such lawsuit, as described in more detail below in “ITEM 3. LEGAL PROCEEDINGS”, and we may be the target of this type of litigation in the future. Securities litigation against us could result in substantial costs and divert our management’s attention from other business concerns, which could seriously harm our business.

If our common stock is delisted from The NASDAQ Stock Market, our business, financial condition, results of operations and stock price could be adversely affected, and the liquidity of our stock and our ability to obtain financing could be impaired.

On June 14, 2016, we received a notice from The NASDAQ Stock Market LLC, or NASDAQ, notifying us that we were not in compliance with the requirement of NASDAQ Listing Rule 5450(a)(1) for continued listing on The NASDAQ Global Market, or the Minimum Bid Price Listing Rule, as a result of the closing bid price of our common stock being below $1.00 per share for 30 consecutive business days. In accordance with NASDAQ Listing Rule 5810(c)(3)(A), we had 180 calendar days, or until December 12, 2016, to regain compliance with the Minimum Bid Price Listing Rule. To regain compliance, the closing bid price of our common stock had to be at least $1.00 per share for a minimum of 10 consecutive business days. On November 1, 2016, we received a notice from NASDAQ that we had regained compliance with the Minimum Bid Price Listing Rule. Subsequently, on December 19, 2016, we received a notice from NASDAQ notifying us that we were again not in compliance with the Minimum Bid Price Listing Rule as a result of the closing bid price of our common stock being below $1.00 per share for 30 consecutive business days. In accordance with NASDAQ Listing Rule 5810(c)(3)(A), we have 180 calendar days, or until June 19, 2017, to regain compliance with the Minimum Bid Price Listing Rule. If we do not regain compliance during such period, we may be eligible for an additional compliance period of 180 calendar days, provided that we meet NASDAQ’s continued listing requirement for market value of publicly held shares and all other initial listing standards for The NASDAQ Capital Market, other than the minimum bid price requirement, and provide written notice to NASDAQ of our intention to cure the deficiency during the second compliance period. If we do not regain compliance during the initial compliance period and are not eligible for an additional compliance period, NASDAQ will provide notice that our common stock will be subject to delisting from The NASDAQ Stock Market. In that event, we may appeal such determination to a hearings panel. Our Board of Directors has approved, and we have proposed that our stockholders approve at our 2017 Annual Meeting of Stockholders to be held on May 23, 2017, or the Annual Meeting, an amendment to our certificate of incorporation to effect a 15-for-1 reverse stock split that is designed to result in an increase in the per share trading price of our common stock above $1.00 per share. If our stockholders approve this proposal, we intend to implement it promptly following the Annual Meeting. There can be no assurance that upon any such implementation of the reverse stock split that we will regain compliance with the Minimum Bid Price Listing Rule and that our common stock will remain listed on The NASDAQ Stock Market.

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Any delisting of our common stock from The NASDAQ Stock Market could adversely affect our ability to attract new investors, decrease the liquidity of our outstanding shares of common stock, reduce our flexibility to raise additional capital, reduce the price at which our common stock trades, and increase the transaction costs inherent in trading such shares with overall negative effects for our stockholders. In addition, the delisting of our common stock could deter broker-dealers from making a market in or otherwise seeking or generating interest in our common stock, and might deter certain institutions and persons from investing in our securities at all. Furthermore, the delisting of our common stock from The NASDAQ Stock Market would constitute a breach under certain of our financing agreements, including agreements governing our outstanding convertible indebtedness, which could result in an acceleration of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under our other outstanding indebtedness, permitting acceleration of such other outstanding indebtedness as well. For these reasons and others, the delisting of our common stock from The NASDAQ Stock Market could materially adversely affect our business, financial condition and results of operations.

The concentration of our capital stock ownership with insiders will limit the ability of other stockholders to influence corporate matters and presents risks related to the operations of our significant stockholders.

As of March 31, 2017:

• our executive officers and directors and their affiliates together held approximately 9% of our outstanding common stock;

• Maxwell (Mauritius) Pte Ltd, or Temasek (which has a designee on our Board of Directors), held approximately 18% of our outstanding common stock; and

• Total (which has a designee on our Board of Directors) held approximately 22% of our outstanding common stock.

Furthermore, Total and Temasek each hold certain of our convertible promissory notes, which are convertible into approximately 22,350,261 and 2,670,370 shares of our common stock, respectively, as of March 31, 2017. Total and Temasek also hold certain warrants pursuant to which they may purchase shares of our common stock. This significant concentration of share ownership may adversely affect the trading price of our common stock because investors often perceive disadvantages in owning stock in companies with stockholders with significant interests. Also, these stockholders, acting together, will be able to control our management and affairs and matters requiring stockholder approval, including the election of directors and the approval of significant corporate transactions, such as mergers, consolidations or the sale of all or substantially all of our assets, and may not act in the best interests of our other stockholders. Consequently, this concentration of ownership may have the effect of delaying or preventing a change of control, including a merger, consolidation or other business combination involving us, or a change in our management or Board of Directors, or discouraging a potential acquirer from making a tender offer or otherwise attempting to obtain control of the Company, even if such actions would benefit our other stockholders.

In addition, our commercial partners, including Total, hold a significant portion of our capital stock and have various rights in connection with their security ownership in us. These stockholders may have interests that are different from those of our other stockholders, including commercial transactions between our company and such commercial partners or their affiliates. While we have a related-party transactions policy which requires certain approvals of any transaction between our company and a significant stockholder or its affiliates, there can be no assurance that such stockholders will act in the best interests of our other stockholders, which could harm our results of operations and cause our stock price to decline.

The market price of our common stock could be negatively affected by future sales of our common stock.

If our existing stockholders, particularly our largest stockholders, our directors, their affiliates, or our executive officers, sell a substantial number of shares of our common stock in the public market, the market price of our common stock could decrease significantly. The perception in the public market that these stockholders might sell our common stock could also depress the market price of our common stock and could impair our future ability to obtain capital, especially through an offering of equity securities.

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We have in place, or have agreed to file, registration statements for the resale of certain shares of common stock held by, or issuable to, certain of our largest stockholders. All common stock sold pursuant to an offering covered by such registration statement will be freely transferable.

In addition, shares issued or issuable under our equity incentive plans have been registered on Form S-8 registration statements and may be freely sold in the public market upon issuance, except for shares held by affiliates who have certain restrictions on their ability to sell.

Conversion of our outstanding convertible promissory notes or the exercise of outstanding warrants to purchase our common stock will dilute the ownership interest of existing stockholders or may otherwise depress the market price of our common stock.

The conversion of some or all of our outstanding convertible promissory notes or the exercise of some or all of outstanding warrants to purchase our common stock will dilute the ownership interests of existing stockholders. In particular, the exercise of certain warrants which have a $0.01 per share exercise price may significantly dilute the economic ownership interest of our existing stockholders. In addition, any sales in the public market of the shares of our common stock issuable upon such conversion or exercise could adversely affect prevailing market prices of our common stock. Furthermore, the existence of our outstanding convertible promissory notes (including anti-dilution conversion price adjustment provisions contained therein which could lead to additional shares of common stock being issuable upon conversion) and warrants may encourage short selling by market participants because the anticipated conversion of such notes into, or exercise of such warrants for, shares of our common stock could depress the market price of our common stock.

If securities or industry analysts do not publish or cease publishing research or reports about us, our business or our market, or if they change their recommendations regarding our stock adversely, our stock price and trading volume could decline.

The trading market for our common stock will be influenced by the research and reports that industry or securities analysts may publish about us, our business, our market or our competitors. If any of the analysts who cover us change their recommendation regarding our stock adversely, or provide more favorable relative recommendations about our competitors, our stock price would likely decline. If any analyst who may cover us were to cease coverage of our company or fail to regularly publish reports on us, we could lose visibility in the financial markets, which in turn could cause our stock price or trading volume to decline.

We do not expect to declare any dividends in the foreseeable future.

We do not anticipate declaring any cash dividends to holders of our common stock in the foreseeable future. In addition, certain of our equipment leases and credit facilities currently restrict our ability to pay dividends. Consequently, investors may need to rely on sales of their common stock after price appreciation, which may never occur, as the only way to realize any future gains on their investment. Investors seeking cash dividends should not purchase our common stock.

Anti-takeover provisions contained in our certificate of incorporation and bylaws, as well as provisions of Delaware law, could impair a takeover attempt.

Our certificate of incorporation and bylaws contain provisions that could delay or prevent a change in control of our company. These provisions could also make it more difficult for stockholders to elect directors and take other corporate actions. These provisions include:

• a staggered board of directors;

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• authorizing the board of directors to issue, without stockholder approval, preferred stock with rights senior to those of our common stock;

• authorizing the board of directors to amend our bylaws, to increase the number of directors and to fill board vacancies until the end of the term of the applicable class of directors;

• prohibiting stockholder action by written consent;

• limiting the liability of, and providing indemnification to, our directors and officers;

• eliminating the ability of our stockholders to call special meetings; and

• requiring advance notification of stockholder nominations and proposals. 

Section 203 of the Delaware General Corporation Law prohibits, subject to some exceptions, “business combinations” between a Delaware corporation and an “interested stockholder,” which is generally defined as a stockholder who becomes a beneficial owner of 15% or more of a Delaware corporation's voting stock, for a three-year period following the date that the stockholder became an interested stockholder. We have agreed to opt out of Section 203 through our certificate of incorporation, but our certificate of incorporation contains substantially similar protections to our company and stockholders as those afforded under Section 203, except that we have agreed with Total that it and its affiliates will not be deemed to be “interested stockholders” under such protections.

In addition, we have an agreement with Total which provides that, so long as Total holds at least 10% of our voting securities, we must inform Total of any offer to acquire us or any decision of our Board of Directors to sell our company, and we must provide Total with information about the contemplated transaction. In such events, Total will have an exclusive negotiating period of fifteen business days in the event the Board of Directors authorizes us to solicit offers to buy Amyris, or five business days in the event that we receive an unsolicited offer to purchase us. This exclusive negotiation period will be followed by an additional restricted negotiation period of ten business days, during which we are obligated to continue to negotiate with Total and will be prohibited from entering into an agreement with any other potential acquirer.

These and other provisions in our certificate of incorporation and our bylaws that became effective upon the completion of our initial public offering under Delaware law and in our agreements with Total could discourage potential takeover attempts, reduce the price that investors might be willing to pay in the future for shares of our common stock and result in the market price of our common stock being lower than it would be without these provisions.

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

On December 28, 2016, we entered into an Exchange Agreement (or the Fidelity Exchange Agreement) with the holders of our outstanding 3% Senior Unsecured Convertible Promissory Notes due 2017 (or the Fidelity Notes). Pursuant to the Fidelity Exchange Agreement, the holders agreed to exchange (or the Fidelity Exchange) all outstanding Fidelity Notes, together with accrued and unpaid interest thereon, for approximately $19.1 million in aggregate principal amount of our 9.50% Convertible Senior Notes due 2019 (or the Additional 2015 144A Notes), representing an exchange ratio of approximately 1:1.25 (i.e., each $1.00 of Fidelity Notes would be exchanged for approximately $1.25 of Additional 2015 144A Notes). The closing of the Fidelity Exchange occurred on January 11, 2017. At the closing, we issued approximately $19.1 million in aggregate principal amount of Additional 2015 144A Notes to the holders in exchange for the cancellation of the outstanding Fidelity Notes. We did not receive any cash proceeds from the Fidelity Exchange.

An exchange agent was used in connection with the exchange of the Fidelity Notes and the issuance of the Additional 2015 144A Notes. The Additional 2015 144A Notes were issued in a private placement pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act of 1933, as amended (or the “Securities Act”) and Regulation D promulgated under the Securities Act. The holders participating in the Fidelity Exchange acquired the Additional 2015 144A Notes for investment purposes only and without intent to resell, were able to fend for themselves in these transactions, and are accredited investors as defined in Rule 501 of Regulation D promulgated under Section 3(b) of the Securities Act. These holders had adequate access, through their relationships with us, to information about us. The shares of our common stock issuable upon conversion of the Additional 2015 144A Notes have not been registered under the Securities Act and may not be offered or sold in the United States absent registration or an applicable exemption from registration requirements.

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ITEM 3. DEFAULTS UPON SENIOR SECURITIES

Not applicable.

ITEM 4. MINE SAFETY DISCLOSURES

Not applicable.

ITEM 5. OTHER INFORMATION

Not applicable.

ITEM 6. EXHIBITS

The exhibits listed in the Exhibit Index included herein at page 123 (other than exhibits 32.01, 32.02 and 101) are filed as part of this Quarterly Report on Form 10-Q and such Exhibit Index is incorporated herein by reference.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

Dated: May 15, 2017	AMYRIS, INC.
	/s/  JOHN G. MELO
	John G. Melo
	Director, President and Chief Executive Officer
	(Principal Executive Officer)

Dated: May 15, 2017
	/s/  KATHLEEN VALIASEK
	Kathleen Valiasek
	Chief Financial Officer
	(Principal Financial Officer)

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EXHIBIT INDEX

Exhibit		Previously Filed				Filed
No.	Description	Form	File No.	Filing Date	Exhibit	Herewith
3.01	Restated Certificate of Incorporation	10-Q	001-34885	November 10, 2010	3.01
3.02	Certificate of Amendment, dated May 9, 2013, to Restated Certificate of Incorporation	S-8	333-188711	May 20, 2013	4.02
3.03	Certificate of Amendment, dated May 12, 2014, to Restated Certificate of Incorporation	10-Q	001-34887	August 8, 2014	3.02
3.04	Certificate of Amendment, dated September 18, 2015, to Restated Certificate of Incorporation	S-3/A	333-206331	November 4, 2015	3.03
3.05	Certificate of Amendment, dated May 18, 2016, to Restated Certificate of Incorporation	10-Q	001-34885	August 9, 2016	3.05
3.06	Restated Bylaws	10-Q	001-34885	November 10, 2010	3.02
4.01	Specimen of Common Stock Certificate	S-1	333-166135	July 6, 2010	4.01
4.02	Amended and Restated Investors’ Rights Agreement, dated June 21, 2010, among registrant and its security holders listed therein	S-1	333-166135	June 23, 2010	4.02
4.03	First Amendment to Amended and Restated Investors' Rights Agreement, dated February 23, 2012, among registrant and registrant's security holders listed therein	S-3	333-180005	March 9, 2012	4.06
4.04	Amendment No. 2 to Amended and Restated Investors' Rights Agreement, dated December 24, 2012, among registrant and registrant's security holders listed therein	10-K	001-34885	March 28, 2013	4.04
4.05	Amendment No. 3 to Amended and Restated Investors' Rights Agreement, dated March 27, 2013, among registrant and registrant's security holders listed therein	10-Q	001-34885	May 9, 2013	4.02
4.06	Amendment No. 4 to Amended and Restated Investors' Rights Agreement, dated October 16, 2013, among registrant and registrant's security holders listed therein	10-K	001-34885	April 2, 2014	4.06
4.07	Amendment No. 5 to Amended and Restated Investors' Rights Agreement, dated December 24, 2013, among registrant and registrant's security holders listed therein	10-K	001-34885	April 2, 2014	4.07
4.08	Amendment No. 6 to Amended and Restated Investors’ Rights Agreement dated July 29, 2015 among registrant and registrant’s security holders listed therein	S-3	333-206331	August 12, 2015	4.17
4.09 a	Amended and Restated Letter Agreement re: Certain Registration Rights dated May 8, 2014 between registrant and the purchasers listed therein	10-Q	001-34885	August 8, 2014	4.01
4.10	Warrant to Purchase Stock, dated December 23, 2011, issued to ATEL Ventures, Inc.	10-K	001-34885	February 28, 2012	4.07
4.11	Side Letter, dated June 21, 2010, between registrant and Total Gas & Power USA, SAS	S-1	333-166135	June 23, 2010	4.19
4.12	Agreement, dated February 23, 2012, among registrant, Maxwell (Mauritius) Pte Ltd, Naxyris SA, Biolding Investment SA and Sualk Capital Ltd.	10-Q	001-34885	May 9, 2012	4.02
4.13	Securities Purchase Agreement, dated February 24, 2012, among registrant and certain investment funds affiliated with Fidelity Investments Institutional Services Company, Inc. listed therein (each, a Fidelity Purchaser)	S-3	333-180005	March 9, 2012	4.02
4.14	Form of Unsecured Senior Convertible Promissory Note issued by registrant to the Fidelity Purchasers in the amounts set forth next to each Fidelity Purchaser's name on Schedule I of Exhibit 4.13 hereof	S-3	333-180005	March 9, 2012	4.03
4.15	Registration Rights Agreement, dated February 27, 2012, among registrant and the Fidelity Purchasers	S-3	333-180005	March 9, 2012	4.04
4.16	Exchange Agreement, dated December 28, 2016, among registrant and certain Fidelity Purchasers	10-K	001-34885	April 17, 2017	4.16

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4.17 c	Form of Common Stock Purchase Agreement among registrant and certain investors	10-Q	001-34885	August 8, 2012	4.01
4.18	Securities Purchase Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.01
4.19	Registration Rights Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS	10-Q	001-34885	November 9, 2012	4.03
4.20	1.5% Senior Secured Convertible Note dated July 29, 2015 (RS-9) issued by registrant to Total Energies Nouvelles Activités USA (RS-9)	10-Q	001-34885	November 9, 2015	4.21
4.21	1.5% Senior Convertible Note, dated March 21, 2016 (RS-10) issued by registrant to Total Energies Nouvelles Activités USA	10-Q	001-34885	May 10, 2016	4.19
4.22	First Amendment, dated February 27, 2017, to 1.5% Senior Convertible Note, dated March 21, 2016 (RS-10) issued by registrant to Total Energies Nouvelles Activités USA	10-Q				X
4.22 a	Securities Purchase Agreement, dated December 24, 2012, between registrant and certain investors listed therein	10-K	001-34885	March 28, 2013	4.16
4.23 a	Follow-On Investment Agreement, dated December 24, 2012, between registrant and Biolding Investment SA	10-K	001-34885	March 28, 2013	4.17
4.24	Securities Purchase Agreement, dated March 27, 2013, between registrant and Biolding Investment SA	10-Q	001-34885	May 9, 2013	4.01
4.25	Securities Purchase Agreement (including Form of Tranche I Senior Convertible Note and Form of Tranche II Senior Convertible Note) , dated August 8, 2013, between registrant, Maxwell (Mauritius) Pte Ltd and Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS)	10-Q	001-34885	November 5, 2013	4.01
4.26 a	Amendment No. 1 dated October 16, 2013, to the Securities Purchase Agreement, dated August 8, 2013, between registrant and other parties named therein	10-K	001-34885	April 2, 2014	4.24
4.27	Tranche I Note Amendment and Amendment No. 2 dated December 24, 2013, to the Securities Purchase Agreement, dated August 8, 2013, between registrant and other parties named therein	10-K	001-34885	April 2, 2014	4.25
4.28 ad	5% Unsecured Convertible Note dated October 16, 2013 issued to Total Energies Nouvelles Activités USA	10-Q	001-34885	May 9, 2014	4.04
4.29 ae	10% Unsecured Convertible Note dated January 15, 2014 issued to Total Energies Nouvelles Activités USA	10-Q	001-34885	May 9, 2014	4.06
4.30	Securities Purchase Agreement, dated September 20, 2013, between registrant and Naxyris S.A.	10-Q	001-34885	November 5, 2013	4.03
4.31	Securities Purchase Agreement, dated March 28, 2014 between registrant and Kuraray Co. Ltd.	10-Q	001-34885	May 9, 2014	4.01
4.32	Loan and Security Agreement, dated March 29, 2014 between registrant and Hercules Technology Growth Capital, Inc.	10-Q	001-34885	May 9, 2014	4.02
4.33	First Amendment, dated June 12, 2014, to Loan and Security Agreement dated March 29, 2014 between registrant and Hercules Technology Growth Capital, Inc.	10-Q	001-34885	August 8, 2014	4.06
4.34	Second Amendment, dated March 31, 2015, to Loan and Security Agreement dated March 29, 2014 between registrant and Hercules Technology Growth Capital, Inc.	10-Q	001-34885	May 7, 2015	10.05
4.35	Third Amendment, dated November 30, 2015, to Loan and Security Agreement dated March 29, 2014 between registrant and Hercules Technology Growth Capital, Inc.	10-K	001-34885	March 30, 2016	4.37

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4.36	Fourth Amendment, dated October 6, 2016, to Loan and Security Agreement dated March 29, 2014 between registrant and Stegodon Corporation, as assignee of Hercules Capital, Inc.	10-K	001-34885	April 17, 2017	4.36
4.37	Fifth Amendment, dated January 10, 2017, to Loan and Security Agreement, dated March 29, 2014, between registrant and Stegodon Corporation, as assignee of Hercules Capital, Inc.					X
4.38	Indenture, dated May 29, 2014, between registrant and Wells Fargo Bank, National Association, as Trustee	8-K	001-34885	May 29, 2014	4.01
4.39	6.5% Convertible Senior Note due 2019, dated May 29, 2014, issued by registrant to Morgan Stanley & Co. LLC	10-Q	001-34885	August 8, 2014	4.02
4.40 f	6.5% Convertible Senior Note due 2019, dated May 29, 2014, issued by registrant to Maxwell (Mauritius) Pte Ltd.	10-Q	001-34885	August 8, 2014	4.03
4.41	Registration Rights Agreement, dated February 24, 2015, between the registrant and Nomis Bay Ltd	8-K	001-34885	February 26, 2015	4.01
4.42 g	Voting Agreement, dated July 24, 2015, between registrant and Foris Ventures, LLC	10-Q	001-34885	November 9, 2015	4.43
4.43	Securities Purchase Agreement, dated July 24, 2015, between registrant and the Purchasers listed therein	10-Q	001-34885	November 9, 2015	4.44
4.44 h	Warrant to Purchase Stock issued on July 24, 2015	S-3	333-206331	August 12, 2015	4.21
4.45	Exchange Agreement, dated July 29, 2015, between registrant and the Investors therein	10-Q	001-34885	November 9, 2015	4.46
4.46	Maturity Treatment Agreement dated July 29, 2015, between registrant and the Investors listed therein	10-Q	001-34885	November 9, 2015	4.47
4.47	Letter Agreement dated as of July 29, 2015 among registrant and registrant’s security holders listed therein	S-3	333-206331	August 12, 2015	4.20
4.48	Warrant to Purchase Stock issued July 29, 2015 by the registrant to Total Energies Nouvelles Activités USA	S-3	333-206331	August 12, 2015	4.22
4.49	Warrant to Purchase Stock issued July 29, 2015 by the registrant to Total Energies Nouvelles Activités USA	S-3	333-206331	August 12, 2015	4.23
4.50	Warrant to Purchase Stock issued July 29, 2015 by the registrant to Maxwell (Mauritius) PTE Ltd	S-3	333-206331	August 12, 2015	4.24
4.51	Warrant to Purchase Stock issued July 29, 2015 by the registrant to Maxwell (Mauritius) PTE Ltd	S-3	333-206331	August 12, 2015	4.25
4.52	Warrant to Purchase Stock issued July 29, 2015 by the registrant to Maxwell (Mauritius) PTE Ltd	S-3	333-206331	August 12, 2015	4.26
4.53	Indenture dated October 20, 2015 between registrant and Wells Fargo Bank, National Association, as Trustee	8-K	001-34885	October 20, 2015	4.01
4.54	9.50% Convertible Senior Note due 2019 dated October 20, 2015 issued by registrant to Cede & Co.	10-K	001-34885	March 30, 2016	4.56
4.55	First Supplemental Indenture, dated January 11, 2017, between registrant and Wells Fargo Bank, National Association, as Trustee					X
4.56	9.50% Convertible Senior Note due 2019, dated January 11, 2017, issued by registrant to Cede & Co.					X
4.55	Registration Rights Agreement dated October 20, 2015 between the registrant and the registrant’s security holders listed therein	8-K	001-34885	October 20, 2015	4.02
4.56	Note and Warrant Purchase Agreement, dated February 12, 2016, between registrant and the purchasers listed therein	10-Q	001-34885	May 10, 2016	4.50
4.57 i	Unsecured Promissory Note, dated February 12, 2016, between registrant and Foris Ventures, LLC	10-Q	001-34885	May 10, 2016	4.51
4.58 j	Warrant to Purchase Stock, dated February 12, 2016, between registrant and Foris Ventures, LLC	10-Q	001-34885	May 10, 2016	4.52j

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4.59	Form of Convertible Note	8-K	001-34885	May 10, 2016	4.1
4.60	Note Purchase Agreement, dated June 24, 2016, between registrant and Foris Ventures, LLC	10-Q	001-34885	August 9, 2016	4.50
4.61	Secured Promissory Note, dated June 24, 2016  issued by registrant to Foris Ventures, LLC	10-Q	001-34885	August 9, 2016	4.51
4.62	Form of Additional Note	8-K	001-34885	September 9, 2016	4.1
4.63	Warrant to Purchase Common Stock, dated August 6, 2016, between registrant and Ginkgo Bioworks, Inc.	10-Q	001-34885	November 9, 2016	4.58
4.64	Note Purchase Agreement, dated October 21, 2016, between registant and Foris Ventures, LLC	10-K	001-34885	April 17, 2017	4.63
4.65	Secured Promissory Note, dated October 21, 2016, issued by registrant to Foris Ventures, LLC	10-K	001-34885	April 17, 2017	4.64
4.66 a	Credit Agreement, dated October 26, 2016, between registrant and Guanfu Holding Co., Ltd.	10-K	001-34885	April 17, 2017	4.65
4.67	Note, dated December 31, 2016, issued by registrant to Wutian Supply Chain Corporation Limited	10-K	001-34885	April 17, 2017	4.66
4.68	Note Purchase Agreement, dated October 27, 2016, between registrant and Ginkgo Bioworks, Inc.	10-K	001-34885	April 17, 2017	4.67
4.69	Secured Promissory Note , dated October 27, 2016, issued by registrant to Ginkgo Bioworks, Inc.	10-K	001-34885	April 17, 2017	4.68
4.70	Warrant to Purchase Stock, issued November 16, 2016, by the registrant to Nenter & Co., Inc.	S-3	333-215318	December 23, 2016	4.15
4.71	Form of Convertible Note	8-K	001-34885	December 2, 2016	4.1
4.72	Purchase Money Promissory Note, issued December 5, 2016, by registrant to Salisbury Partners, LLC	10-K	001-34885	April 17, 2017	4.71
4.73	Purchase Money Promissory Note, issued December 19, 2016, by registrant to Nikko Chemicals Co. Ltd.	10-K	001-34885	April 17, 2017	4.72
10.01 k	Credit Facility Agreement, dated October 11, 2010, between Financiadora de Estudos E Projetos - FINEP and Anyris Brasil S.A.					X
10.02	Modification No. 3, dated June 20, 2016, to the Technology Investment Agreement, dated September 22, 2015, between registrant and The Defense Advanced Research Projects Agency (DARPA)					X
10.03	First Amendment, dated February 14, 2017, to the Amended and Restated Jet Fuel License Agreement, dated March 21, 2016, between registrant and Total Amyris BioSolutions B.V.					X
10.04	First Amendment, dated February 14, 2017, to the License Agreement regarding Diesel Fuel in the EU, dated March 21, 2016, between registrant and Total Energies Nouvelles Activités USA					X
10.05	Amendment Number One, dated February 16, 2017, to the Amyris, Inc. 2010 Employee Stock Purchase Plan					X
10.06	Amendment #2, dated February 28, 2017, to the Second Amendment to the Technology, License, Development, Research and Collaboration Agreement between registrant and Total Energies Nouvelles Activités USA SAS					X
10.07	Side Letter, dated February 28, 2017, amending the Technology License, Development, Research and Collaboration Agreement, dated July 30, 2012, between registrant and Total Gas & Power USA, SAS					X
10.08	Amendment, dated March 6, 2017, to Offer Letter, dated November 23, 2016, between registrant and Kathleen Valiasek					X
31.01	Certification of Chief Executive Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002					X

126

31.02	Certification of Chief Financial Officer pursuant to Securities Exchange Act Rules 13a-14(c) and 15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002	X
32.01 m	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
32.02 m	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X
101 n	The following materials from registrant's Quarterly Report on Form 10-Q for the quarter ended March 31, 2017, formatted in XBRL (Extensible Business Reporting Language): (i) the Consolidated Statements of Operations; (ii) the Consolidated Balance Sheets; (iii) the Consolidated Statements of Comprehensive Income; (iv) the Consolidated Statements of Convertible Preferred Stock, Redeemable Noncontrolling Interest and Equity (Deficit); (v) the Consolidated Statements of Cash Flows; and (vi) Notes to Consolidated Financial Statements	X

127

a	Portions of this exhibit, which have been granted confidential treatment by the Securities and Exchange Commission, have been omitted.
b	Portions of this exhibit have been omitted pending a determination by the Securities and Exchange Commission as to whether these portions should be granted confidential treatment.
c	Substantially identical Common Stock Purchase Agreements, each dated May 18, 2012, were entered into with five separate investors.  Registrant has filed the form of such Common Stock Purchase Agreements, which is substantially identical in all material respects to all of such Common Stock Purchase Agreements, except as to the parties thereto and the number of shares being purchased.
d	Registrant issued substantially identical 5% Unsecured Convertible Notes (the "5% Notes") to Total Gas & Power USA, SAS (“Total’), FIAM Target Date Large Cap Stock Commingled Pool (formerly known as Fidelity Pyramis Lifecycle Large Cap Stock Commingled Pool. Fidelity Variable Insurance Products Fund Ill: Growth & Income Portfolio, Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund. Fidelity Securities Fund: Fidelity Growth & Income Portfolio Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund. Fidelity Commonwealth Trust: Fidelity Large Cap Stock Fund, and Maxwell (Mauritius) Pte Ltd on October 16. 2013. Registrant has filed the 5% Note issued to Total. and has included with Exhibit 4.04 a schedule (Schedule A to Exhibit 4.04 of registrant’s Form 10-Q filed on May 9, 2014) identifying each of the 5% Notes and setting forth the material detail in which the other 5% Note(s) differ from the filed 5% Note (i.e. the Purchasers. the amounts of the 5% Notes. and the conversion price).
e	Registrant issued substantially identical 10% Unsecured Convertible Notes (the" 10% Notes") to Total Wolverine Flagship Fund Trading Limited and Maxwell (Mauritius) Pte Ltd on January 15 2014. Registrant has filed the 10% Note issued to Total and has included with Exhibit 4.06. a schedule (Schedule A to Exhibit 4.06 of registrant’s Form 10-Q filed on May 9, 2014) identifying each of the 10% Notes and setting forth the material details in which the other 10% Note(s) differ from the filed 10% Note (i.e. the purchasers and the amounts of the 10% Notes).
f	Registrant issued substantially identical 6.5% Senior Convertible Notes due 2019 (the “6.5% Notes”) to Maxwell (Mauritius) Pte Ltd. (“Temasek”), Total Energies Nouvelles Activités USA, and Foris Ventures, LLC on May 29, 2014. Registrant has filed the 6.5% Note issued to Temasek, and has included, with such exhibit, a schedule (Schedule A to Exhibit 4.03 of registrant's Form 10-Q filed August 8, 2014) identifying each of the 6.5% Notes and setting forth the material details in which the other 6.5% Notes differ from the filed 6.5% Note (i.e., the note number, the purchasers, and the amounts of the 6.5% Notes).
g	Substantially identical Voting Agreements, each dated July 31, 2015, were entered into with five separate investors.  Registrant has filed Voting Agreement entered into by registrant and Foris Ventures LLC, which is substantially identical in all material respects to all of such Voting Agreements, except as to the parties thereto.
h	Registrant issued substantially identical warrants to the purchasers under that certain Securities Purchase Agreement entered into on July 24. 2015~ Registrant has filed the warrant issued to Total Energies Nouvelles Activites USA and has included with such Exhibit a schedule (Schedule A to Exhibit 4.03 of registrants Form 10-Q filed on August 8, 2015) identifying each of the warrants and setting forth the material details in which the other warrants differ from the filed form of warrant (i.e. the names of the purchasers. the certificate numbers and the respective amounts of shares underlying the warrants).
i	Substantially identical Unsecured Promissory Notes, each dated February 15, 2016 (the “Notes”), were entered into with three separate investors.  Registrant has filed the Note entered into by registrant and Foris Ventures LLC, which is substantially identical in all material respects to all of such Notes except as to the parties thereto and the value of the Notes.
j	Substantially identical Warrants to Purchase Stock, each dated February 15, 2016 (the “Warrants”), were entered into with three separate investors.  Registrant has filed the Warrant entered into by registrant and Foris Ventures LLC, which is substantially identical in all material respects to all of such Warrants, except as to the parties thereto and the amount of underlying shares.
k	Translation to English from Portuguese or Dutch, as applicable, in accordance with Rule 12b-12(d) of the regulations promulgated by the Securities and Exchange Commission under the Securities Exchange Act of 1934, as amended (or the Exchange Act).
m	This certification shall not be deemed “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.
n	Pursuant to applicable securities laws and regulations, registrant is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions of the federal securities laws as long as registrant has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fails to comply with the submission requirements. These interactive data files are deemed not filed or part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act, are deemed not filed for purposes of section 18 of the Exchange Act and otherwise are not subject to liability under these sections.

128

EX-4.22

Exhibit 4.22

FIRST AMENDMENT TO 1.5% SENIOR CONVERTIBLE NOTE (RS-10)

This First Amendment to 1.5% Senior Convertible Note (RS-I 0) (this "Amendment") is made and entered into as of February 27, 2017, by and between Amyris, Inc., a Delaware corporation (the "Company") and Total Energies Nouvelles Activites USA (f.k.a. Total Gas & Power USA, SAS) (the "Investor").

RECITALS

WHEREAS, on March 21, 2016 the Company issued to the Investor a 1.5% Senior Convertible Note (RS-10) in the principal amount of $3,700,000 (the "Note"), which Note is attached hereto as Exhibit A.

WHEREAS, the Company and the Investor desire to amend the Note as set forth herein.

WHEREAS, pursuant to Section 7 of the Note, the Note may be amended with the written consent of the Company and the Investor.

NOW, THEREFORE, for good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties hereby agree as follows:

1.         Amendment of Section 2(b) of the Note. Section 2(b) of the Note is hereby deleted in its entirety and replaced with the following:

(b)       Scheduled Payment of Principal. Unless paid, converted or cancelled and extinguished earlier in accordance with the terms hereof, the Company shall deliver to the Investor cash in the amount of the Face Amount, together with all accrued and unpaid interest on this Note, on May 15, 2017 (the "Final Maturity Date") and this Note shall be retired and canceled.

2.       Amendment of Section 14 of the Note. Investor hereby designates the following address for purposes of receiving notice under the Note.:

c/o Total Raffinage Chimie

2, place Jean Millier - La Defense 6

92078 Paris La Defense Cedex

France

Attn:

Fax. No.:

Email:

With a copy to (which shall not constitute notice):

Legal Department

Total Energies Nouvelles Activites USA

24 Cours Michelet

92800 Courbevoie

France

Attn: Department Head

3.        Full Force and Effect. Except as expressly modified by this Amendment, the terms of the Note shall remain in full force and effect.

4.        Integration. This Amendment and the Note constitute the entire agreement and understanding of the parties with respect to the subject matter hereof, and supersede all prior understandings and agreements, whether oral or written, between or among the parties hereto with respect to the specific subject matter hereof.

5.        Counterparts; Facsimile. This Amendment may be executed in one (1) or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. This Amendment may be executed and delivered by facsimile, or by email in portable document format (.pdf), and delivery of any signature page by such method will be deemed to have the same effect as if the original signature had been delivered to the other party.

[Remainder of Page intentionally left blank)

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

AMYRIS, INC.
By:	/s/ John Melo
Name:	John Melo
Title:	President & Chief Executive Officer

[Signature Page to First Amendment to R&D Note]

IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the date first above written.

TOTAL ENERGIES NOUVELLES ACTIVITES USA
(F.K.A. TOTAL GAS & POWER USA, SAS)
By:	/s/ Christophe Vuillez
Name:	Christophe Vuillez
Title:	Attorney in fact

[Signature Page to First Amendment to R&D Note]

Exhibit A

See attached.

EX-4.37

Exhibit 4.37

January 10, 2017

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, CA 94608

Attention: John Melo, President and Chief Executive Officer

RE: Amendment to Loan and Security Agreement

Dear Mr. Melo:

Reference is made to that certain Loan and Security Agreement dated as of March 29, 2014, as amended on June 12, 2014, March 31, 2015, November 30, 2015 and October 6, 2016 (as amended, the “LSA”), by and between Amyris, Inc., a Delaware corporation (the “Parent”), and each of its Subsidiaries that has delivered a Joinder Agreement (collectively, “Borrower”), the other financial institutions or entities from time to time parties to the LSA (collectively, referred to as “Lender”) and Stegodon Corporation, a Delaware corporation, as assignee of Hercules Capital, Inc., a Maryland corporation, in its capacity as administrative agent for itself and Lender (in such capacity, the “Agent”). Capitalized terms used but not otherwise defined herein have the meaning set forth in the LSA.

In connection with certain waivers of the debt and transfer covenants under the LSA granted by Lender, Borrower, the Agent and Lender have agreed to amend Section 2.2(d) (“Term Loan – Payment”) of the LSA, as well as make certain updates to the LSA, all as set forth herein.

For good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, based upon the mutual covenants contained herein, Borrower, the Agent and Lender, in accordance with Section 11.3(b) of the LSA, hereby amend the LSA (this “Amendment”) as follows:

I.        The definition of “Fidelity Unsecured Convertible Debt” is hereby deleted in its entirety and the following is substituted therefor:

“Fidelity Unsecured Convertible Debt” means the Indebtedness evidenced by those 9.50% Convertible Senior Notes issued on or about January 11, 2017 with a maturity date of April 15, 2019 in the original principal amount of $19,136,000.

II.        New definitions of “Earned Incentive Payments” and “Incentive Payments” are hereby inserted into Section 1 of the LSA in appropriate alphabetical order:

“Earned Incentive Payments” has the meaning ascribed to such term in the Ginkgo Collaboration Agreement.

“Incentive Payments” has the meaning ascribed to such term in the Ginkgo Collaboration Agreement.

III.        Section 2.2(d) (“Term Loan – Payment”) of the LSA is hereby deleted in its entirety and the following is substituted therefor:

“Payment. Borrower will pay interest on each Term Loan Advance on the first Business Day of each month, beginning the month after the (i) Closing Date with respect to the Closing Date Term Loan Advance, (ii) First Amendment Effective Date with respect to the Additional Term Loan Advance and (iii) the Third Amendment Effective Date for the Third Amendment Term Loan Advance. At its sole discretion, Lender will either (i) initiate debit entries to the Borrower’s account as authorized on the ACH Authorization on each payment date of all periodic interest obligations payable to Lender under each Term Loan Advance and any costs and expenses reimbursable to Lender, (ii) submit a written invoice to Borrower for all amounts due by Borrower on each payment date of all periodic interest obligations payable to Lender under each Term Loan Advance and any costs and expenses reimbursable to Lender, which invoice must be paid by Borrower within five days of receipt or (iii) submit other written instructions to Borrower regarding the proper method for payment of such periodic interest obligations and costs and expenses. In addition, Borrower shall pay to the Agent, for the benefit of Lender, (i) promptly following Parent’s receipt thereof, all Net Profits earned by and actually received by Parent under the Ginkgo Collaboration Agreement, up to a maximum of $1,000,000 in any calendar month and (ii) promptly following Parent’s receipt thereof, all Earned Incentive Payments and/or Incentive Payments earned by and actually received by Parent that are owed by Ginkgo Bioworks, Inc. under the Ginkgo Collaboration Agreement, up to a maximum of $3,000,000 in the aggregate, and in each case any such payments shall be applied to the principal balance outstanding under the LSA on the first Business Day of the month following payment (except for any such payments that are received on the first Business Day of the month, which shall be applied to the principal balance outstanding under the LSA on such date). For the sake of clarification, any such payments of Net Profits, Earned Incentive Payments or Incentive Payments made to the Agent, for the benefit of Lender, in accordance with this paragraph shall not be subject to any Prepayment Charge under Section 2.5 hereof. The entire Term Loan Advance principal balance outstanding and all accrued but unpaid interest hereunder shall be due and payable on the Term Loan Maturity Date. Borrower shall make all payments due under this Agreement without setoff, recoupment or deduction and regardless of any counterclaim or defense.”

IV. The last paragraph of Section 7.1 (“Covenants of Borrower - Financial Reports”) of the LSA is hereby deleted in its entirety and the following is substituted therefor:

“The executed Compliance Certificate may be sent via e-mail to provided, that if e-mail is not available or sending the Compliance Certificate via email is not possible, it shall be sent via facsimile to Agent at: , attention . All Financial Statements required to be delivered pursuant to clauses (a), (b) and (c) shall be sent via e-mail to provided, that if e-mail is not available or sending such Financial Statements via e-mail is not possible, they shall be sent via facsimile to Agent at: , attention .”

V. Sections 11.2(a), 11.2(b) and 11.2(c) (“Miscellaneous - Notice”) of the LSA are hereby deleted in their entirety and the following is substituted therefor:

“(a) If to Agent:

STEGODON CORPORATION

Attention:

12 Saint Paul Street, #1

Cambridge, MA 02139

Email:

Facsimile:

(b)        If to Lender:

STEGODON CORPORATION

Attention:

12 Saint Paul Street, #1

Cambridge, MA 02139

Email:

Facsimile:

2

(c) If to Borrower:

AMYRIS, INC.

Attention: General Counsel

5885 Hollis Street, Suite 100

Emeryville, CA 94608

Facsimile: ”

Within five (5) days following receipt of an invoice, Borrower shall pay the Agent’s reasonable out-of-pocket costs, including reasonable attorneys’ fees, incurred in connection with the LSA.

Except to the extent of this Amendment, the LSA shall remain unaltered and in full force and effect. This Amendment shall not be a waiver of any existing default or breach of a covenant unless specified herein.

This Amendment shall be limited precisely as written and shall not be deemed (a) to be a waiver or modification of any other term or condition of the LSA or of any other instrument or agreement referred to therein or to prejudice any right or remedy which Lender may now have or may have in the future under or in connection with the LSA or any instrument or agreement referred to therein; or (b) to be a consent to any future amendment or modification of any instrument or agreement the execution and delivery of which is consented to hereby, or to any waiver of any of the provisions thereof.

The Borrower acknowledges and agrees that it remains obligated to pay all principal, interest, reimbursement obligations, fees, and other amounts owing to the Agent and Lender under and in respect of the Loan Documents when due and payable in accordance with the terms thereof.

The Borrower hereby acknowledges and agrees that as of the date hereof, the Borrower has outstanding Secured Obligations to the Agent and the Lender which include indebtedness to the Agent and Lender in an aggregate outstanding principal amount equal to $28,565,748.86 plus accrued interest and fees. The Borrower hereby acknowledges and agrees that, to the best of its knowledge as of the date hereof, the liens and security interests granted in favor of the Agent and/or the Lender under the terms of the Loan Documents are perfected, effective, enforceable, and valid and such liens and security interests are, in each case, a first priority lien and security interest subject to Permitted Liens. Notwithstanding the foregoing, each of the Agent and the Lender acknowledges and agrees that Borrower is not responsible for perfecting or ensuring such liens are effective and enforceable.

The Borrower hereby acknowledges and agrees that as of the date hereof: (a) it does not have any claim or cause of action related to the LSA, the Loan Documents or any other agreement between or among Borrower, the Agent and/or the Lender against the Agent or the Lender (or any of their respective directors, officers, employees, agents, subsidiaries, affiliates, attorneys, attorneys’ consultants, predecessors, successors or assigns); (b) it does not have any offset right, counterclaim, or defense of any kind against the Secured Obligations or any portion thereof; and (c) each of the Agent and the Lender has heretofore properly performed and satisfied in a timely manner all of its obligations and commitments to the Borrower. For and in consideration of the agreements contained in this Amendment and other good and valuable consideration, the Borrower unconditionally and irrevocably releases, waives, and forever discharges each of the Agent and the Lender, together with their respective predecessors, successors, assigns, subsidiaries, affiliates, agents, employees, directors, officers, attorneys and attorneys’ consultants (collectively, the “Released Parties”), from the following, in each case only as related to the LSA, the Loan Documents and any other agreement between or among Borrower, the Agent and/or the Lender: (x) any and all liabilities, obligations, duties, promises, or indebtedness of any kind (if any) of the Released Parties to the Borrower or any of its affiliates, which existed, arose, or occurred at any time from the beginning of the world to the date of this Amendment, and (y) all claims, offsets, causes of action, suits, or defenses of any kind whatsoever (if any), which the Borrower or any of its affiliates might otherwise have against the Released Parties, or any of them, in either case (x) or (y) on account of any condition, act, omission, event, contract, liability, obligation, indebtedness, claim, cause of action, defense, circumstance, or matter of any kind, which existed, arose, or occurred at any time from the beginning of the world to the date of this Amendment. Notwithstanding anything to the contrary herein, the Borrower does not hereby release, waive, or forever discharge the Released Parties from any claims, offsets, causes of action, suits or defenses of any kind relating to any conduct or action by the Agent or Lender that is illegal under federal, state or local law.

2

Without limitation, each party hereto acknowledges that it has been advised by its attorneys concerning, and is familiar with, the California Civil Code Section 1542. Section 1542 of the California Civil Code provides as follows:

A general release does not extend to claims which the creditor does not know or suspect to exist in his or her favor at the time of the executing of the release, which if known by him or her must have materially affected his or her settlement with the debtor.

Each party hereto expressly waives any and all rights under California Civil Code Section 1542 and under any other federal or state statute or law of similar effect as to all matters released pursuant to this Amendment.

This Amendment shall become effective upon the receipt of a fully executed Amendment.

This Amendment may be executed in two or more counterparts, each of which shall constitute an original, but all of which, when taken together, shall constitute but one instrument, and shall become effective when one or more counterparts have been signed by each party hereto and delivered to the other party. Facsimile signatures shall be deemed originals for all purposes hereunder. This Amendment shall be governed by, and construed and enforced in accordance with, the laws of the State of California, excluding conflict of laws principles that would cause the application of laws of any other jurisdiction.

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]

4

IN WITNESS WHEREOF, Borrower, the Agent and the Lender have duly executed and delivered this Amendment as of the day and year first above written.

AGENT AND LENDER:
STEGODON CORPORATION, as Agent and as
AGENT AND LENDER
STEGODON CORPORATION, as Agent and as
Lender
Signature:	/s/ Austin Che
Print Name:	Austin Che
Title:	President
BORROWER
AMYRIS, INC.
Signature:
Print Name:
Title:
AMYRIS FUELS, INC.
By Amyris, Inc., its sole manager
Signature:
Print Name:
Title:

[Signature Page to LSA Amendment]

IN WITNESS WHEREOF, Borrower, the Agent and the Lender have duly executed and delivered this Amendment as of the day and year first above written.

AGENT AND LENDER:
STEGODON CORPORATION, as Agent and as
AGENT AND LENDER
STEGODON CORPORATION, as Agent and as
Lender
Signature:
Print Name:
Title:
BORROWER
AMYRIS, INC.
Signature:	/s/ John Melo
Print Name:	John Melo
Title:	President and CEO
AMYRIS FUELS, INC.
By Amyris, Inc., its sole manager
Signature:	/s/ John Melo
Print Name:	John Melo
Title:	President and CEO

[Signature Page to LSA Amendment]

EX-4.55

Exhibit 4.55

FIRST SUPPLEMENTAL INDENTURE

First Supplemental Indenture, dated as of January 11, 2017 (this “First Supplemental Indenture”), between Amyris, Inc., a Delaware corporation (the “Company”) and Wells Fargo Bank, National Association, as trustee (the “Trustee”).

W I T N E S S E T H:

WHEREAS, the Company has heretofore executed and delivered to the Trustee an indenture, dated as of October 20, 2015 (the “Indenture”), that governs the Company’s outstanding 9.50% Convertible Senior Notes due 2019 (the “Notes”);

WHEREAS, Sections 13.01(i) and (vi) of the Indenture provide that the Company and the Trustee may enter into one or more indentures supplemental thereto without the consent of any Holders in order to cure any ambiguity, omission, defect or inconsistency and make any change that does not adversely affect the rights of any Holder, respectively, in each case as determined in good faith by the Company and evidenced in an Officers’ Certificate;

WHEREAS, the execution and delivery of this First Supplemental Indenture has been duly authorized and all conditions and requirements necessary to make this First Supplemental Indenture a valid and binding agreement of Company have been duly performed and complied with;

WHEREAS, pursuant to Section 13.01 of the Indenture, the Company has delivered a resolution of its Boards of Directors (as defined in the Indenture) authorizing the execution of this First Supplemental Indenture, and in accordance with Section 13.03 and Section 14.02 of the Indenture has delivered an Officers’ Certificate and an Opinion of Counsel (each as defined in the Indenture) to the Trustee stating that the execution of this First Supplemental Indenture is authorized or permitted by the Indenture, that this First Supplemental Indenture is the legal, valid and binding obligation of the Company, enforceable against it in accordance with the terms of this First Supplemental Indenture, subject to customary exceptions and that all conditions precedent and covenants, if any, provided for in the Indenture relating to the execution of this First Supplemental Indenture have been complied with;

WHEREAS, the Company, pursuant to the foregoing authority, proposes in and by this First Supplemental Indenture to amend the Indenture, and requests that the Trustee join in the execution of this First Supplemental Indenture; and

WHEREAS, pursuant to Section 13.01 of the Indenture, the Trustee is authorized to execute and deliver this First Supplemental Indenture.

NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the receipt of which is hereby acknowledged, the Company and the Trustee mutually covenant and agree for the benefit of each other and the equal and ratable benefit of the Holders of the Notes as follows:

1. Capitalized Terms. Capitalized terms used herein without definition shall have the meanings assigned to them in the Indenture.

2. Amendment of Section 6.04 of the Indenture. Section 6.04 of the Indenture shall be deleted in its entirety and replaced with the following:

Section 6.04 Limitations on Issuance of Shares Due to Market Regulation. Notwithstanding anything to the contrary in this Indenture or in the Notes, the Company shall not be obligated to issue shares of Common Stock upon conversion of the Notes in connection with an Early Conversion Payment or otherwise, and shall not be entitled to issue shares of Common Stock in connection with payment of interest or in connection with any anti-dilution terms described hereunder, to the extent (and only to the extent) the issuance of all such shares of Common Stock would exceed, (1) in the case of the Initial Notes, 38,415,626 in the aggregate (which number is approximately and no greater than 19.99% of the Company’s outstanding shares of Common Stock on October 14, 2015, without giving effect to the issuance of shares of Common Stock underlying the Initial Notes) and (2) in the case of any Additional Notes, a number in the aggregate equal to (and in no event greater than) 19.99% of the Company’s outstanding shares of Common Stock on the date of the definitive agreement providing for the issuance of such Additional Notes, without giving effect to the issuance of shares of Common Stock underlying such Additional Notes (as applicable, the “Exchange Cap”); provided, however, that the Exchange Cap for the Additional Notes issued on January 11, 2017 shall be reduced by an amount equal to the number of shares of Common Stock issued under or in connection with (A) the Credit Agreement, dated as of October 26, 2016, between the Company and Guanfu Holding Co., Ltd. and (B) the Securities Purchase Agreement, dated as of December 1, 2016, between the Company and Nomis Bay Ltd. The Exchange Cap limitation shall not apply in the event that the Company obtains the approval of its holders of Common Stock for issuances of shares of Common Stock in excess of such amount in accordance with NASDAQ Market Rule 5635. The Company will settle such amount in excess of the Exchange Cap in cash and not in shares of Common Stock by wire transfer of U.S. dollars in immediately available funds to the account designated by the Holder, in an amount equal to the product of (x) the number of shares of Common Stock which would have been issuable upon conversion but cannot be issued as a result of the Exchange Cap and (y) the simple average of the daily VWAP for Common Stock for the ten consecutive VWAP Trading Days ending on and included the VWAP Trading Day immediately prior to the Conversion Date.

4 Ratification of Indenture; Supplemental Indenture Part of Indenture. Except as expressly amended hereby, the Indenture is in all respects ratified and confirmed and all the terms, conditions and provisions thereof shall remain in full force and effect. This First Supplemental Indenture shall form a part of the Indenture for all purposes, and every Holder of Notes heretofore or hereafter authenticated and delivered shall be bound hereby.

5. Severability. In case any provision in this First Supplemental Indenture, the Indenture or in the Notes shall be invalid, illegal or unenforceable, the validity, legality and enforceability of the remaining provisions shall not in any way be affected or impaired thereby.

6. Governing Law. THIS FIRST SUPPLEMENTAL INDENTURE WILL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK, WITHOUT REGARD FOR THE CONFLICTS OF LAWS PRINCIPLES THEROF. Waiver of Jury Trial. EACH OF THE COMPANY, HOLDERS AND TRUSTEE HEREBY IRREVOCABLY WAIVES, TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW, ANY AND ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING ARISING OUT OF OR RELATING TO THIS FIRST SUPPLEMENTAL INDENTURE, THE INDENTURE, THE NOTES OR THE TRANSACTIONS CONTEMPLATED HEREBY OR THEREBY.

7. Counterparts. The parties hereto may sign any number of copies of this First Supplemental Indenture. Each signed copy shall be an original, but all of them together represent the same agreement. The exchange of copies of this First Supplemental Indenture and of signature pages by facsimile or portable document format (“PDF”) transmission shall constitute effective execution and delivery of this First Supplemental Indenture as to the parties hereto and may be used in lieu of the original First Supplemental Indenture for all purposes. Signatures of the parties hereto transmitted by facsimile or PDF shall be deemed to be their original signatures for all purposes.

2

8. Effect of Headings. The Section headings herein are for convenience only and shall not affect the construction hereof.

9. The Trustee. The Trustee shall not be responsible in any manner whatsoever for or in respect of the validity or sufficiency of this First Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by the Company. This First Supplemental Indenture is executed and accepted by the Trustee subject to all the terms and conditions set forth in the Indenture with the same force and effect as if those terms and conditions were repeated at length herein and made applicable to the Trustee with respect hereto. In entering into this First Supplemental Indenture, the Trustee shall be entitled to the benefit of every provision of the Indenture relating to the conduct or affecting the liability or affording protection to the Trustee, whether or not elsewhere herein so provided.

10. Successors. This First Supplemental Indenture shall be binding on the Company, the Trustee and the Holders and their respective successors and assigns, and shall inure to the benefit of such parties and their respective successors and assigns.

[Remainder of Page Intentionally Blank]

3

IN WITNESS WHEREOF, the parties hereto have caused this First Supplemental Indenture to be duly executed, all as of the date first above written.

AMYRIS, INC.
By:	/s/ John Melo
Name:	John Melo
Title:	President and Chief Executive Officer
WELLS FARGO BANK,
NATIONAL ASSOCIATION
as Trustee
By:
Name:
Title:

[Signature Page to First Supplemental Indenture]

IN WITNESS WHEREOF, the parties hereto have caused this First Supplemental Indenture to be duly executed, all as of the date first above written.

AMYRIS, INC.
By:
Name:
Title:
WELLS FARGO BANK,
NATIONAL ASSOCIATION
as Trustee
By:	/s/ Maddy Hughes
Name:	Maddy Hughes
Title:	Vice President

[Signature Page to First Supplemental Indenture]

EX-4.56

Exhibit 4.56

NO AFFILIATE (AS DEFINED IN RULE 144 UNDER THE SECURITIES ACT) OF THE COMPANY OR PERSON THAT HAS BEEN AN AFFILIATE (AS DEFINED IN RULE 144 UNDER THE SECURITIES ACT) OF THE COMPANY DURING THE IMMEDIATELY PRECEDING THREE MONTHS MAY RESELL THIS NOTE OR A BENEFICIAL INTEREST HEREIN.

THIS SECURITY IS A GLOBAL SECURITY WITHIN THE MEANING OF THE INDENTURE HEREINAFTER REFERRED TO AND IS REGISTERED IN THE NAME OF A DEPOSITARY OR A NOMINEE THEREOF. THIS SECURITY MAY NOT BE EXCHANGED IN WHOLE OR IN PART FOR A SECURITY REGISTERED, AND NO TRANSFER OF THIS SECURITY IN WHOLE OR IN PART MAY BE REGISTERED, IN THE NAME OF ANY PERSON OTHER THAN SUCH DEPOSITARY OR A NOMINEE THEREOF, EXCEPT IN THE LIMITED CIRCUMSTANCES DESCRIBED IN THE INDENTURE.

UNLESS THIS CERTIFICATE IS PRESENTED BY AN AUTHORIZED REPRESENTATIVE OF THE DEPOSITORY TRUST COMPANY (“DTC”), A NEW YORK CORPORATION, TO THE COMPANY OR ITS AGENT FOR REGISTRATION OF TRANSFER, EXCHANGE OR PAYMENT, AND ANY CERTIFICATE ISSUED IS REGISTERED IN THE NAME OF CEDE & CO. OR IN SUCH OTHER NAME AS IS REQUESTED BY AN AUTHORIZED REPRESENTATIVE OF DTC (AND ANY PAYMENT IS MADE TO CEDE & CO. OR TO SUCH OTHER ENTITY AS IS REQUESTED BY AN AUTHORIZED REPRESENTATIVE OF DTC), ANY TRANSFER, PLEDGE OR OTHER USE HEREOF FOR VALUE OR OTHERWISE BY OR TO ANY PERSON IS WRONGFUL IN AS MUCH AS THE REGISTERED OWNER HEREOF, CEDE & CO., HAS AN INTEREST HEREIN.

AMYRIS, INC.

9.50% Convertible Senior Notes due 2019

No. A-2		U.S. $19,136,000
CUSIP NO.	03236M AG6
ISIN NO.	US03236MAG69

Amyris, Inc., a company duly incorporated and validly existing under the laws of the state of Delaware in the United States of America (herein called the “Company”), which term includes any successor corporation under the Indenture referred to on the reverse hereof), for value received hereby promises to pay to CEDE & CO, or registered assigns, the principal sum of NINETEEN MILLION ONE HUNDRED AND THIRTY SIX THOUSAND UNITED STATES DOLLARS (U.S. $19,136,000) (which amount may from time to time be increased or decreased by adjustments made on the records of the Trustee, as custodian for the Depositary, in accordance with the rules and procedures of the Depositary and in accordance with the below referred Indenture) on April 15, 2019. The Principal Amount of Physical Notes and interest thereon (to the extent paid in cash), as provided on the reverse hereof, shall be payable at the Corporate Trust Office and at any other office or agency maintained by the Company for such purpose. In the case of cash payment, the Paying Agent will pay principal of any Note and interest thereon, and, in the case of payment made in Common Stock, the Transfer Agent will issue Common Stock in payment of principal (or conversion) on any Note and interest thereon, as provided on the reverse hereof, in immediately available funds, in the case of a cash payment, or in Common Stock, in the case of payment in shares of Common Stock, to The Depository Trust Company or its nominee, as the case may be, as the registered holder of such global note, on each Interest Payment Date, Fundamental Change Purchase Date or other payment date, as the case may be.

Reference is made to the further provisions of this Note set forth on the reverse hereof, including, without limitation, provisions giving the Holder the right to convert this Note into shares of Common Stock of the Company and to the ability and obligation of the Company to purchase this Note upon certain events, in each case, on the terms and subject to the limitations referred to on the reverse hereof and as more fully specified in the Indenture. Such further provisions shall for all purposes have the same effect as though fully set forth at this place. Capitalized terms used but not defined herein shall have such meanings as are ascribed to such terms in the Indenture. In the case of any conflict between this Note and the Indenture, the provisions of the Indenture shall control.

This Note shall not be valid or become obligatory for any purpose until the certificate of authentication hereon shall have been manually signed by the Trustee or a duly authorized authenticating agent under the Indenture.

IN WITNESS WHEREOF, the Company has caused this instrument to be duly executed.

	AMYRIS, INC.
	By:	/s/ John Melo
		Name: John Melo
		Title: President and Chief Executive Officer
	By:	/s/ Kathleen Valiasek
		Name: Kathleen Valiasek
		Title: Chief Financial Officer
Date: January 11, 2017

CERTIFICATE OF AUTHENTICATION

This is one of the Notes referred to in the within-mentioned Indenture.
Dated: January 11, 2017
	WELLS FARGO BANK, NATIONAL
	ASSOCIATION, as Trustee
	By:	/s/ Madelyn Hughes
		Authorized Signatory

AMYRIS, INC.

9.50% Convertible Senior Notes due 2019

This Note is one of a duly authorized issue of Notes of the Company, designated as its 9.50% Convertible Senior Notes due 2019 (the “Notes”), initially limited in aggregate principal amount to $57,605,000, which amount may from time to time be increased or decreased by adjustments made on the records of the Trustee, as custodian for the Depositary, in accordance with the rules and procedures of the Depositary and in accordance with the below referred Indenture) all issued or to be issued under and pursuant to an Indenture dated as of October 20, 2015 (the “Indenture”) between the Company and Wells Fargo Bank, National Association, as Trustee (the “Trustee”), to which the Indenture and all indentures supplemental thereto reference is hereby made for a description of the rights, limitations of rights, obligations, duties and immunities thereunder of the Trustee, the Company and the Holders of the Notes. The Indenture provides that Additional Notes may be issued thereunder, if certain conditions are met.

Interest. This Note will bear interest at a rate of 9.50% per year. Interest on this Note will accrue from, and including, October 15, 2016, or from the most recent date to which interest has been paid or duly provided for. Interest will be payable semiannually in arrears on each Interest Payment Date, beginning April 15, 2017.

Method of Payment. The Company may elect to pay interest entirely in cash or entirely in Common Stock. The Company may elect to pay interest in Common Stock, subject to the Exchange Cap limitation in Section 6.04. If the Company elects to pay interest in cash it shall be made in money of the United States of America that at the time of payment is legal tender for payment of public and private debts. If the Company elects to pay interest in shares of Common Stock, the number of shares issuable will be based upon a price equal to 92.5% of the simple average of the daily VWAP per share for Common Stock for the Averaging Period, as calculated and determined by the Company. On or before the fifth Trading Day before the start of the applicable Averaging Period, the Company shall notify the Holders, the Trustee and the Transfer Agent of whether it will make such interest payment in cash or in shares of Common Stock; provided that, if no such notice is given, the Company shall be deemed to have notified the Holders that it will pay interest in cash. If the Company chooses to make such payment in shares of Common Stock, on or before the third Trading Day following the applicable Interest Payment Date, the Company shall (X) provided that the Transfer Agent is participating in The Depository Trust Company Fast Automated Securities Transfer Program and the Holder or its designee has an account with DTC, credit the number of shares of Common Stock payable as an interest payment to such Holder’s or its designee’s balance account with DTC through its Deposit/Withdrawal at Custodian system, or (Y) if the Transfer Agent is not participating in the DTC Fast Automated Securities Transfer Program and the Holder or its designee has an account with DTC, issue and dispatch by overnight courier to each Holder, a certificate, registered in the Company’s share register in the name of such Holder or its designee, for the number of shares of Common Stock to which such Holder is entitled in connection with such payment.

Pursuant to Section 8.03 of the Indenture and Section 2(c) of the Registration Rights Agreement, in certain circumstances, the Holders of Notes shall be entitled to receive Additional Interest. Payments of the Fundamental Change Repurchase Price, principal and interest that are not made when due will accrue interest per annum at the then-applicable interest rate for the Notes from the required date of payment.

Interest will be paid to the person in whose name a Note is registered at the Close of Business on the April 1 or October 1 (whether or not such date is a Business Day), as the case may be, immediately preceding the relevant Interest Payment Date. Interest on the Notes will be computed on the basis of a 360-day year composed of twelve 30-day months.

Interest will cease to accrue on a Note upon its maturity, conversion or repurchase in connection with a Fundamental Change.

Ranking. The Notes constitute a general unsecured and unsubordinated obligation of the Company.

No Redemption at the Option of the Company. The Notes may not be redeemed at the option of the Company and no sinking fund is provided for the Notes.

Purchase at the Option of the Holder Upon a Fundamental Change. Subject to the terms and conditions of the Indenture, the Company shall become obligated, at the option of the Holder, to repurchase the Notes if a Fundamental Change occurs at any time prior to the Maturity Date at 100% of the Principal Amount together with accrued and unpaid interest to, but excluding, the Fundamental Change Purchase Date, which amount will be paid in cash.

Withdrawal of Fundamental Change Purchase Notice. Holders have the right to withdraw, in whole or in part, any Fundamental Change Purchase Notice by delivering to the Paying Agent a written notice of withdrawal in accordance with the provisions of the Indenture, or in the case of Notes held in book entry form, in accordance with the Applicable Procedures of DTC. The right to withdraw the Fundamental Change Purchase Notice will terminate at the Close of Business on the Business Day immediately preceding the relevant Fundamental Change Purchase Date.

Payment of Fundamental Change Purchase Price. If money sufficient to pay the Fundamental Change Purchase Price of all Notes or portions thereof to be purchased on a Fundamental Change Purchase Date is deposited with the Paying Agent on the Fundamental Change Purchase Date, such Notes will cease to be outstanding and interest will cease to accrue on such Notes (or portions thereof) immediately after the Close of Business on such Fundamental Change Purchase Date, and the Holder thereof shall have no other rights as such (other than the right to receive the Fundamental Change Purchase Price upon surrender of such Note).

Conversion. Subject to and upon compliance with the provisions of the Indenture (including without limitation the conditions of conversion of this Note set forth in Article 6 thereof), the Holder hereof has the right, at its option, to convert the Principal Amount hereof or any portion of such principal which is $1,000 or an integral multiple of $1,000 in excess thereof, into shares of Common Stock at the Applicable Conversion Rate. The Conversion Rate is initially 446.8707 shares of Common Stock per $1,000 Principal Amount of Notes (equivalent to an initial Conversion Price of approximately $2.24), subject to adjustment in certain events described in the Indenture. Upon conversion, the Company will deliver shares of Common Stock, and the Early Conversion Payment, if applicable, as set forth in the Indenture. No fractional shares will be issued upon any conversion, but a payment in cash will be made, as provided in the Indenture, in respect of any fraction of a share which would otherwise be issuable upon the surrender of any Notes for conversion. Notes in respect of which a Holder is exercising its right to require repurchase on a Fundamental Change Purchase Date may be converted only if such Holder withdraws the related election to exercise such right in accordance with the terms of the Indenture.

In the event of a deposit or withdrawal of an interest in this Note, including an exchange, transfer, repurchase or conversion of this Note in part only, the Trustee, as custodian of the Depositary, shall make an adjustment on its records to reflect such deposit or withdrawal in accordance with the rules and procedures of the Depositary.

Limitations on Issuance due to Market Regulation. Notwithstanding any provision herein to the contrary, if the payment of interest (including Additional Interest) in Common Stock, or issuance of shares of Common Stock upon conversion of the Notes, would result in the Company exceeding the Exchange Cap, then the Company shall make interest payments, or settle its obligation on conversion, in cash. The Exchange Cap limitation shall not apply in the event that the Company obtains stockholder approval for issuances of shares of Common Stock in excess of such amount and satisfies the requirements of NASDAQ Market Rule 5635. In the event that a Holder seeks to convert such Holder’s Notes into shares of Common Stock in excess of the Exchange Cap, the Company will notify such Holder within three Business Days that the Exchange Cap has been exceeded and that the Company will instead settle such amount in excess of the Exchange Cap in cash and not in shares of Common Stock. In such case, the Company will, by wire transfer of U.S. dollars in immediately available funds to the account designated by the Holder, pay cash to the Holder in an amount equal to the product of (x) the number of shares of Common Stock which would have been issuable upon conversion but cannot be issued as a result of the Exchange Cap and (y) the simple average of the Daily VWAP for Common Stock for the ten consecutive VWAP Trading Days ending on and including the VWAP Trading Day immediately prior to the Conversion Date.

Acceleration of Maturity. Subject to certain exceptions in the Indenture, if an Event of Default shall occur and be continuing, the Principal Amount plus interest through such date on all the Notes may be declared due and payable in the manner and with the effect provided in the Indenture.

Supplement Indentures with Consent of Holders; Waiver of Past Defaults. The Indenture permits, with certain exceptions as therein provided, the amendment thereof and the modification of the rights and obligations of the Company and the rights of the Holders of the Notes under the Indenture at any time by the Company and the Trustee with the consent of the Holders of not less than a majority in aggregate Principal Amount of the outstanding Notes. The Indenture also contains provisions permitting the Holders of specified percentages in aggregate Principal Amount of the outstanding Notes, on behalf of the Holders of all the Notes, to waive compliance by the Company with certain provisions of the Indenture and certain past Defaults under the Indenture and their consequences. Any such consent or waiver by the Holder of any provision of or applicable to this Note shall be conclusive and binding upon such Holder and upon all future Holders of this Note and of any Note issued upon the registration of transfer hereof or in exchange herefor or in lieu hereof, whether or not notation of such consent or waiver is made upon this Note.

Registration of Transfer and Exchange. As provided in the Indenture and subject to certain limitations therein set forth, the transfer of this Note is registrable in the Register, upon surrender of this Note for registration of transfer at the office or agency of the Company in the United States, duly endorsed by, or accompanied by a written instrument of transfer in form satisfactory to the Company and the Registrar duly executed by, the Holder hereof or his attorney duly authorized in writing, and thereupon one or more new Notes, of authorized denominations and for the same aggregate Principal Amount, will be issued to the designated transferee or transferees.

No service charge shall be made for any such registration of transfer or exchange, but the Company and the Registrar may require payment of a sum sufficient to cover any tax or other governmental charge payable in connection therewith.

Prior to due presentment of this Note for registration of transfer, the Company, the Trustee and the Registrar and any agent of the Company or the Trustee may treat the Person in whose name this Note is registered as the owner hereof for all purposes, whether or not this Note be overdue, and neither the Company, the Trustee nor any such agent shall be affected by notice to the contrary.

Denominations. The Notes are issuable only in registered form in denominations of $1,000 and any integral multiple of $1,000 in excess thereof, as provided in the Indenture and subject to certain limitations therein set forth. Notes are exchangeable for a like aggregate Principal Amount of Notes of a different authorized denomination, as requested by the Holder surrendering the same.

This Note and any claim, controversy or dispute arising under or related to this Note shall be governed by and construed in accordance with the laws of the State of New York.

All terms used in this Note that are defined in the Indenture shall have the meanings assigned to them in the Indenture.

EX-10.01

Exhibit 10.01

[English translation from Portuguese]

INOVA BRASIL PROGRAM

Reference No. 0434/08

CREDIT FACILITY AGREEMENT BY AND BETWEEN
FINANCIADORA DE ESTUDOS E PROJETOS – FINEP
AND AMYRIS BRASIL S/A.

Stamp: FINANCIADORA DE ESTUDOS E
PROJETOS – FINEP, AGREEMENT CODE No.
0|2|10|0520|00

Stamp: Registry of Deeds and
Documents/Campinas, microfilm
1123292

By this private instrument, FINANCIADORA DE ESTUDOS E PROJETOS – FINEP, a state-owned company operated by the Ministry of Science and Technology, with head office in Brasília, Federal District, and which provides services in this city, at Praia Flamengo 200 – parte, Federal Taxpayer Registration CNPJ No. 33.749.086/0001-09, hereinafter referred to as FINEP, and AMYRIS BRASIL S.A., a corporation with head office in the City of Campinas, State of São Paulo, at Rua James Clerk Maxwell, n° 315, CEP 13069-380, Federal Taxpayer Registration CNPJ No. 09.379.224/0001-20, hereinafter referred to as BORROWER, by their legal representatives:

SECTION ONE PRICE

FINEP hereby extends to BORROWER a credit facility in the amount of up to six million four hundred and thirty-five thousand Brazilian Reais (R$6,435,000.00) as part of the global cost of the PROJECT identified in Section Two, in the total amount of

twenty million nine hundred and eighty-one thousand nine hundred and ninety-nine Brazilian Reais and ninety-one cents (R$20,981,999.91).

SECTION TWO PURPOSE

The purpose of the credit facility extended hereunder is to partially fund expenses incurred to develop the PROJECT “RESEARCH AND DEVELOPMENT OF FERMENTATION PROCESS FOR PILOT PRODUCTION OF SUGARCANEBASED BIODIESEL”, hereinafter simply referred to as PROJECT (FINEP reference No. 0434/08), pursuant to Resolution No. 0167/10, issued on May 10, 2010 by FINEP’S Executive Board, in accordance with the Disbursement Scheduled approved by FINEP.

SECTION THREE AVAILABILITY OF FUNDS

1. Subject to the financial and budgetary availability of FINEP, which is subject to the definition of funds for its investments, the credit facility contemplated herein shall be

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extended in four (4) disbursements, upon compliance with the conditions established in Section Five, which disbursements shall be available for withdrawal as follows:

1^st disbursement: one million seven hundred and fifty-five thousand Brazilian Reais (R$1,755,000.00) after execution hereof;

2^nd disbursement: one million five hundred and sixty thousand Brazilian Reais (R$1,560,000.00) one hundred and eighty (180) days after release of the first disbursement;

3^rd disbursement: one million five hundred and sixty thousand Brazilian Reais (R$1,560,000.00) one hundred and eighty (180) days after release of the second disbursement;

4^th disbursement: one million five hundred and sixty thousand Brazilian Reais (R$1,560,000.00) one hundred and eighty (180) days after release of the third disbursement.

1. During the period of use of funds, BORROWER agrees to keep a checking account informed to FINEP for release of the funds obtained hereunder, as provided in Section Five, item 1 of this Agreement.

2. The disbursements not made within the estimated period shall be automatically rescheduled for the immediate following equivalent period. Should the late disbursement be reasonably caused by BORROWER for two (2) consecutive periods, a new Disbursement Schedule shall be approved by FINEP, subject to FINEP’S financial and budgetary availability.

3. The date of execution hereof shall be deemed the reference date with regard to the periods contemplated in the Disbursement Schedule.

4. The installments provided and not completely used within thirty (30) months as of the date of execution hereof shall be automatically cancelled.

5.1. At the request of BORROWER, FINEP may, at its sole discretion, extend the terms for use of the disbursements or revoke cancellation of any disbursement, provided FINEP accepts BORROWER’S reasons, which shall be submitted in writing.

SECTION FOUR CONSIDERATION

BORROWER hereby irrevocably and irreversibly agrees to share the PROJECT development costs described in Section Two above with proprietary funds in the minimum amount of fourteen million five hundred and forty-six thousand nine hundred and ninety-nine Brazilian Reais and ninety-one cents (R$14,546,999.91).

SECTION FIVE

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Reference No. 0434/08

CONDITIONS FOR THE DISBURSEMENT OF FUNDS

1. The first disbursement shall be conditional upon performance of the following actions, by BORROWER, within up to sixty (60) days as of execution hereof:

a) prove transcription of this Agreement in one of the Registries of Deeds and Documents of the head office of BORROWER;

b) inform the checking account for release of the funds;

c) present a Debt Clearance Certificate relating to Social Security and Third-Party Contributions issued by the Federal Revenue Office;

d) present an insurance policy covering movable property (machinery / equipment);

1.1. BORROWER’S failure to comply with the obligations listed above within the agreed term shall result in automatic termination hereof and shelving of the PROJECT.

2. The following disbursements shall be conditional upon submission of the following documents by BORROWER to FINEP:

a) statement of the expenses incurred from the funds previously released by FINEP;

b) statement of the use of proprietary funds in the minimum amount of:

i) eleven million one hundred and forty-four thousand six hundred and fourteen Brazilian Reais and fifty-nine cents (R$11,144,614.59)

for release of the second disbursement;

ii) one million one hundred and thirty-four thousand and eighty-five cents (handwritten: Brazilian Reais – initialed) (R$1,134,085.00) for release of the third disbursement;

iii) one million one hundred and thirty-four thousand and eighty-five cents (handwritten: Brazilian Reais – initialed) (R$1,134,085.00) for release of the fourth disbursement;

c) partial report on the progress of the PROJECT;

d) Debt Clearance Certificate relating to Social Security and Third-Party Contributions issued by the Federal Revenue Office;

e) bank letters of guarantee in accordance with the provisions of Section Twelve hereof, in the following amounts:

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Reference No. 0434/08

i) For the second disbursement, a bank letter of guarantee in the minimum amount of one hundred and forty-four thousand two hundred and sixty-six Brazilian Reais and seventy-eight cents (R$144,266.78), plus charges hereunder, which bank letter of guarantee shall be valid until thirty (30) days after the maturity date of the last amortization installment; ii) For the third disbursement, a bank letter of guarantee in the minimum amount of one million five hundred and sixty thousand Brazilian Reais (R$1,560,000.00), plus charges hereunder, which bank letter of guarantee shall be valid until thirty (30) days after the maturity date of the last amortization installment; iii) For the fourth disbursement, a bank letter of guarantee in the minimum amount of one million five hundred and sixty thousand Brazilian Reais (R$1,560,000.00), plus charges hereunder, which bank letter of guarantee shall be valid until thirty (30) days after the maturity date of the last amortization installment;

3. Within up to one hundred and eighty (180) days after the last disbursement, BORROWER shall provide FINEP with:

a) statement of the expenses incurred from the funds previously released by FINEP;

b) statement of the use of proprietary funds – compensation – in the minimum amount of one million one hundred and thirty-four thousand two hundred and fifteen Brazilian Reais and thirty-two cents (R$1,134,215.32);

c) one (1) copy of the Final Report on the PROJECT, along with an up to 200-word summary for external disclosure purposes, which shall provide information relating to the results of the PROJECT, and which shall highlight up to six (6) keywords identifying the contents of these results;

1. The expense statements mentioned in items 2 and 3 of this Section shall discriminate the expenses incurred with the PROJECT, identifying the underlying event, the amount and the number of the corresponding tax invoice or similar document.

2. FINEP shall only release the installments in case it understands that the documents referred to in items 1 and 2 above are satisfactory.

SECTION SIX CHARGES

1. For purposes of the provisions hereof, the following terms are defined:

a) SPREAD – Percentage amount corresponding to the remuneration of the invested capital;

b) TJLP – Long-Term Interest Rate, as disclosed by the Central Bank of Brazil;

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Reference No. 0434/08

c) REDUCTION FACTOR – Non-capitalized portion of the TJLP, currently established as six percent (6%) per year;

d) CAPITALIZATION FACTOR – Corresponds to the result of the adjustment to the TJLP at the reduction factor;

e) EQUALIZATION – Instrument that allows reduction of the charges hereunder to be paid by BORROWER to FINEP;

f) EQUALIZATION FACTOR – Based on Administrative Regulation – MCT No. 727, of November 24, 2005 (published in the Brazilian Federal Register on November 25, 2005), it adjusts the total amount of interest owed under each transaction, including the portion relating to the TJLP and the portion relating to the SPREAD.

g) DEFAULT – For purposes of article 4 of the Administrative Regulation – MCT No. 727, of November 24, 2005 (published in the Brazilian Federal Register on November 25, 2005), the company that fails to comply with its obligations to FINEP within up to twenty (20) days after the contractual maturity date relating to each installment of interest and/or amortization is deemed to be in financial default. Two successive or alternate late payments in the same fiscal year shall result in loss of the fixed interest rate benefit. In addition, with regard to technical default and for purposes of the aforementioned article, companies that fail to comply with the contractual obligations and to observe the contractual terms for more than ninety (90) days shall loose the fixed interest rate benefit.

2. The principal amount of the debt shall accrue interest at the rate of five percent (5%) per year.

2.1. The charges contemplated in item 2 result from the deduction of the equalization factor relating to the TJLP from the charges owed corresponding to the sum of the five percent (5%)-spread per year and the TJLP.

2.2. The amount determined in accordance with the provisions of item 2 of this Section shall be due on a monthly basis during the grace period. During the amortization period, the aforementioned amount shall be due jointly with the installments of the principal amount and upon termination or liquidation of the Agreement.

3. In the event of loss of the fixed interest rate benefit,a spread of five percent (5%) per year above the TJLP shall be charged, in which case the criterion contemplated in items I and II below shall apply:

I -TJLP in excess of six percent (6%) per year:

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a) The amount corresponding to the portion of the TJLP in excess of six percent (6%) per year shall be capitalized on a daily basis and assessed by means of application of the following term of capitalization to the outstanding balance, taking into consideration all financial events occurred during such period:

n/360

FC= [1 + TJLP)/1.06], where:

FC -Capitalization Factor;

TJLP -Long-Term Interest Rate, as disclosed by the Central Bank of Brazil, expressed in decimals;

n – number of days from the date of the financial event to the date of capitalization, maturity or liquidation of the obligation. Financial event means any and all financial fact that results or may result in a change in the outstanding balance.

The currency URTJ-01 shall be used as operational support for this term of capitalization. The daily rate shall be obtained by means of application of the FC factor on the rate of the preceding date, where n=1.

b) SPREAD of five percent (5%) per year above the TJLP, as mentioned in item 3 of this Section, plus the reduction factor (six percent per year – 6%) shall apply to the outstanding balance on the maturity date of the interests mentioned in item 3.1 below, or on the date of termination or liquidation hereof. For purposes of daily calculation of interest, the number of days between the date of each financial event and the aforementioned maturity dates shall be taken into consideration.

c) The amount referred to in item I, letter “a” of this Section, which shall be capitalized and incorporated in the principal amount of the debt, shall be payable simultaneously to the installments of principal.

II -TJLP equal or inferior to six percent (6%) per year:

a) The capitalization factor of the outstanding balance shall be one (1);

b) SPREAD of five percent (5%) per year plus the TJLP shall apply to the outstanding balance on the maturity date of the interests mentioned in item 3.1 below, or on the date of termination or liquidation hereof. For purposes of daily calculation of interest, the number of days between the date of each financial event and the aforementioned maturity dates shall be taken into consideration.

3.1. The amount determined in accordance with the provisions of items I and II of this Section, as the case may be, shall be due on a monthly basis during the grace period. During the amortization period, the aforementioned amount shall be payable simultaneously to the

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installments of the principal and upon termination or liquidation of the Agreement.

4. In the event of default or in case the amount offered is not sufficient for liquidation of at least one installment of the debt, a special account shall be opened with FINEP in the name of BORROWER, where the amount of the installments in default plus the charges contemplated in the following items shall be recorded as debit. All payments made by BORROWER shall be accepted as partial payments of the debt. This procedure, however, shall not result in novation of the debt and may not be claimed as a sufficient reason to suspend or suppress the default or immediate claim to the obligation, subject to the provision of Section Seven – LOSS OF THE FIXED INTEREST RATE BENEFIT.

4.1. A fine of up to ten percent (10%) shall immediately apply to the amount of the obligations in default. Such fine shall be calculated in accordance with the number of days in default, as explained in the following table:

4.2. The defaulting BORROWER shall also be subject to the payment of interest on late payment of one percent (1%) per month, levied on the overdue amount, in addition to the fine referred to in subsection 4.1 above, which shall be calculated per day of delay.

Number of Days in Default	Fine
One (1)	One percent (1%)
Two (2)	Two percent (1%)
Three (3)	Three percent (3%)
Four (4)	Four percent (4%)
Five (5)	Five percent (5%)
Six (6)	Six percent (6%)
Seven (7)	Seven percent (7%)
Eight (8)	Eight percent (8%)
Nine (9)	Nine percent (9%)
Ten (10)	Ten percent (10%)

4.3. The installments coming due shall be subject to the charges contemplated herein.

4.4. Should the entire amount due be immediately claimed, the outstanding balance shall accrue the amounts contemplated in the preceding subsections of this Section.

5. The amount corresponding to one percent (1%) of the credit facility shall be used to cover inspection and supervision expenses. This percentage shall be applied on the amount of each disbursement and shall be deducted upon actual release of the corresponding disbursement.

6. In the event of any change in the statutory fund remuneration criteria, the remuneration contemplated herein shall observe the new remuneration criteria relating

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to such funds that, in addition to preserving the actual value of the transaction, shall remunerate it at the same preceding levels. In this case, the new criterion shall only be owed as of the date on which FINEP gives BORROWER written notice of such change.

SECTION SEVEN LOSS OF THE FIXED INTEREST RATE BENEFIT

1. Any default as defined in Section Six, item 1, letter “g” shall result in full loss of the fixed interest rate benefit until the end of the term of effectiveness hereof, effective as of the date of the default, which loss of the fixed interest rate benefit shall relate to the outstanding installments coming due, so that the outstanding balance shall be recalculated as of that date, upon elimination of the benefit, as provided in Section Six, item 3.

1.1. Loss of the fixed interest rate benefit shall also apply as a result of a technical and/or financial default hereunder and/or in any other instrument executed by and among BORROWER and FINEP.

SECTION EIGHT OUTSTANDING BALANCE

The outstanding balance shall be composed of the sum of the amount of the disbursements plus the charges established in Section Six.

SECTION NINE GRACE PERIOD AND AMORTIZATION

1. The charges contemplated in Section Six shall be due during the twenty (20)-month grace period, which is the period from the date of execution hereof and the maturity date of the first amortization installment.

2. The outstanding balance shall be paid to FINEP in eighty-one (81) monthly and successive installments, each of which in the amount of the outstanding balance divided by the number of amortization installments coming due. The maturity date of the first installment shall be July 15, 2012 and the other installments shall be due on the same day of the following months. The maturity date of the last installment shall be March 15, 2019.

3. Failure to receive the collection notice shall not exempt BORROWER from the obligation to pay the outstanding installments on the dates stated herein.

4. Whenever the maturity date of the principal and charges falls on a Saturday, Sunday or national holiday, including bank holiday, such amount shall be paid on the first following business day.

SECTION TEN OTHER OBLIGATIONS OF BORROWER

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In order to use the credit facility and until final payment of the whole debt resulting therefrom, BORROWER agrees to comply with the following obligations, in addition to other obligations established elsewhere in this Agreement:

a) to answer by mail any request of information sent by FINEP within up to thirty (30) days as of the date of request, with regard to the progress of the works or the outcome of the PROJECT, without prejudice to the inspection to be carried out by FINEP;

b) to keep for a term of five (5) years, in am exclusive file available to FINEP, the evidentiary documents relating to the expenses listed in the statements referred to in items 2 and 3 of Section Five, it being understood that FINEP may deduct from the credit facility amount the amounts relating to expenses that have not been proved, which have been unsatisfactorily proved or which are not allowed. BORROWER shall submit to FINEP proof of the aforementioned expenses within thirty (30) days as of the request made by FINEP by mail.

c) to refrain from obtaining credit facilities or from performing actions that directly or indirectly result in a reduced ability to make payments without the prior and express consent of FINEP, except for actions performed in the ordinary course of business;

d) to inform FINEP of any event that results in a reduction in its ability to make payments or in the amount of the guarantees;

e) to immediately inform FINEP in writing of any event that results in the reduction in, insufficiency or impossibility of the guarantee offered, in order for FINEP to adopt the applicable measures. In this case, BORROWER shall reinforce or substitute the guarantee within thirty (30) days as of the written notice sent by FINEP by telegram, certified mail or via the Registry of Deeds and Documents, or by means of a court notice, which shall neither result in novation nor in release of the joint obligors/guarantors.

f) to pay with proprietary funds all expenses required for formalization hereof;

g) to grant FINEP full inspection authority concerning the execution hereof, especially with regard to the use of the funds actually released, but also with regard to the amounts invested as compensation;

h) to grant FINEP all facilities and access required for analysis of BORROWER’S legal, technical, economic and financial condition, including, at the discretion of FINEP, to contract audit services;

i) to keep FINEP informed of the outcome of the financed PROJECT, especially with regard to the amount of the investments actually made upon implementation of the FINAL PROJECT, on the dates established herein or upon request;

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j) to mention, whenever it announces the PROJECT contemplated herein, FINEP’S cooperation as lender, including at the place of execution thereof;

k) to prominently display in its establishment and in all promotion materials resulting from execution of PROJECT, by means of a plate in accordance with the model, dimensions and inscription informed on FINEP’S website (http://www.finep.gov.br), the text below or other text provided by FINEP:

“VENTURE FINANCED BY FINANCIADORA DE ESTUDOS E PROJETOS – FINEP”

l) to participate in the costs for preparation of the PROJECT with the additional amounts required for completion thereof;

m) to maintain its head office and management in Brazil, informing FINEP of any change therein, even if within the Brazilian territory;

n) to inform FINEP of all changes in its capital stock and/or corporate structure within ten days after registration thereof with the applicable Commercial Registry or Civil Registry of Legal Entities;

o) to annually send its balance sheet;

p) to comply with the provisions of the laws relating to the Brazilian Environmental Policy, as well as to perform, during the term of effectiveness hereof, any action to avoid or remedy damages to the environment that may be caused by the financed PROJECT;

q) to regularly comply with its obligations to the environmental authorities during the term of effectiveness hereof.

SECTION ELEVEN NET AND CLEAR DEBT

BORROWER is required to acknowledge as proof of its debt all withdrawals, requests, receipts and money orders or similar documents issued or signed by BORROWER, as well as any accounting entry made by FINEP in this regard, and FINEP is required to acknowledge as proof of its credit all receipts or communications issued or signed by FINEP with regard to amounts received to the credit of BORROWER, in order to ensure that the debt is net and clear at all times, including interest and other expenses that shall add to the principal amount of the debt, provided BORROWER'S right to require verification of this proof and to be refunded for any possible credit.

SECTION TWELVE GUARANTEES

1. In order to guarantee the payment of any obligations hereunder, such as the principal amount, interest, contractual fine and fine, BORROWER hereby provides to FINEP:

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1.1. A chattel mortgage on the forty-eight (48) chattels described and identified in EXHIBIT I hereto, free and clear of any judicial or extrajudicial lien.

1.1.1. The aforementioned chattels shall remain in the possession of BORROWER, which hereby agrees to maintain them in a perfect state of conservation, safety and operation, making the required repairs as requested by FINEP, which may inspect the chattels at any time.

1.1.2. The alienation, encumbrance, lease or assignment of, or change in, the aforementioned chattels without the prior and express consent of FINEP shall be prohibited.

1.1.3. BORROWER hereby declares that it has peaceable and uncontested possession of the chattels, free and clear of any liens or encumbrances, including tax liens.

1.2. Three (3) BANK LETTERS OF GUARANTEE in the amount of each release, plus charges, issued by a financial institution previously approved by FINEP, which hereby agrees on its behalf and on the best terms of the law, as GUARANTOR and primary obligor and jointly and severally liable with BORROWER, upon waiver of the benefits contemplated in articles 827 and 333, sole paragraph of the Brazilian Civil Code (Law 10406, of January 10, 2002), on its behalf and on behalf of its successors, until final payment of the debt.

1.2.1. In order to comply with the provisions of the preceding item, BORROWER shall submit to FINEP bank letters of guarantee previously approved by FINEP, the maturity date of which shall be thirty (30) days after the maturity date of the last installment of the credit facility agreement, as stated in Section Five, item 2, letter “e” hereof.

1.2.2. The bank letters of guarantee shall be an integral and inseparable part hereof.

1.2.3. The guarantees provided under this Section shall be deemed indivisible with regard to the amount of the debt.

3. BORROWER agrees not to perform any action that could reduce the amount of the guarantee provided hereunder.

3.1. BORROWER shall immediately inform FINEP in writing of the occurrence of any event rendering the guarantees offered hereunder insufficient or unviable, and BORROWER hereby agrees to reinforce or substitute the guarantees within thirty (30) days as of the notice sent by FINEP by fax, telegram or certified mail or via the Registry of Deeds and Documents, or by means of a court notice, under penalty of FINEP being able to terminate this

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Agreement by operation of law, regardless of any other warning, notice or judicial or extrajudicial notification.

1. FINEP may agree with BORROWER on the substitution, reinforcement, release or even waiver of the guarantees offered hereunder, which shall not result in novation or in the release of the joint obligors or guarantors.

2. Should FINEP have to foreclose the securities agreed hereunder or in any possible amendment hereto, including the chattel mortgage, the guarantor(s) or joint obligors, if any, shall remain jointly and severally liable for the outstanding balance, even after the judicial or extrajudicial sale of the securities, and they hereby agree to settle such outstanding balance on the date required by FINEP, including in the events of early maturity hereof, regardless of any other judicial or extrajudicial warning or notice.

3. The securities shall be covered against all risks by an insurance policy provided by a Brazilian insurance company to which they may be subject, for an amount that shall never be lower than the appraisal carried out by FINEP, and BORROWER shall present the corresponding insurance policy before the first disbursement.

6.1. The insurance policy shall state that FINEP is a beneficiary to the insurance, and it shall also provide that the insured may not reserve the right to substitute the beneficiary without the consent of FINEP.

6.2. Within up to thirty (30) days before termination of the insurance, BORROWER shall provide FINEP with a proof that the insurance of the securities has been renewed and send FINEP the corresponding renewed policies, the premiums of which shall have been paid.

6.3. Should BORROWER fail to comply with the obligation contemplated in the preceding item, FINEP is hereby authorized to insure the asset in the name and on account of BORROWER, which hereby appoints FINEP as its representative, with the required powers to take out the insurance, and it further agrees to pay or reimburse the premiums owed, the amount of which shall be added to the outstanding balance hereof, for purposes of calculating interest and other charges, provided FINEP’S right to declare the early maturity of the debt.

6.4. In the event of loss, FINEP may, at its sole discretion, invest the amount of the compensation for payment of the outstanding balance hereunder, wholly or in part, and any remaining amount shall be reimbursed to BORROWER.

6.5. No amendment to the special conditions of the insurance policies approved by FINEP may be made without the prior written consent of FINEP.

6.6. BORROWER further agrees not to perform, accept or allow any action that could suspend, impair or prevent any insurance taken out by BORROWER or by FINEP.

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SECTION THIRTEEN SUSPENSION OF DISBURSEMENTS

Should FINEP decide to declare the early maturity of the debt, it may, upon express notice to BORROWER, suspend disbursement of the funds in view of the noncompliance with any obligation assumed hereunder or upon occurrence of any of the following events, it being understood that BORROWER shall provide information or cure the default within at most thirty (30) days:

a) use of the borrowed funds for purposes other than agreed or in noncompliance with the Disbursement Schedule referred to in Section Two;

b) late payment of any amount owed to FINEP;

c) inaccuracy of information provided to FINEP by BORROWER, for purposes of obtaining the credit extended hereunder or during performance hereof;

d) negligent interruption of the PROJECT;

e) other events that, at the discretion of FINEP, cause the compliance by BORROWER with the obligations assumed hereunder or the achievement of the goals for which the credit has been extended unsafe or impossible;

f) failure to comply with any obligation assumed by BORROWER hereunder;

g) in the event of judicial reorganization or agreement with creditors, adjudication of bankruptcy or protest in respect of any negotiable instrument with regard to BORROWER and/or its guarantor(s), except in the event of mistaken protest and/or submission of reasonable grounds for the protest.

SECTION FOURTEEN EARLY MATURITY OF THE DEBT

Failure to comply with any obligation assumed hereunder or occurrence of any of the events contemplated in the preceding Section, either before or after full disbursement of the amount mentioned in Section One, shall grant FINEP, regardless of judicial or extrajudicial notice, the right to terminate this Agreement, in which case the whole debt hereunder shall become immediately due, as calculated in accordance with the provisions of Section Seven hereof.

SECTION FIFTEEN CONTRACTUAL FINE

Should FINEP resort to the courts to receive its credit, BORROWER shall pay ten percent (10%) of the outstanding debt as contractual fine. This fine may not be reduced and it shall be due together with the principal and ancillary amounts.

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SECTION SIXTEEN FAILURE TO EXERCISE RIGHTS

No late exercise or failure to exercise any rights or powers granted to FINEP under the law or hereunder and no forbearance of late compliance with the obligations assumed by BORROWER shall result in novation, and none of these actions may be construed as a waiver of such rights or powers, which may be exercised at any time at the sole discretion of FINEP.

SECTION SEVENTEEN PLACE OF PAYMENT

BORROWER shall pay all amounts due hereunder, either relating to amortization or to the payment of ancillary amounts, at FINEP’S office in the City of Rio de Janeiro, or wherever informed by FINEP by means of a collection notice, in Brazilian currency or by means of checks drawn to the order of FINEP.

SECTION EIGHTEEN JURISDICTION

The parties hereby elect the courts of the City of Rio de Janeiro to resolve any dispute hereunder, provided FINEP’S right to choose the courts of its head office.

The pages of this Agreement are initiated by Priscilla Mouta Nunes, counsel to FINEP, who is enrolled with the Brazilian Bar Association, Rio de Janeiro Chapter, under No. 134.164, upon authorization of the undersigned legal representatives.

IN WITNESS WHEREOF, the parties execute this instrument in two (2) counterparts of equal contents and form, for one sole effect, together with the undersigned witnesses.

Rio de Janeiro, November 10, 2010.

By FINANCIADORA DE ESTUDOS E PROJETOS – FINEP

By	/s/ Luis Manuel Rebelo Fernandes	/s/ Eduardo Moreira da Costa
	Luis Manuel Rebelo Fernandes	Eduardo Moreira da Costa
	Chief Executive Officer	Officer
	CPF:	CPF:
	ID:	ID:

By BORROWER – AMYRIS BRASIL S/A:

(sgd) (sgd) [illegible] Collier Felipe Moreira Caram CPF: 218.950.128-80 CPF: 033.724.916-82

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WITNESSES:
/s/ Rômulo Carvalho	/s/ Tiago Ribeiro Mendes
Name: Rômulo Carvalho	Tiago Ribeiro Mendes
CPF:	CPF:

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EXHIBIT I

ASSETS SUBJECT TO CHATTEL MORTGAGE

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Asset		Brand	Model	Series
1.	15-L Fermenter	Tecnal	Techbio 15	08080019, 08080016, 08080014, 09010173, 08080015
2.	15-L Fermenter	Tecnal	Techbio 15	09060040, 09050040, 09060039, 08080018, 09060039
3.	Ultra freezer	Sanyo	MDF-U33V	890122
4.	Centrifuge	Sorval	Evolution RC #728211	U28Y-421522-VT
5.	Image Digitizer	Kodak	Gel Logic 1500	C96173
6.	Refrigerated centrifuge	Eppendorf	5810R	5811XM341440
7.	Sugar analyzer	YSI Life Sciences	7100 MBS	08G000035
8.	Lyophilizer	Matrin Christ	Alpha 2-4 LD Plus	14392, 31115102
9.	HPLC -ion chromatograph	Dionex	ICS-3000	061775, 08100804, 08100727, 08100879
10.	Gas chromatograph	Agilent	7890A	CN10844150, CN84251033
11.	ATAGO Spectropolarimeter	ATAGO	AP-300	082702M
12.	Shaker	Thermo Scientific	Labline MaxQ 5000 #SHKE5000-7	1.41408E+12
13.	300-L Fermenter	Sartorius	Biostat D300-DCU	L04329-1, -2
14.	300-L Fermenter	Sartorius	Biostat D300-DCU	L04329-1, -3
15.	Hydrogenator	PARR Instruments	9003 TRS	9003T-0811-8795
16.	Gas chromatograph	Agilent	G3440AX	CN10923004, USK0085016
17.	Continuous centrifuge	Alfa-laval	LAPX 404	9160
18.	Continuous centrifuge	Alfa-laval	DX 203B-24-60	4174354/2008
19.	LPG vertical boilers – 8kgf/cm2 500 kg/h	Domel	VSVG 495 -GLP	81609361, 08169362
20.	LPG vertical boilers – 8kgf/cm2 500 kg/h	Domel	VSVG 495 -GLP	81609361, 08169363

Reference No. 0434/08

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21.	Centrifuge DX409	JDF	DX 409 B34	4001403
22.	Frings Shaker	Frings	TRG 1000	1554
23.	Dechlorine Filter 2,000L/H, Carbon Steel	Equipar	-	7611
24.	Water and Oil Tank 9,000 liters, Stainless Steel 304	Equipar	-	7618
25.	Honey Storage Tank 15,000 Liters, Carbon Steel	Equipar	-	7609
26.	Water Storage Tank 10,000 Liters, Carbon Steel	Equipar	-	7610
27.	Must Storage Tank 3,500 Liters, Stainless Steel 304	Equipar	-	7612
28.	Clarified Must Storage Tank 3,500 Liters, Stainless Steel	Equipar	-	7613
29.	Hybrid Fermentation Tank (SIP) 5,000 Liters, Stainless Steel 304	Equipar	-	7615
30.	Bubble Colum Fermentation Tank (SIP) 5,000 Liters	Equipar	-	7616
31.	Aseptic Must Pressure Vessel (SIP) 7,000 Liters, Stainless Steel	Equipar	-	7614
32.	Pre-Fermentation Pressure Vessel with Shaker (SIP) 4,000 Liters	Equipar	-	7617
33.	Compressor 6.8m3/min Water Cooled	Equipar	-	API781184
34.	Bearing Structure – Cooling Tower – Amyris Ma	Equipar	-	Not applicable
35.	Fermenter Access Platform, Stainless Steel 304	Equipar	-	Not applicable
36.	Electrical protection panel (CMM) and Transformer – Amyris D	Equipar	-	Not applicable
37.	Water and Oil Tank 600 Liters, Stainless Steel 304	Equipar	-	7839
38.	CIP Tank with Shaker, Heating, Insulation, 2,500 L, A	Equipar	-	7625
39.	CIP Tank with Shaker, 200 L, Stainless Steel 304 – Tag TQ 14	Equipar	-	7626
40.	CIP Tank with Shaker, 200 L, Stainless Steel 304 – Tag TQ 15	Equipar	-	7648

41.	CIP Tank with Shaker, Heating, Insulation, 2,500 L, A	Equipar	-	7647
42.	CIP Tank with Shaker, Heating, Insulation, 2,500 L, A	Equipar	-	7646
43.	FENE Oil Storage Tank 600 Liters, Stainless Steel 304	Equipar	-	7621
44.	Cold Vinasse Tank 1,000 Liters, Stainless Steel 304	Equipar	-	7619
45.	Cold Vinasse Tank 15,000 Liters, Fiberglass	Equipar	-	10857
46.	Cooling Tower 90,000 L/H	Equipar	-	0005/08
47.	Oil Condenser Pressure Vessel – Exchanging Area 1.0m2	Equipar	-	7624
48.	Compressed Air Pressure Vessel 3,000 Liters, Carbon Steel	Equipar	-	OP7627

EX-10.02

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

Exhibit 10.02

MODIFICATION P00003 TO THE TECHNOLOGY INVESTMENT AGREEMENT

Between

AMYRIS, INC.,

5885 Hollis Street Suite 100

Emeryville, CA 94608

And

The Defense Advanced Research Projects Agency

675 North Randolph Street

Arlington, VA 22203-2114

Concerning

Improving the Timeline for Scaling Up Molecules from Proof Of Concept to Market Reducing Time and Cost

(Mgs TO Kgs)

Agreement No.: HR0011-15-3-0001

DARPA Order No.: HR0011621265

Total Amount of the Agreement:	$	50,721,349
Total Estimated Government Funding of the Agreement:	$	35,160,011
Contractor Share Contribution	$	15,551,338
Funds Obligated:	$	23,324,088
Funds Obligated by this Modification	$	6,648,707

Recipient Identification Number/Codes:	DUNS: 185930182
	CAGE: 47QN9
	TIN: 55-0856151

Authority: 10 U.S.C. § 2371

All provisions, terms, and conditions set forth in this Agreement are applicable and in full force and effect except as specified otherwise herein.

FOR AMYRIS, INC.	FOR THE UNITED STATES OF AMERICA, THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY
/s/ Joel R. Cherry	/s/ Michael S. Mutty
Joel R. Cherry, President, R&D	Michael S. Mutty Agreements Officer Contracts Management Office
6/20/2016	6/20/2016
(Date)	(Date)

HR0011-15-3-0001

P00003

In order to incorporate changes to the Technology Investment Agreement identified below, replace Attachment 1 Statement of Work with Revision 2, replace Attachment 3 Total Agreement Funding Plan and Payable Milestones and Corresponding Payment Schedule with Revision 3, replace Attachment 5 List of Intellectual Property Assertions by the Performer with Revision 1, replace Attachment 6 List of Property Greater than $5,000 with Revision 1, and provide additional incremental funding, the parties agree to the following changes:

1. The Technology Investment Agreement is revised to: 1) revise the Technology Investment Agreement Table of Contents page to annotate Agreement Revision 3 and page number revisions tied to the changes made in paragraph 1. above and to annotate Attachment 1 - Revision 2, Attachment 3 - Revision 3, Attachment 5 - Revision 1, and Attachment 6 - Revision 1; 2) remove revision identification and incremental funding data from the cover page to Article V, Obligation and Payment, subparagraph C. previously titled Accounting and Appropriation Data; now titled Agreement Value, Agreement Funding and Accounting and Appropriation Data; 3) incorporate additional incremental funding; 4) incorporate under Article VII: Patent Rights, subparagraph A. Allocation of Principal Rights, subparagraph numbering and a new subparagraph 3. to incorporate Flavor and/or Fragrance exclusion language; and 5) add a new subparagraph (e) to subparagraph B.1 of Article IX: Foreign Access to Technology, in order to add an exception solely regarding Flavor and/or Fragrance uses. Changes are shown below.

Change 1)

TABLE OF CONTENTS – Revision 3

ARTICLES		PAGE
ARTICLE I	Scope of the Agreement	3
ARTICLE II	Term	7
ARTICLE III	Management of the Project	10
ARTICLE IV	Agreement Administration	11
ARTICLE V	Obligation and Payment	12
ARTICLE VI	Disputes	16
ARTICLE VII	Patent Rights	17
ARTICLE VIII	Data Rights	21
ARTICLE IX	Foreign Access to Technology	22
ARTICLE X	Title to and Disposition of Property	23
ARTICLE XI	Civil Rights Act	24
ARTICLE XII	Security	24
ARTICLE XIII	Subcontractors	24
ARTICLE XIV	Key Personnel	24
ARTICLE XV	Order of Precedence	25
ARTICLE XVI	Execution	25
ARTICLE XVII	Applicable Law	25
ARTICLE XVIII	Severability	25
ARTICLE XIX	Data Sharing Plan and Status Reporting	25

ATTACHMENTS

ATTACHMENT 1 – Revision 2	Statement of Work
ATTACHMENT 2	Report Requirements
ATTACHMENT 3 – Revision 3	Total Agreement Funding Plan and Payable Milestones and Corresponding Payment Schedule
ATTACHMENT 4	Funding Schedule
ATTACHMENT 5 – Revision 1	List of Intellectual Property Assertions by the Performer
ATTACHMENT 6 – Revision 1	List of Property Greater than $5,000
ATTACHMENT 7	Certifications for Agreement No. HR0011-15-3-0001

HR0011-15-3-0001

P00003

Change 2) and Change 3)

C.       Agreement Value, Agreement Funding and Accounting and Appropriation Data

Agreement Value

Total Amount of the Agreement: $50,721,349

Total Estimated Government Funding of the Agreement: $35,160,011

Agreement Funding

TIA Award: $ 6,035,686

P00002 $10,639,695

P00003 $ 6,648,707

Total Funds Obligated: $23,324,088

Accounting and Appropriation Data

TIA Award

CLIN/SLIN/ACRN: 0001/01/AA

LOA: 012199 097 0400 000 N 20152016 D 1320 BLTM66 2015.MBT-02.CORE.A DARPA 255

FUNDING AMOUNT: $6,035,686

P00002

CLIN/SLIN/ACRN: 0001/01/AB

LOA: 012199 097 0400 000 N 20162017 D 1320 BLTM66 2016.MBT-02.CORE.A DARPA 255

FUNDING AMOUNT: $10,639,695

P00003

CLIN/SLIN/ACRN: 0001/01/AB

LOA: 012199 097 0400 000 N 20162017 D 1320 BLTM66 2016.MBT-02.CORE.A DARPA 255

FUNDING AMOUNT: $6,648,707

Change 4)

ARTICLE VII: PATENT RIGHTS

A.       Allocation of Principal Rights

1. Unless the Performer shall have notified DARPA (in accordance with subparagraph B.2 below) that the Performer does not intend to retain title, the Performer shall retain the entire right, title, and interest throughout the world to each Subject Invention consistent with the provisions of this Article and 35 U.S.C. § 202. With respect to any Subject Invention in which the Performer retains title, the Government shall have a nonexclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the Government the Subject Invention throughout the world.

2. With regard to Inventions made under this Agreement that are not Subject Inventions, i.e. Inventions relating to genetically modified organisms, strains, or any compounds or products made by or from such organisms or strains that are conceived or first actually reduced to practice in the performance of the Program, the Government retains a right to request from Performer a nonexclusive, nontransferable, irrevocable license, on fair and reasonable terms, to such Inventions to have such Inventions practiced on behalf of the Government throughout the world. The Government will provide Performer with written notice identifying the specific Invention to which it is requesting such license. Prior to granting such license, the Parties agree to negotiate in good faith fair and reasonable terms under which the Performer would be the exclusive supplier/manufacturer to the Government of the desired compound or product under the Government’s license. Upon agreement of such fair and reasonable terms between the Performer and the Government, the Performer shall grant the Government the nonexclusive license described

HR0011-15-3-0001

P00003

above to such identified Inventions. In the event that no agreement is reached between Performer and Government with regard to said fair and reasonable terms on Performer’s supply/manufacturing rights, Performer shall nonetheless grant the Government a nonexclusive, nontransferable, irrevocable license, on fair and reasonable terms, to such Inventions to have such Inventions practiced on behalf of the Government throughout the world. Failure to reach agreement on fair and reasonable terms will be resolved in accordance with Article VI. Disputes.

3. Notwithstanding anything to the contrary in subparagraph A.2 above, the Parties agree that any license to the Government to any Inventions made under this Agreement that are not Subject Inventions expressly excludes any and all rights to make, have made, use, sell, offer for sale, or import any compound or product as, or in, a Flavor or Fragrance, unless the Parties reasonably determine that a national security interest requires the Government to use such compound or product as, or in, a Flavor or Fragrance, in which case subparagraph A.2 will also be applicable to such use. As used in this paragraph, “Flavor” means an ingredient(s) whose intended or primary functionality (individually or as part of a blend with auxiliary materials) is to impart, modify, boost or enhance a desirable taste, flavor or sensation, or to conceal, modify or minimize an undesirable taste, flavor or sensation, in materials designed for consumption (including food, beverages, drugs, tobacco and any animal feed). As used in this paragraph, “Fragrance” means an ingredient(s) whose intended or primary functionality (individually or as part of a blend with auxiliary materials) is to impart, modify, boost or enhance a desirable scent or odor or to conceal, modify or minimize an undesirable scent or odor, in consumer and industrial grade products.

Change 5)

ARTICLE IX: FOREIGN ACCESS TO TECHNOLOGY

B. 1.(e) a license and transfer of Technology solely to make, have made, use, offer for sale, sell, or import a compound or product as, or in, a Flavor (as defined in Article VII.A.3) or Fragrance (as defined in Article VII.A.3).

2. Attachment 1 Statement of Work - Revision 2 is issued to remove Subtask F.2.5 (Month 6), modify Subtask F.3.5 (Month 12) and add Subtask F.3.6 (Month 12).

3. Attachment 3 Total Agreement Funding Plan and Payable Milestones and Corresponding Payment Schedule - Revision 3 is issued to move funding associated with the Statement of Work change identified in paragraph 2. Above and incorporate the incremental funding line of accounting designation in the CLIN/SLIN/ ACRN column, as shown in bold in the Attachment.

4. Attachment 5 List of Intellectual Property Assertions by the Performer is deleted and replaced with Attachment 5 - Revision 1 in order to incorporate changes in Arzeda Tables 3 and 4; incorporate Agilent Technologies, Inc. Tables 5 and 6; incorporate Ruprecht-Karls-Universität Heidelberg, Professor Oliver Trapp, and/or Trapp ChemTech Inc. Tables 7 and 8, as listed below by title:

Table 5	List of Technical Data and Computer Software of Agilent Technologies, Inc.
Table 6	Exemplary, Non-limiting List of Patents and Patent Applications, Pending or Issued as of, September 11, 2015, of Agilent Technologies, Inc.
Table 7	List of Technical Data and Computer Software of Ruprecht-Karls-Universität Heidelberg, Professor Oliver Trapp, and/or Trapp ChemTech Inc.
Table 8	Exemplary, Non-limiting List of Patents and Patent Applications, Pending or Issued as of, September 11, 2015, of Ruprecht-Karls-Universität Heidelberg, Professor Oliver Trapp, and/or Trapp ChemTech Inc.

5. Attachment 6 List of Property Greater than $5,000 is deleted and replaced with Attachment 6 - Revision 1 in order to incorporate the following Modules H, I, and K changes:

Delete:

H	[*	1	$424,530	$424,530
H	[*	1	$20,258	$20,258

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

P00003

H	[*	1	$33,440	$33,440
Add:
H	[*	1	$399,344	$399,344
H	[*	1	$5,411	$5,411
H	[*	1	$33,848	$33,848
H	[*	1	$26,919	$26,919
H	[*	1	$18,456	$18,456
H	[*	1	$61,923	$61,923
H	[*	1	$14,690	$14,690
H	[*	2	$14,358	$28,716
I	[*	1	$93,000	$93,000
I	[*	2	$12,050	$24,100
K	[*	1	$8,477	$8,477

6. All provisions, terms, and conditions set forth in this Agreement are applicable and in full force and effect except as specified otherwise herein.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

TECHNOLOGY INVESTMENT AGREEMENT

BETWEEN

AMYRIS, INC.,

5885 HOLLIS STREET SUITE 100

EMERYVILLE, CALIFORNIA 94608

AND

THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY

675 NORTH RANDOLPH STREET

ARLINGTON, VA 22203-2114

CONCERNING

IMPROVING THE TIMELINE FOR SCALING UP MOLECULES FROM PROOF OF CONCEPT

TO MARKET REDUCING TIME AND COST

(MGS TO KGS)

Agreement No.: HR0011-15-3-0001 – Revision 3

DARPA Order No.: HR0011518718

Total Amount of the Agreement: $50,721,349

Total Estimated Government Funding of the Agreement: $35,160,011

Funds Obligated: See Article V.C

Authority: 10 U.S.C. § 2371

This Agreement is entered into between the United States of America, hereinafter called the Government, represented by The Defense Advanced Research Projects Agency (DARPA), and AMYRIS, INC., a corporation organized and existing under the laws of the State of Delaware with its principal place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608 pursuant to and under U.S.

Federal law.

FOR AMYRIS, INC	FOR THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY
/s/ Joel R Cherry       6/20/2016	/s/ Michael S. Mutty   2016.06.20
(Signature & Date)	(Signature & Date)
Joel R. Cherry, President R&D	Michael S. Mutty Agreements Officer
(Name, Title)	(Name, Title)

Agreement HR0011-15-3-0001

TABLE OF CONTENTS

ARTICLES		PAGE
ARTICLE I	Scope of the Agreement	3
ARTICLE II	Term	7
ARTICLE III	Management of the Project	10
ARTICLE IV	Agreement Administration	11
ARTICLE V	Obligation and Payment	12
ARTICLE VI	Disputes	15
ARTICLE VII	Patent Rights	16
ARTICLE VIII	Data Rights	19
ARTICLE IX	Foreign Access to Technology	21
ARTICLE X	Title to and Disposition of Property	22
ARTICLE XI	Civil Rights Act	23
ARTICLE XII	Security	23
ARTICLE XIII	Subcontractors	23
ARTICLE XIV	Key Personnel	23
ARTICLE XV	Order of Precedence	23
ARTICLE XVI	Execution	23
ARTICLE XVII	Applicable Law	24
ARTICLE XVIII	Severability	24
ARTICLE XIX	Data Sharing Plan and Status Reporting	24

ATTACHMENTS

ATTACHMENT 1 – Revision 2	Statement of Work
ATTACHMENT 2	Report Requirements
ATTACHMENT 3 – Revision 3	Total Agreement Funding Plan and Payable Milestones and Corresponding Payment Schedule
ATTACHMENT 4	Funding Schedule
ATTACHMENT 5 – Revision 1	List of Intellectual Property Assertions by the Performer
ATTACHMENT 6 – Revision 1	List of Property Greater than $5,000
ATTACHMENT 7	Certifications for Agreement No. HR0011-15-3-0001

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ARTICLE I: SCOPE OF THE AGREEMENT

A.       Background

Performer is a leader in applying synthetic biology technologies to engineer living organisms into manufacturing platforms that are able to produce a wide variety of target molecules, many of which are impossible to produce through traditional manufacturing processes. While current technologies are highly advanced, they suffer from a lack of integration and automation. By focusing on the same principles that made the United States the leaders in traditional manufacturing, namely standardized engineering and efficiency gains through automation, the Performer seeks, through funding in this Agreement, to develop a state of the art open bio-fabrication facility that will shorten the scale-up time and cost by using biology to produce molecules. Many of these molecules are directly relevant to the DoD mission due to their unique chemical properties that enable their use as fuels, lubricants, anti-fouling agents, antibiotics, and adhesives while also providing building blocks for novel families of materials. DARPA’s interest in synthetic biology rises from its potential application to manufacturing. Biological manufacturing is in its infancy and the work required to reduce the time, effort, and cost needed to develop a new microbe is risky and at odds with the work needed to bring a product to market which is the chief goal of any company seeking to capitalize on the technology. The Agreement supports research with a long-term perspective that will enable academic and commercial participants to perform cutting edge research with less effort and cost than ever before. In addition to producing molecules relevant to the DoD, the commercial opportunities are immense since virtually any molecule made through traditional manufacturing processes can be replicated using biology as a catalyst. Although engineering cellular factories has been intermittently successful, the cost and time required for success have been prohibitive. The Performer’s new technological approach will develop new molecules and materials while at the same time improving efficacy and efficiency. As a result of these improvement, the United States will reduce production time to under three years and at less than $10M per molecule while simultaneously handling 100 molecules, a 20X improvement. To achieve these innovations, the Performer will focus on technology development addressing metabolic pathway and enzyme design, strain construction, phenotypic measurements, large-scale data analysis, and strain optimization. To ensure success, the Performer will complement its expertise in strain engineering by partnering with companies and academic laboratories that are leaders in their field. Upon the completion of this agreement, the capacity to perform biological engineering will far surpass current capabilities. The United States will possess state of the art facilities for design and biomanufacturing of existing and novel molecules and materials.

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B.       Definitions

Affiliate: means, with respect to an entity, any person or entity that directly or indirectly, through one or more intermediaries, controls, is controlled by, or is under common control with such first entity. For purposes of this definition, “control”, “controlled by”, and “under common control with” mean (i) the possession, directly or indirectly, of the power to direct the management or policies of an entity, whether through the ownership of voting securities, by contract relating to voting rights or corporate governance, or otherwise or (ii) the ownership, directly or indirectly, of more than fifty percent (50%) of the voting securities or other ownership interest of an entity.

Agreement: The body of this Agreement and Attachments 1 – 7, which are expressly incorporated in and made a part of the Agreement.

Collaborators: A third party in a contractual arrangement with the Performer or with a Subcontractor, whether executed before or after the Effective Date, under which arrangement the Performer or a Subcontractor has agreed to jointly research, develop and/or commercialize a technology or product with such third party and has an “active role” in such arrangement. For the avoidance of doubt, an “active role” by the Performer or a Subcontractor is a contractual relationship (1) that involves more than the mere transfer of intellectual property and (2) where the Performer or a Subcontractor has a significant participation in decision making and/or funding of the activities.

Data: Recorded information, regardless of form or method of recording, which includes but is not limited to, scientific or technical data, software, trade secrets, and mask works, in each case developed or generated by the Performer or its Subcontractors in performing the Program under this Agreement. The term “Data” does not include financial, administrative, cost, pricing or management information.

Effective Date: means November 1, 2015.

Foreign Firm or Institution: A firm or institution organized or existing under the laws of a country other than the United States, its territories, or possessions. The term includes, for purposes of this Agreement, any agency or instrumentality of a foreign government; and firms, institutions or business organizations which are owned or substantially controlled by foreign governments, firms, institutions, or individuals.

Government: The United States of America, as represented by DARPA.

Government Purpose Rights: The rights to use, duplicate, or disclose Data, in whole or in part and in any manner, for Government Purposes only, and to have or permit others to do so for Government Purposes only.

Government Purpose: Any activity in which the Government is a party, including cooperative agreements with international or multi-national defense organizations or sales or transfers by the Government to foreign governments or international organizations. Government Purposes include competitive procurement, but do not include the rights to use, modify, reproduce, release, perform, display, or disclose Data for commercial purposes or authorize others to do so.

Invention: Any invention or discovery which is or may be patentable or otherwise protectable under Title 35 of the United States Code.

Know-How: All information including, but not limited to discoveries, formulas, materials, Inventions, processes, ideas, approaches, concepts, techniques, methods, software, programs, documentation, procedures, firmware, hardware, technical data, specifications, devices, apparatus and machines.

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Limited Rights: The rights to use, modify, reproduce, release, perform, display, or disclose Data, in whole or in part, within the Government. The Government may not, without the written permission of the Party asserting limited rights, release or disclose applicable Data outside the Government, use the applicable Data for manufacture, or authorize the applicable Data to be used by another party, except that the Government may reproduce, release, or disclose such Data or authorize the use or reproduction of the applicable Data by persons outside the Government if -

(i) The reproduction, release, disclosure , or use is:

A. Necessary for emergency repair and overhaul; or

B. A release or disclosure to

1. A covered Government support contractor in performance of its covered Government support contract for use, modification, reproduction, performance, display or release or disclosure to a person authorized to receive Limited Rights Data; or

2. A foreign government, of such Data other than detailed manufacturing or process Data, when use of such Data by the foreign government is in the interest of the Government and is required for evaluational or informational purposes;

(ii) The recipient of the applicable Data is subject to a prohibition on the further reproduction, release, disclosure, or use of the Data; and

(iii) The Performer, or its subcontractor asserting the restriction is notified of such reproduction, release, disclosure, or use.

Made: Relates to any Invention means the conception or first actual reduction to practice of such Invention.

Parties: The Government (represented by DARPA) and the Performer.

Payable Milestone: A Program-related task or tasks identified in Attachment 3 for which a corresponding payment (also identified in Attachment 3) will be made by the Government to the Performer upon the Government’s verification, in accordance with this Agreement, that the Performer (or a Subcontractor) accomplished such task(s).

Performer: AMYRIS, INC. a corporation organized and existing under the laws of the State of

Delaware with its principal place of business at 5885 Hollis Street, Suite 100, Emeryville, California

94608

Practical Application: To manufacture, in the case of a composition of product, to practice, in the case of a process or method, or to operate, in the case of a machine or system; and, in each case, under such conditions as to establish that the Subject Invention is capable of being utilized and that its benefits are, to the extent permitted by law or Government regulations, available to the public on reasonable terms. For the avoidance of doubt, the Parties acknowledge that “Practical Application” under this Agreement may not include actual commercialization of Subject Invention(s) hereunder because such Subject Invention(s) are likely to be Tools (e.g., it is envisioned that the Tools resulting from the research carried out under this Agreement will later – outside of this Agreement - be used by the Performer and its Subcontractors to develop commercial products).

Program: Research and development being conducted by the Performer and its Subcontractors under this Agreement, as set forth in Article I, paragraph C and in Attachment 1, Statement of Work.

Property: Any tangible personal property other than property actually consumed during the execution of work under this Agreement.

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Subcontractor: Those persons or entities that, per a written agreement with the Performer, will perform certain of the Payable Milestones. As of the date of this Agreement, the Subcontractors consist of Agilent Technologies, Inc., Arzeda Corporation, m2p-labs GmbH, Ruprecht-Karls-Universität Heidelberg, and Bruker Corporation.

Subject Invention: Any Invention conceived or first actually reduced to practice in the performance of the Program under this Agreement that is capable of use as a Tool for making or altering a genetically modified organism; provided however, any Inventions, regardless when conceived or reduced to practice, covering a genetically modified organism, a strain, or any compound or product made by or from an organism or strain shall not be considered “Subject Inventions” hereunder. For the avoidance of doubt, no Inventions conceived or reduced to practice prior to the Effective Date, excluding subject inventions conceived or first actually reduced to practice under the Amyris Living Foundries TIA HR0011-12-3-0006, shall be considered performed “under this Agreement.”

Technology: Discoveries, innovations, Know-How and Inventions, whether patentable or not, including computer software, recognized under U.S. law as intellectual creations to which rights of ownership accrue, including, but not limited to, patents, trade secrets, maskworks, and copyrights, developed under this Agreement.

Term: has the meaning set forth in Article II, paragraph A.

Tools: Software, analytical methods, standard operating procedures, and workflow processes.

Unlimited Rights: Rights to use, duplicate, release, or disclose Data, in whole or in part, in any manner and for any purposes whatsoever, and to have or permit others to do so.

C.       Scope

1.       The Performer shall perform the Program, which is intended to build an open BioFab that shortens the timeline for scaling up molecules from proof of concept to market to two to three years, reduces the cost of such development to less than $10 million per molecule, and simultaneously handles a hundred molecules. Success will be demonstrated by delivering 1 kg of material for 10 molecules generated by an integrated pipeline that enables the biological production of metric tons of any subsequent molecule in two to three years. The Program shall be carried out in accordance with the Statement of Work incorporated in this Agreement as Attachment 1. The Performer shall submit or otherwise provide all documentation required by Attachment 2, Report Requirements.

2.       The Performer shall be paid for each Payable Milestone accomplished in accordance with the Schedule of Payments and Payable Milestones set forth in Attachment 3 and the procedures of Article V. The Schedule of Payments and Payable Milestones set forth in Attachment 3 may be revised or updated in accordance with Article III, subject to mutual agreement of the Parties.

3.       The Government and the Performer estimate that the Statement of Work for this Agreement can only be accomplished with the Performer’s provision during the Term of the “Performer Contribution”, as detailed in the Total Agreement Funding Plan set forth in Attachment 3 and the Funding Schedule set forth in Attachment 4. The Total Agreement Funding Plan and the Funding Schedule may be revised or updated in accordance with Article III, subject to mutual agreement of the Parties. The Performer intends and, by entering into this Agreement, undertakes to cause the Performer Contribution to be provided. However, if either the Government or the Performer is unable to provide its respective funding (in the case of the Government) or the Performer Contribution (in the case of the Performer) for the Program, the other Party

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Agreement HR0011-15-3-0001

may reduce its funding or Performer Contribution, whichever is applicable to it, for the Program by a proportional amount. Throughout the Term, the Parties, through the Performer’s routine reports to the Government, will monitor the Performer’s satisfaction of the Performer Contribution and will promptly address, in good faith, any divergence or shortfall in the final Performer Contribution amount anticipated by the Performer (e.g., the Performer purchases Property for the Program at a price significantly cheaper than what was anticipated when establishing the Performer Contribution) and its effect, if any, on the Government’s funding obligation under this Agreement.

D.       Goals / Objectives

1.       The goal of this Agreement is for the Performer to investigate and build a BioFab that scales up molecules from proof of concept to market in less time and at less cost, as described under Scope above. The goal is to accomplish this by incorporating radical innovations into key modules at each stage of the Design-Build-Test-Learn cycle as described in detail Amyris Proposal “Mgs to Kgs” dated February 3, 2015. The modules will be interdependent and align within an integrated pipeline. The foundation is a set of measurement technologies with various levels of risk. In addition to new algorithms for pathway prediction, data analysis and hypothesis generation, the BioFab’s testing and optimization of up to 450 molecules from a large metabolic space will require a paradigm shift from a high-throughput, single-molecule screening platform to a high throughput, molecule-agnostic screening platform that is predictive of performance to a large scale. To address the gaps in throughput, quality and scale, a testing platform that utilizes a tiered approach to promote strains will be developed. Although individual tiers exist in some form at various institutions and companies (including at the Performer), there is not a single platform that has managed to encompass all of them into a single pipeline at the proposed scale.

2.       The Government will have continuous involvement with the Performer. The Government will also obtain access to research results and certain rights in Data and Subject Inventions pursuant to Articles VII and VIII. Government and the Performer are bound to each other by a duty of good faith and best research effort in achieving the goals of the Program.

3.       This Agreement is an "other transaction" pursuant to 10 U.S.C. § 2371. The Parties agree that the principal purpose of this Agreement is for the Government to support and stimulate the Performer to provide its best effort in advanced research and technology development and not for the acquisition of property or services for the direct benefit or use of the Government. The Performer will be paid a fixed amount for each Payable Milestone accomplished in accordance with the Payable Milestones and Corresponding Payment Schedule set forth in Attachment 3 and the procedures of Article V. The Parties agree that the amount payable to Performer for an accomplished Payable Milestone will be unaffected by whether Performer ends up expending more or less effort to accomplish such Payable Milestone than the Parties assumed would be required to accomplish it. This Agreement is not intended to be, nor shall it be construed as, by implication or otherwise, a partnership, a corporation, or other business organization.

ARTICLE II: TERM

A.       Term of this Agreement

The Program commences upon the Effective Date and continues for forty-eight (48) months, unless extended as described in paragraph C below, (the “Term”) and is split into three development and operational phases described below and depicted in the table:

“Dev” – in the first twenty-four months, the initial set of strain designs and testing will be generated using existing infrastructure and processes, while simultaneously developing the new technology platforms simultaneously;

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Agreement HR0011-15-3-0001

“DevOps” – newly developed technology platforms will be transferred to pipeline operations as part of the beta-testing transition process;

“Ops” – once the technology transfer is completed, the new technologies will be part of standard operations.

If all Government funds committed for the Program and the Performer Contribution are expended prior to the expiration of the Term, the Parties have no obligation to continue performance of the Program and may elect to cease development at that point.

Provisions of this Agreement, which, by their express terms or by necessary implication, apply for periods of time other than specified herein, shall be given effect, notwithstanding this Article.

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[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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B.       Termination Provisions

Subject to a reasonable determination that the Program will not produce beneficial results commensurate with the expenditure of resources, either Party may terminate this Agreement by written notice to the other Party, provided that such written notice is preceded by consultation between the Parties. In the event of a termination of the Agreement under this paragraph B, it is agreed that disposition of Data shall be in accordance with the provisions set forth in Article VIII, Data Rights. The Government and the Performer will negotiate in good faith a reasonable and timely adjustment of all outstanding issues between the Parties as a result of termination under this paragraph B. Failure of the Parties to agree to a reasonable adjustment will be resolved pursuant to Article VI, Disputes. The Government has no obligation to pay the Performer beyond the last completed and paid Payable Milestone if the Performer decides to terminate under this paragraph B. For the avoidance of doubt, any termination under this paragraph B by either Party does not require repayment by the Performer of any Payable Milestone amounts already received by the Performer.

C.       Extending the Term

The Parties may extend, by mutual written agreement, the Term if funding availability and research opportunities reasonably warrant. Any extension shall be formalized through modification of the Agreement by the DARPA Agreements Officer and the Performer’s Administrator.

ARTICLE III: MANAGEMENT OF THE PROJECT

A.       Management and Program Structure

The Performer shall be responsible for the overall technical and program management of the Program, and technical planning and execution shall remain with the Performer. The DARPA Agreements Officer’s Representative, in consultation with the DARPA Program Manager or DARPA management, shall provide recommendations to Program developments and technical collaboration and be responsible for the review and verification of the Payable Milestones.

B.       Program Management Planning Process

Program planning will consist of an Annual Program Plan with inputs and review from the Performer and DARPA management, containing the detailed schedule of research activities and Payable Milestones. The Annual Program Plan will consolidate quarterly adjustments in the Program’s research schedule, including revisions/modification to Payable Milestones.

1.       Initial Program Plan: The Performer will follow the initial program plan that is contained in the Statement of Work, Attachment 1, and in the Payable Milestones and Corresponding Payment Schedule, Attachment 3.

2.       Overall Program Plan Annual Review

(a)       The Performer, with DARPA Agreements Officer’s Representative review, in consultation with the DARPA Program Manager or DARPA management, will prepare an overall Annual Program Plan in the last month of each Agreement year (i.e., October). The Annual Program Plan will be presented and reviewed at an annual site review, to be held within the sixty (60) days of each subsequent Agreement year, which will be attended by the Performer’s Key Personnel (as defined in Article XIV), the DARPA Agreements Officer’s Representative, senior DARPA management (as appropriate), and other DARPA program managers and personnel (as appropriate). The Performer, with DARPA participation and review,

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will prepare a final Annual Program Plan following such annual site review as more fully described in Attachment 2, Report Requirements.

(b)       The Annual Program Plan provides a detailed schedule of the Program’s research activities, commits the Performer to use its best efforts to meet specific performance objectives, includes forecasted expenditures and describes the Payable Milestones. The Annual Program Plan will consolidate all prior adjustments in the Program’s research schedule, including revisions/modifications to the Payable Milestones. Recommendations for changes, revisions or modifications to the Agreement which result from this annual review process shall be made in accordance with the provisions of Article III, paragraph C.

C.        Modifications

1.       As a result of the Parties’ meetings (in person or videoconference) or annual reviews or at any other time during the Term, the Program’s research progress or results or other changes in circumstances (e.g., availability of required materials or equipment from external vendors, legal freedom to operate, etc.) may indicate that a change in the Statement of Work and/or the Payable Milestones would be beneficial to Program’s objectives. Recommendations for modifications, including justifications to support any changes to the Statement of Work and/or the Payable Milestones, will be documented in a letter and submitted by the Performer to the DARPA Agreements Officer’s Representative with a copy to the DARPA Agreements Officer. This documentation letter will detail the technical, chronological, and financial impact of the proposed modification to the Program. The Performer shall approve any Agreement modification. The Government is not obligated to pay for additional or revised Payable Milestones until the Payable Milestones and Corresponding Payment Schedule, Attachment 3, is formally revised by the DARPA Agreements Officer and made part of this Agreement.

2.       The DARPA Agreements Officer’s Representative shall be responsible for the review and verification of any recommendations to revise or otherwise modify the Agreement, the Statement of Work, the Payable Milestones and Corresponding Payment Schedule, or any other proposed changes to the terms and conditions of this Agreement.

3.       For minor or administrative Agreement modifications (e.g., changes in the paying office or appropriation data, changes to Government or the Performer’s personnel identified in the Agreement, etc.), no signature is required by the Performer.

ARTICLE IV: AGREEMENT ADMINISTRATION

Unless otherwise provided in this Agreement, approvals permitted or required to be made by the Government may be made only by the DARPA Agreements Officer. Administrative and contractual matters under this Agreement shall be referred to the following representatives of the Parties:

A.Government Points of Contact:

DARPA Agreements Officer:

DARPA Program Manager:

DARPA Agreements Officer’s Representative (AOR):

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DARPA Administrative Agreements Officer (AAO):

DARPA Assistant Director, Program Management (ADPM)

B.       Performer Points of Contact

Administrator:

, Program Manager, R&D,

Contracting:

, General Counsel,

Program Manager:

, PI,

BioAnalytics Group Leader:

, Co-PI,

Each Party may change its representatives named in this Article by written notification to the other Party. The Government will effect the change as stated in Article III, C.3 above.

ARTICLE V: OBLIGATION AND PAYMENT A. Obligation

1.       The Government’s liability to make payments to the Performer is limited to only those funds obligated under the Agreement or by modification to the Agreement. The Government may obligate funds to the Agreement incrementally.

2.       If modification of a Payable Milestone becomes necessary in performance of this Agreement, pursuant to Article III, paragraph C, the DARPA Agreements Officer and the Performer’s Administrator shall execute a revised Payable Milestones and Corresponding Payment Schedule consistent with the then current Annual Program Plan.

B.       Payments for Accomplished Payable Milestones

1.       The Performer has, and agrees to maintain, an established accounting system, which complies with Generally Accepted Accounting Principles and the requirements of this Agreement and shall ensure that appropriate arrangements have been made for receiving, distributing and accounting for all funding. An acceptable established accounting system is one in which all cash receipts and disbursements are controlled and documented properly.

2.       Once the Performer accomplishes a Payable Milestone, the Performer may seek payment from the Government of the corresponding payment amount in the Payable Milestones and Corresponding Payment Schedule in Attachment 3. The Performer shall document the accomplishment of such Payable Milestone by submitting or otherwise providing the Payable Milestones Report required by Attachment 2, Part F. After written verification of the accomplishment of such Payable Milestone by the DARPA

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Agreements Officer’s Representative and approval by the DARPA Agreements Officer, the associated invoice will be submitted to the payment office via Wide Area Workflow (“WAWF”), as detailed in subparagraph B.6 of this Article. If a Payable Milestone is composed of more than one task (e.g., Payable Milestones 2, 6, 7, etc.), all such tasks in such Payable Milestone must be fully accomplished before the Performer may seek payment for such Payable Milestone. However, if a task in a single task Payable Milestone (or all of the tasks in a multi-task Payable Milestone) cannot be completed by the applicable Milestone (MS) Month set forth in Attachment 3, the Performer will document such event in its Monthly Technical Status Report, and the Parties will execute a contract modification to incorporate required changes in Attachment 3, and in Attachments 1 and 4, as applicable. For clarity, the “MS Month” column set forth in Attachment 3 sets forth the Parties’ good faith estimate of the date by which a Payable Milestone will be accomplished, but it is not a deadline for accomplishing the applicable Payable Milestone. In addition, missing the MS Month does not prevent the Performer from subsequently accomplishing the applicable Payable Milestone and has no effect on the corresponding payment amount in Attachment 3 once accomplished.

If deemed necessary by the DARPA Agreements Officer, payment approval for the final Payable Milestone will be made after reconciliation of actual Government funding for the Program with the actual Performer Contribution amount. While there will be this final Government reconciliation and accounting of the Performer Contribution amount, the Parties agree that the quarterly accounting of the Performer Contribution, as reported in the quarterly Business Status Report submitted in accordance with Attachment 2, will not, nor is it necessarily intended or required to, uniformly or proportionally track or match the estimated schedule of the Performer Contribution set forth in either Attachments 3 or 4.

3.       Subject to change only through written Agreement modification, payment shall be made to the address of the Performer’s Administrator set forth below.

AMYRIS, INC., 5885 Hollis Street, Suite 100, Emeryville, California 94608

4.       Payments will be made by the cognizant Defense Agencies Financial Services office, as indicated below, within thirty (30) calendar days of an accepted invoice in WAWF. WAWF is a secure web-based system for electronic invoicing, receipt and acceptance. The WAWF application enables electronic form submission of invoices, government inspection, and acceptance documents in order to support DoD’s goal of moving to a paperless acquisition process. Authorized DoD users are notified of pending actions by e-mail and are presented with a collection of documents required to process the contracting or financial action. It uses Public Key Infrastructure (“PKI”) to electronically bind the digital signature to provide non-reputable proof that the user (electronically) signed the document with the contents. Benefits include online access and full spectrum view of document status, minimized re-keying and improving data accuracy, eliminating unmatched disbursements and making all documentation required for payment easily accessible.

The Performer is required to utilize the WAWF system when processing invoices and receiving reports under this Agreement. The Performer shall (i) ensure an Electronic Business Point of Contact is designated in Central Contractor Registration at http://www.ccr.gov and (ii) register to use WAWF–RA at the https://wawf.eb.mil site, within ten (10) calendar days after award of this Agreement. Step by step procedures to register are available at the https://wawf.eb.mil site. The Performer is directed to use the “2-in-1” format when processing invoices.

a.       For the Issue By DoDAAC enter HR0011

b. For the Admin DoDAAC and Ship To fields, enter S0507A.

c.       For the Service Acceptor field, enter HR0011, Extension 01.

d.       Leave the Inspect by DoDAAC, Ship From Code DoDAAC and LPO DoDAAC fields blank unless otherwise directed by the DARPA Agreements Officer or DARPA Administrative Agreements

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Officer.

e.       The following guidance is provided for invoicing processed under this Agreement through WAWF:

• The DARPA Agreements Officer’s Representative identified at Article IV "Agreement Administration" shall continue to formally inspect and accept the deliverable Payable Milestone reports. To the maximum extent practicable, the DARPA Agreements Officer’s Representative shall review the Payable Milestone report(s) and either: 1) provide a written notice of rejection to the Performer which includes feedback regarding deficiencies requiring correction or 2) written notice of acceptance to the DARPA Administrative Agreements Officer, DARPA Program Manager and DARPA Agreements Officer.

• Acceptance within the WAWF system shall be performed by the DARPA Agreements Officer upon receipt of a confirmation email, or other form of transmittal, from the DARPA Agreements Officer’s Representative.

• The Performer shall send an email notice to the DARPA Agreements Officer’s Representative and DARPA Agreements Officer upon submission of an invoice in WAWF (this can be done from within WAWF).

• Payments shall be made by DFAS-CO/WEST (HQ0339)

• The Performer agrees, when entering invoices entered in WAWF to utilize the CLINs associated with each Payable Milestone as delineated at Attachment 3. The description of the CLIN shall include reference to the associated milestone number along with other necessary descriptive information. The Performer agrees that the Government may reject invoices not submitted in accordance with this provision.

Note for DFAS: The Agreement shall be entered into the DFAS system by CLIN – Milestone association as delineated at Attachment 3. The Agreement is to be paid out by CLIN – Milestone association. Payments shall be made using the CLIN (MS)/ACRN association as delineated at Attachment 3.

5.       Payee Information: As identified at Central Contractor Registration.

•      Cage Code: 47QN9

•      DUNS: 185930182

•      TIN: 55-0856151

6.       Financial Records and Reports: The Performer shall maintain adequate records to account for accomplishment of all Payable Milestones for which payment is received by the Performer under this Agreement and shall maintain adequate records to account for the Performer Contribution provided under this Agreement. Upon completion or termination of this Agreement, whichever occurs earlier, the Performer’s Administrator shall furnish to the DARPA Agreements Officer a copy of the Final Report required by Attachment 2, Part E. The Performer’s relevant financial records are subject to examination or audit on behalf of DARPA by the Government for a period not to exceed three (3) years after expiration or earlier termination of the Term. The DARPA Agreements Officer or designee shall have direct access to sufficient records and information of the Performer to ensure accomplishment of the Payable Milestones for which payment was received by the Performer under this Agreement and satisfaction of the Performer Contribution under this Agreement. Such audit, examination, or access shall be performed during business

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hours on business days upon reasonable, prior written notice and shall be subject to the security requirements of the audited party. For clarity, where the labor component of the Performer Contribution is based upon a fixed price hourly commercial rate(s) documented in a contract (e.g., GSA Schedule contract), the examination or audit of the labor component of such costs shall be limited to a review of hours worked and shall not include a review of the rates.

C.       Agreement Value, Agreement Funding and Accounting and Appropriation Data

Agreement Value

Total Amount of the Agreement: $50,721,349

Total Estimated Government Funding of the Agreement: $35,160,011

Agreement Funding

TIA Award	$ 6,035,686
P00002	$10,639,695
P00003	$ 6,648,707
Total Funds Obligated	$23,324,088

Accounting and Appropriation Data

TiA Award

CLIN/SLIN/ACRN: 0001/01/AA

LOA: 012199 097 0400 000 N 20152016 D 1320 BLTM66 2015.MBT-02.CORE.A DARPA 255

FUNDING AMOUNT: $6,035,686

P00002

CLIN/SLIN/ACRN: 0001/01/AB

LOA: 012199 097 0400 000 N 20162017 D 1320 BLTM66 2016.MBT-02.CORE.A DARPA 255

FUNDING AMOUNT: $10,639,695

P00003

CLIN/SLIN/ACRN: 0001/01/AB

LOA: 012199 097 0400 000 N 20162017 D 1320 BLTM66 2016.MBT-02.CORE.A DARPA 255

FUNDING AMOUNT: $6,648,707

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ARTICLE VI: DISPUTES

A.       General

The Parties shall communicate with one another in good faith and in a timely and cooperative manner when raising issues under this Article.

B.       Dispute Resolution Procedures

1.       Any dispute, disagreement, or misunderstanding between the Government and the Performer concerning questions of fact or law arising from or in connection with this Agreement, and, whether or not involving an alleged breach of this Agreement, may be raised only under this Article.

2.       Whenever disputes, disagreements, or misunderstandings arise, the Party aggrieved by such dispute, disagreement, or misunderstanding shall provide written notice to the other Party involved identifying the matter in dispute and inviting the other Party involved in the dispute to attempt to resolve the issue(s) involved by discussion and mutual agreement as soon as practicable. If the aggrieved Party does not provide the notification made under subparagraph B.3 of this Article within three (3) months of becoming aware of the dispute, disagreement, or misunderstanding, then such dispute, disagreement, or misunderstanding will not constitute the basis for relief under this Article unless the Director of DARPA in the interests of justice waives this requirement.

3.       Failing resolution by mutual agreement described above, the aggrieved Party shall document the dispute, disagreement, or misunderstanding by notifying the other Party (through the DARPA Agreements Officer or the Performer’s Administrator, as the case may be) in writing of the relevant facts, identify unresolved issues, and specify the clarification or remedy sought. Within five (5) business days after providing such notice to the other Party, the aggrieved Party may, in writing, request a joint decision by the DARPA Senior Procurement Executive and a senior executive (no lower than Vice President, Legal) appointed by the Performer. The other Party shall submit a written position on the matter(s) in dispute within thirty (30) calendar days after being notified in writing that a joint decision has been requested regarding the dispute, disagreement, or misunderstanding. The DARPA Senior Procurement Executive and the Performer’s senior executive shall conduct a review of the matter(s) in dispute and render a decision in writing within thirty (30) calendar days of receipt of such other Party’s written position. Any such joint decision is final and binding.

4.       In the absence of a joint decision, upon written request to the Director of DARPA, made within thirty (30) calendar days of the expiration of the time for a joint decision under subparagraph B.3 above, the dispute, disagreement, or misunderstanding shall be further reviewed. The Director of DARPA may elect to conduct this review personally or through a designee or jointly with a senior executive (no lower than Vice President, Legal) appointed by the Performer. Following the review, the Director of DARPA or designee will resolve the issue(s) and notify the Parties in writing. Such resolution is not subject to further administrative review and, to the extent permitted by law, shall be final and binding.

C.       Limitation of Damages

Claims for damages of any nature whatsoever pursued under this Agreement shall be limited to direct damages only up to the aggregate amount of Government funding disbursed as of the time the dispute arises. In no event shall the Government be liable for claims for consequential, punitive, special and incidental damages, claims for lost profits, or other indirect damages.

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ARTICLE VII: PATENT RIGHTS

A.       Allocation of Principal Rights

1. Unless the Performer shall have notified DARPA (in accordance with subparagraph B.2 below) that the Performer does not intend to retain title, the Performer shall retain the entire right, title, and interest throughout the world to each Subject Invention consistent with the provisions of this Article and 35 U.S.C. § 202. With respect to any Subject Invention in which the Performer retains title, the Government shall have a nonexclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the Government the Subject Invention throughout the world.

2. With regard to Inventions made under this Agreement that are not Subject Inventions, i.e. Inventions relating to genetically modified organisms, strains, or any compounds or products made by or from such organisms or strains that are conceived or first actually reduced to practice in the performance of the Program, the Government retains a right to request from Performer a nonexclusive, nontransferable, irrevocable license, on fair and reasonable terms, to such Inventions to have such Inventions practiced on behalf of the Government throughout the world. The Government will provide Performer with written notice identifying the specific Invention to which it is requesting such license. Prior to granting such license, the Parties agree to negotiate in good faith fair and reasonable terms under which the Performer would be the exclusive supplier/manufacturer to the Government of the desired compound or product under the Government’s license. Upon agreement of such fair and reasonable terms between the Performer and the Government, the Performer shall grant the Government the nonexclusive license described above to such identified Inventions. In the event that no agreement is reached between Performer and Government with regard to said fair and reasonable terms on Performer’s supply/manufacturing rights, Performer shall nonetheless grant the Government a nonexclusive, nontransferable, irrevocable license, on fair and reasonable terms, to such Inventions to have such Inventions practiced on behalf of the Government throughout the world. Failure to reach agreement on fair and reasonable terms will be resolved in accordance with Article VI. Disputes.

3. Notwithstanding anything to the contrary in subparagraph A.2 above, the Parties agree that any license to the Government to any Inventions made under this Agreement that are not Subject Inventions expressly excludes any and all rights to make, have made, use, sell, offer for sale, or import any compound or product as, or in, a Flavor or Fragrance, unless the Parties reasonably determine that a national security interest requires the Government to use such compound or product as, or in, a Flavor or Fragrance, in which case subparagraph A.2 will also be applicable to such use. As used in this paragraph, “Flavor” means an ingredient(s) whose intended or primary functionality (individually or as part of a blend with auxiliary materials) is to impart, modify, boost or enhance a desirable taste, flavor or sensation, or to conceal, modify or minimize an undesirable taste, flavor or sensation, in materials designed for consumption (including food, beverages, drugs, tobacco and any animal feed). As used in this paragraph, “Fragrance” means an ingredient(s) whose intended or primary functionality (individually or as part of a blend with auxiliary materials) is to impart, modify, boost or enhance a desirable scent or odor or to conceal, modify or minimize an undesirable scent or odor, in consumer and industrial grade products.

B.       Invention Disclosure, Election of Title, and Filing of Patent Application

1.       The Performer shall disclose each Subject Invention to DARPA within four (4) months after the inventor discloses it in writing to Performer’s personnel responsible for patent matters or, in the case of no internal writing from the inventor, within two (2) months after Performer files a provisional application for it; provided however, that in the event the Performer does not file a provisional application, Performer shall disclose the Subject Invention to the Government within two (2) months of determining that a particular set of experiments and or data qualify as a Subject Invention. The disclosure to the Government shall be in the

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form of a written report and shall identify the Agreement under which the Subject Invention was Made and the identity of the inventor(s). It shall be sufficiently complete in technical detail to convey a clear understanding to the extent known at the time of the disclosure, of the nature, purpose, operation, and the physical, chemical, biological, or electrical characteristics of the Subject Invention. The disclosure shall also identify any publication, sale, or public use of the Subject Invention and whether a manuscript describing the Subject Invention has been submitted for publication and, if so, whether it has been accepted for publication at the time of disclosure. The Performer shall also submit to the Government an annual listing of Subject Inventions.

2.       If the Performer determines that it does not intend to retain title to any such Subject Invention, the Performer shall notify the Government, in writing, within eight (8) months of disclosure to DARPA. However, in any case where publication, sale, or public use has initiated the one (1)-year statutory period wherein valid patent protection can still be obtained in the United States, the period for such notice may be shortened by DARPA to a date that is no more than sixty (60) calendar days prior to the end of the statutory period.

3.       The Performer shall file its initial patent application on a Subject Invention to which it elects to retain title within one (1) year after election of title or, if earlier, prior to the end of the statutory period wherein valid patent protection can be obtained in the United States after a publication, or sale, or public use. The Performer may elect to file patent applications in additional countries (including the European Patent Office and the Patent Cooperation Treaty) within either: (i) ten (10) months of the corresponding initial patent application; or (ii) six (6) months from the date permission is granted by the Commissioner of Patents and Trademarks to file foreign patent applications where such filing has been prohibited by a secrecy order.

4.       Requests for extension of the time for disclosure, election, and filing under Article VII, paragraph B, may, at the discretion of DARPA, and after considering the position of the Performer, be granted.

C.       Conditions When the Government May Obtain Title

Upon DARPA’s written request, the Performer shall convey title to any Subject Invention to DARPA under any of the following conditions:

1.       If the Performer fails to disclose or elects not to retain title to the Subject Invention within the times specified in paragraph B of this Article; provided, that DARPA may request title only within sixty (60) calendar days after learning of: (i) the failure of the Performer to disclose; or (ii) Performer’s election not to retain title, in each case within the specified times.

2.       In those countries in which the Performer fails to file patent applications within the times specified in paragraph B of this Article; provided, that if the Performer has filed a patent application in a country after the times specified in paragraph B of this Article, but prior to its receipt of the written request by DARPA, the Performer shall continue to retain title to the Subject Invention in that country; or

3.       In any country in which the Performer decides not to continue the prosecution of, to pay the maintenance fees on, or defend a reexamination of or opposition proceedings on, a patent application or patent on a Subject Invention.

D.       Minimum Rights to the Performer and Protection of the Performer’s Right to File

1.       The Performer shall retain a nonexclusive, royalty-free, paid-up license throughout the world in each Subject Invention to which the Government obtains title under paragraph C of this Article, except if the

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Performer fails to disclose the Subject Invention within the times specified in paragraph B of this Article. The Performer’s license to such Subject Invention extends to the Performer’s Affiliates and Collaborators, if any, and includes the right to grant sublicenses of the same scope to the extent that the Performer was legally obligated to do so at the time the Agreement was awarded. The license is transferable only with the approval of DARPA, except as noted above regarding Affiliates and Collaborators of Performer or when transferred to the successor of that part of the Performer’s business to which the Subject Invention pertains. DARPA approval for a license transfer requiring DARPA approval shall not be unreasonably withheld or delayed.

2.       The Performer’s license in subparagraph D.1 of this Article may be revoked or modified by DARPA to the extent necessary to achieve expeditious Practical Application of the Subject Invention pursuant to an application for an exclusive license submitted consistent with appropriate provisions at 37 CFR Part 404. This license shall not be revoked in that field of use or the geographical areas in which the Performer continues to practice the general technology developed hereunder in pursuit of commercial goals, including the goal of making the products derived from such platforms reasonably accessible to the public.

3.       Before revocation or modification of the Performer’s license in subparagraph D.1 of this Article, DARPA shall furnish the Performer a written notice of its intention to revoke or modify the license, and the Performer shall be allowed thirty (30) calendar days (or such other time as may be authorized for good cause shown) after the notice to show cause why the license should not be revoked or modified.

E.       Action to Protect the Government’s Interest

1.       The Performer agrees to execute or to have executed and promptly deliver to DARPA all instruments necessary to: (i) establish or confirm the rights the Government has throughout the world in those Subject Inventions to which the Performer elects to retain title; and (ii) convey title to DARPA when requested under paragraph D of this Article and to enable the Government to obtain patent protection throughout the world in that Subject Invention.

2.       The Performer agrees to require, by written agreement, its employees, other than clerical and non-technical employees, to disclose promptly in writing to personnel identified as responsible for the administration of patent matters and in a format suggested by the Performer each Subject Invention Made under this Agreement in order that the Performer can comply with the disclosure provisions of paragraph B of this Article. The Performer shall instruct employees, through employee agreements or other suitable educational programs, on the importance of reporting Subject Inventions in sufficient time to permit the filing of patent applications prior to U.S. or foreign statutory bars.

3.       The Performer shall notify DARPA of any decisions not to continue the prosecution of, pay maintenance fees for, or defend in a reexamination or opposition proceedings on a Subject Invention patent application or patent, in any country, not less than thirty (30) calendar days before the expiration of the response period required by the relevant patent office.

4.       The Performer shall include, within the specification of any United States patent application and any patent issuing thereon covering a Subject Invention, the following statement: “This invention was made with Government support under Agreement HR0011-15-3-0001, awarded by DARPA. The Government has certain rights in the invention.”

F.       Lower Tier Agreements

The Performer shall include this Article VII, suitably modified to identify the Parties and, as applicable, Subcontractors, in all subcontracts or lower tier agreements, regardless of tier, for experimental,

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developmental, or research work under the Program.

G.       Reporting on Utilization of Subject Inventions

1.       Pursuant to Attachment 2, the Performer agrees to submit, during the Term, an annual report on the general subject matter research at Performer or its Collaborators, licensees or assignees in connection with utilization of a Subject Invention or on efforts at obtaining such utilization that is being made by the Performer or its Collaborators, licensees or assignees. Such reports shall include information regarding the general fields of potential products where such Subject Inventions may ultimately assist in commercial sales. The Performer also agrees to provide additional reports as may be requested by DARPA in connection with any march-in proceedings undertaken by DARPA in accordance with paragraph I of this Article. Consistent with 35 U.S.C. § 202(c) (5), DARPA agrees it shall not disclose such information to persons outside the Government without permission of the Performer.

2.       All required reporting shall be accomplished, to the extent possible, using the iEdison reporting website: https://s-edison.info.nih.gov/iEdison/. To the extent any such reporting cannot be carried out by use of i-Edison, reports and communications shall be submitted to the DARPA Agreements Officer and DARPA Administrative Agreements Officer.

H.       Preference for American Industry

Notwithstanding any other provision of this clause, the Performer agrees that it shall not grant to any person the exclusive right to use or sell any Subject Invention in the United States or Canada unless such person agrees that any product embodying the Subject Invention or produced through the use of the Subject Invention shall be manufactured substantially in the United States or Canada, except when such rights are in connection with a Collaborator. However, in individual cases, the requirements for such an agreement beyond what is contemplated herein may be waived by DARPA upon a showing by the Performer: (1) that reasonable but unsuccessful efforts have been made to grant licenses on similar terms to potential licensees that would be likely to manufacture substantially in the United States; or (2) that, under the circumstances, domestic manufacture is not commercially feasible.

I.       March-in Rights

The Performer agrees that, with respect to any Subject Invention in which it has retained title, DARPA has the right to require the Performer, an assignee, or exclusive licensee of a Subject Invention to grant a non-exclusive license to a responsible applicant or applicants, upon terms that are reasonable under the circumstances, and if the Performer, assignee, or exclusive licensee refuses such a request, DARPA has the right to grant such a license itself if DARPA determines that:

1.       Such action is necessary because the Performer, assignee, or exclusive licensee has not taken effective steps, consistent with the intent of this Agreement, to achieve Practical Application of the Subject Invention;

2.       Such action is necessary to alleviate health or safety needs which are not reasonably satisfied by the Performer, assignee, or exclusive licensee;

3.       Such action is necessary to meet requirements for public use and such requirements are not reasonably satisfied by the Performer, assignee, or exclusive licensee; or

4.       Such action is necessary because the agreement required by paragraph I of this Article has not

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been obtained or waived or because a licensee of the exclusive right to use or sell any Subject Invention in the United States is in breach of such agreement.

ARTICLE VIII: DATA RIGHTS

A.       Allocation of Principal Rights

1.       This Agreement shall be performed with mixed Government and Performer funding. The Parties agree that in consideration for Government funding, the Performer intends to reduce to Practical Application Subject Invention(s) developed under this Agreement.

2.       The Performer agrees to retain and maintain in good condition, until two (2) years after completion or termination of this Agreement, all Data necessary to achieve Practical Application of Subject Invention(s).

3.       In the event of exercise of the Government’s “March-in Rights” as set forth under Article VII or in this subparagraph, the Performer agrees that, with respect to Data necessary to achieve Practical Application of the applicable Subject Invention(s), the Government has the right to require the Performer to deliver, within sixty (60) calendar days from the date of the written request and at no additional cost to the Government, all such Data to the Government in accordance with its reasonable directions if the Government determines that:

(a)       Such action is necessary because the Performer, assignee, or exclusive licensee has not taken effective steps, consistent with the intent of this Agreement, to achieve Practical Application of the Subject Invention(s) developed during the performance of this Agreement;

(b)       Such action is necessary to alleviate health or safety needs which are not reasonably satisfied by the Performer, assignee, or exclusive licensee; or

(c)       Such action is necessary to meet requirements for public use and such requirements are not reasonably satisfied by the Performer, assignee, or exclusive licensee.

4.       With respect to all Data delivered in the event of the Government’s exercise of its right under this subparagraph A.3, the Government shall receive Unlimited Rights.

5.        With respect to Data developed, generated or delivered under this Agreement, the Government shall receive Government Purpose Rights.

6. Any data or intellectual property developed or generated exclusively at private expense, either prior to, or outside the scope of, this Agreement, to be utilized or delivered under this Agreement by the Performer and/or its Subcontractors shall be delivered with restrictions as delineated in the List of Intellectual Property Assertions provided in Attachment 5. The Performer reserves the right to add to or modify the data or intellectual property identified in Attachment 5, but agrees that it will not use in the performance of this Agreement any private expense data or intellectual property until Attachment 5 is modified to reflect such additional data or intellectual property, in a contractual document executed by the Contracting Officer.

B.       Marking of Data

Pursuant to paragraph A above, any Data delivered under this Agreement shall be marked with the following legend:

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“Use, duplication, or disclosure is subject to the restrictions as stated in Agreement HR0011-15-3-0001 between DARPA and Amyris, Inc.”

C.       Lower Tier Agreements

The Performer shall include this Article, suitably modified to identify the Parties and, as applicable, Subcontractors, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work under the Program.

ARTICLE IX: FOREIGN ACCESS TO TECHNOLOGY

This Article shall remain in effect during the Term and for two (2) years thereafter.

A.       General

The Parties agree that research findings and technology developments arising under this Agreement may constitute a significant enhancement to the national defense and to the economic vitality of the United States. Accordingly, access to important technology developments under this Agreement by Foreign Firms or Institutions must be carefully controlled. The controls contemplated in this Article are in addition to, and are not intended to change or supersede, the provisions of the International Traffic in Arms Regulation (22 CFR pt. 121 et seq.), the DoD Industrial Security Regulation (DoD 5220.22-R) and the Department of Commerce Export Regulation (15 CFR pt. 770 et seq.)

B.       Restrictions on Sale or Transfer of Technology to Foreign Firms or Institutions

1.       In order to promote the national security interests of the United States and to effectuate the policies that underlie the regulations cited above, the procedures stated in subparagraphs B.2 and B.3 below shall apply to any proposed Transfer of Technology. For purposes of this Article IX, a “Transfer of Technology” means a sale of the Performer or of a Subcontractors, and sales or licensing of Technology, however, the term “Transfer of Technology” does not include:

(a)       sales of products or components incorporating or produced via a Subject Invention(s), or licenses or sales of any genetically modified organism, strain, or compound made by or from such an organism, strain, excluding genetically modified organism, strain or compound made by or from an organism or strain developed under this Program.

(b)       licenses of software or documentation related to sales of products or components described in clause (a), or

(c)       a transfer of Technology to foreign subsidiaries of the Performer for purposes related to this Agreement or to Collaborators, or

(d)       a transfer of Technology to a Foreign Firm or Institution, which is a Subcontractor or an approved source of supply or source for the conduct of research under this Agreement; provided that such transfer shall be limited to that necessary to allow the Foreign Firm or Institution to perform its approved role under this Agreement.

(e) a license and transfer of Technology solely to make, have made, use, offer for sale, sell, or import a compound or product as, or in, a Flavor (as defined in Article VII.A.3) or Fragrance (as defined in Article VII.A.3).

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2.       The Performer shall provide written notice to the DARPA Agreements Officer’s Representative and DARPA Agreements Officer of any proposed Transfer of Technology to a Foreign Firm or Institution by Performer or a Subcontractor at least sixty (60) calendar days prior to the proposed date of transfer. Such notice shall cite this Article and shall state specifically what Technology is to be transferred and the general terms of the transfer. Within thirty (30) calendar days of receipt of the Performer’s written notification, the DARPA Agreements Officer shall advise the Performer whether it consents to the proposed Transfer. If DARPA determines that the proposed Transfer of Technology may have adverse consequences to the national security interests of the United States, the Performer (or, if applicable, a Subcontractor) and DARPA shall jointly endeavor to find alternatives to the proposed Transfer of Technology which obviate or mitigate potential adverse consequences of the Transfer of Technology but which provide substantially equivalent benefits to the Performer (or, if applicable, a Subcontractor). In cases where DARPA does not concur or sixty (60) calendar days after receipt and DARPA provides no decision, the Performer (or, if applicable, Performer on behalf of a Subcontractor) may utilize the procedures under Article VI, Disputes. No such Transfer shall take place until a decision is rendered.

3.       In the event a Transfer of Technology to a Foreign Firm or Institution which is NOT approved by DARPA takes place, the Performer shall: (a) refund to DARPA funds paid by DARPA for the development of such unapproved transferred Technology; and (b) the Government shall have a non-exclusive, nontransferable, irrevocable, paid-up license to practice or have practiced on behalf of the Government such Technology throughout the world for the Government and any and all other purposes, particularly to effectuate the intent of this Agreement. Upon request of the Government, the Performer shall provide written confirmation of such licenses.

C.       Lower Tier Agreements

The Performer shall include this Article, suitably modified to identify the Parties and, as applicable, Subcontractors, in all subcontracts or lower tier agreements, regardless of tier, for experimental, developmental, or research work under the Program.

ARTICLE X: TITLE TO AND DISPOSITION OF PROPERTY

A.       Title to Property

Title to any items of Property acquired under this Agreement with an acquisition value of $5,000 or less shall vest in the Performer (and/or its Subcontractors) upon acquisition with no further obligation of the Parties unless otherwise determined in advance by the DARPA Agreements Officer. The Performer (and/or its Subcontractors) will acquire Property with an acquisition value greater than $5,000 under this Agreement as set forth in Attachment 6 to this Agreement, which Property is necessary to further the research and development goals of this Program and is not for the direct benefit of the Government. Title to this Property shall vest in the Performer (and/or its Subcontractors) upon acquisition. Should any other item of Property with an acquisition value greater than $5,000 be required during the Program, the Performer shall obtain prior written approval of the DARPA Agreements Officer, which approval shall not to be unreasonably withheld or delayed. Title to this later acquired Property shall also vest in the Performer (and/or its Subcontractors) upon acquisition. The Performer (and/or its Subcontractors) shall be responsible for the maintenance, repair, protection, and preservation of all such Property at its own expense.

B.       Disposition of Property with Value >$5,000

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At the completion or termination of the Term, title to (i) items of Property set forth in Attachment 6 and (ii) any other items of Property acquired under the Program with an acquisition value greater than $5,000 shall remain vested with the Performer and, if applicable, its Subcontractors without further obligation to the Government.

ARTICLE XI: CIVIL RIGHTS ACT

This Agreement is subject to the compliance requirements of Title VI of the Civil Rights Act of 1964 as amended (42 U.S.C. 2000-d) relating to nondiscrimination in Federally assisted programs. The Performer has signed a Certifications for Agreement No. HR0011-15-3-0001, a copy of which is attached hereto as Attachment 7, which certifies, among other matters, the Performer’s compliance with the nondiscriminatory provisions of the Act.

ARTICLE XII: SECURITY

The Government does not anticipate the need for the Performer (or its Subcontractors) to develop and/or handle classified information in the performance of this Agreement. No DD254 is currently required for this Agreement.

ARTICLE XIII: SUBCONTRACTORS

The Performer shall make every effort to satisfy the intent of competitive bidding of sub-agreements to the maximum extent practical. The Performer may use foreign entities or nationals as Subcontractors, subject to compliance with the requirements of this Agreement and to the extent otherwise permitted by law.

ARTICLE XIV: KEY PERSONNEL

A.       The Performer shall notify the DARPA Agreements Officer in writing prior to making any change in Key Personnel for the Program. The following individuals are designated as ”Key Personnel” for the purposes of this Agreement:

Name	Role/Title	% Time
	Principal Investigator (PI)	100%
	Co-PI	100%

B.       When replacing any of the Key Personnel identified above, the Performer must demonstrate that the qualifications of the prospective Key Personnel are acceptable to the Government as reasonably determined by the Program Manager. Substitution of Key Personnel shall be documented by modification to the Agreement made in accordance with the procedures outlined in Article III, paragraph C.

ARTICLE XV: ORDER OF PRECEDENCE

In the event of any inconsistency between the terms of this Agreement and language set forth in the Attachments, the inconsistency shall be resolved by giving precedence in the following order: (1) the Agreement; and (2) all Attachments to the Agreement.

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ARTICLE XVI: EXECUTION

This Agreement constitutes the entire agreement of the Parties with respect to the subject matter hereof and supersedes all prior and contemporaneous agreements, understandings, negotiations and discussions among the Parties, whether oral or written, with respect to the subject matter hereof. This Agreement may be revised only by written consent of the Performer and the DARPA Agreements Officer. This Agreement, or modifications thereto, may be executed in counterparts each of which shall be deemed as original, but all of which taken together shall constitute one and the same instrument.

ARTICLE XVII: APPLICABLE LAW

United States federal law will apply to the construction, interpretation, and resolution of any disputes arising out of or in connection with this Agreement.

ARTICLE XIII: SEVERABILITY

In the event that any one or more of the provisions contained herein shall, for any reason, be held to be invalid, illegal or unenforceable in any respect, such invalidity, illegality or unenforceability shall not affect any other provisions of this Agreement, but this Agreement shall be construed as if such invalid, illegal or unenforceable provisions had never been contained herein, unless the deletion of such provision or provisions would result in such a material change so as to cause completion of the transactions contemplated herein to be unreasonable.

ARTICLE XIX: DATA SHARING PLAN AND STATUS REPORTING

It is the goal of the Government that its investment in the tools and capabilities developed under the Program to be multiplied many-fold by adoption and improvement by researchers across the United States. In order to achieve this vision, the Living Foundries program aims to facilitate interoperability and open the field to new entrants.

The Performer shall make available the Tools developed under the Program to the broader synthetic biology community by presenting its Program research Data at public meetings, conferences, and workshops and publishing results in peer-reviewed journal articles. At a minimum, the types of information that will be made available to the broader synthetic biology community are as discussed below:

(i) Data and analysis necessary to evaluate the utility of the Tools developed under the Program, including standard operating procedures and design specifications enabling others to reconstitute the equipment, set up, and approaches developed.

(ii) Details required for technical evaluation of the Tools developed under the Program: full protocols, technical drawings of equipment built and specifications met, Data on accuracy and precision of these systems, and results of procedures performed against large number of samples to investigate the robustness and readiness of the approaches for broader distribution – providing a trained reader with the information needed to recapitulate the methods and results described.

(iii) The Key Personnel shall be reasonably available to consult with third parties seeking to replicate the results.

The Performer shall include as part of required monthly Technical Status Reports in Attachment 2 an

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on-going status of efforts to develop and/or carry out this Intellectual Property and Data Sharing plan. Reporting shall include a summary of Data sharing activities that have taken place during the reporting period, and any Data sharing activities planned to take place within three months of the reporting period.

The Performer shall also include as part of required monthly Technical Status Reports in Attachment 2 a listing of the Performer’s Subject Invention disclosures, Subject Invention patent applications and a brief discussion summarizing plans, if any, to license the resulting Subject Inventions (e.g., intent and rationale regarding whether the Performer intends to seek non-exclusive licensing, exclusive licensing for a particular field of use, or exclusive licensing across the board, etc.).

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Attachment 1

M2K Program

Statement of Work (SOW)

References:

(a) Amyris Proposal “Mgs to Kgs” (M2K) dated February 3, 2015

As detailed in reference (a), the Performer will complete the work set forth below to achieve the Program Goals / Objectives set forth in Technology Investment Agreement HR0011-15-3-0001.

MODULE A: [*]

Task A.1: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 3): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task A.2: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 30): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 36): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 42): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 48): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

MODULE B: [*]

Task B.1: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 3): [*]

Deliverables: [*]

Milestone (Month 12): [*]

Deliverables: [*]

Task B.2: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 3): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 9): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task B.3: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 9): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 15): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 21): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Deliverables: [*]

Milestone (Month 30): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 36): [*]

Metrics/Completion Criteria: [*]

Task B.4: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 3): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task B.5: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Deliverables: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 21): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 30): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 30): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 36): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 42): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

MODULE C: [*]

Task C.1: [*] ( , Arzeda).

Task Objective: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Milestone (Month 3): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 9): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 9): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task C.2: [*] ( , Arzeda).

Task Objective: [*]

Milestone (Month 18): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (month 30): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 42): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

MODULE D: [*]

Task D.1: [*] ( , Arzeda)

Task Objective: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Deliverables: [*]

Task D.2: [*] ( , Arzeda)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 9): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 15): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 21): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task D.3: [*] ( , Arzeda)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverable: [*]

Task D.4: [*] ( , Arzeda)

Task Objective: [*]

Milestone (Month 21): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 21): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task D.5: [*] ( , Arzeda).

Task Objective: [*]

Milestone (Month 30): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 36): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 45): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 48): [*] Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Deliverable: [*]

MODULE E: [*]

Task E.1: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*] Metrics/Completion Criteria: [*]

Deliverables: [*]

Task E.2: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task E.3 (Month 24): [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 18): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

MODULE F: [*]

Task F.1: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 3): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask F.1.1 (Month 3): [*]

Subtask F.1.2 (Month 3): [*]

Subtask F.1.3 (Month 1): [*]

Subtask F.1.4 (Month 3): [*]

Task F.2: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask F.2.1 (Month 3): [*]

Subtask F.2.2 (Month 3): [*]

Subtask F.2.2 (Month 4): [*]

Subtask F.2.4 (Month 5): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Subtask F.2.5 (Month 6): Deleted

Task F.3: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask F.3.1 (Month 3): [*]

Subtask F.3.2 (Month 3): [*]

Subtask F.3.2 (Month 4): [*]

Subtask F.3.4 (Month 10): [*]

Subtask F.3.5 (Month 12): [*]

Subtask F.3.6 (Month 12): [*]

MODULE G: DELETED

MODULE H: [*]

Task H.1: [*] ( , Agilent)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Deliverables: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask H.1.1 (Month 3): [*]

Subtask H.1.2 (Month 15): [*]

Task H.2: [*] ( , Amyris).

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task H.3: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 6): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 12): 1) [*].

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 18) [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask H.3.1 (Month 1): [*]

Task H.4: [*] ( , Agilent)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Deliverables: [*]

Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask H.4.1 (Month 18): [*]

Task H.5: [*] ( , Agilent)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask H.5.1 (Month 2): [*]

Task H.6: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Milestone (Month 30): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

MODULE I: [*]

Task I.1: [*] ( , Univ. of Heidelberg)

Task Objective: [*]

Milestone (Month 9): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask I.1.1 (Month 2): [*]

Subtask I.1.2 (Month 5): [*]

Subtask I.1.3 (month 8): [*]

Task I.2: [*] ( , Univ. of Heidelberg)

Task Objective: [*]

Milestone (month 9): [*]

Metrics/Completion Criteria[*]

Deliverables: [*]

Subtask I.2.1 (Month 1): [*]

Subtask I.2.2 (Month 5): [*]

Subtask I.2.3 (Month 8): [*]

Task I.3: [*] ( , Amyris)

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Task Objective: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask I.3.1 (Month 10): [*]

Task I.4: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask I.4.1 (Month 9): [*]

Subtask I.4.2 (Month 12): [*]

Subtask I.4.3 (month 15): [*]

Task I.5: [*] ( , Univ. of Heidelberg)

Task Objective: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Subtask I.5.1 (Month 10): [*]

Task I.6: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Subtask I.6.1 (Month 9): [*]

Subtask I.6.2 (Month 12): [*]

Subtask I.6.3 (month15): [*]

MODULE J: [*]

Task J.1: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 3): [*]

Deliverables: [*]

Subtask J1.1 (Month 2): [*]

Subtask J1.2 (Month 3): [*]

Milestone (Month 12): [*]

Deliverables: [*]

Subtask J1.2 (Month 6): [*]

Subtask J1.3 (Month 9): [*]

Milestone (Month 18): [*]

Deliverables: [*]

Subtask J1.4 (Month 12): [*]

Subtask J1.5 (Month 15): [*]

Subtask J1.6 (Month 18): [*]

Task J.2: [*] ( , Amyris).

Task Objective: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Milestone (Month 21): [*]

Deliverables: [*]

Subtask J2.1 (Month 20): [*]

Milestone (Month 24): [*]

Deliverables: [*]

Subtask J2.2 (Month 24): [*]

Subtask J2.3 (Month 24): [*]

Task J.3: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 30): [*]

Deliverables: [*]

Subtask J3.1 (Month 27): [*]

Subtask J3.2 (Month 30): [*]

Subtask J3.3 (Month 30): [*]

Milestone (Month 30): [*]

Deliverables: [*]

Subtask J3.4 (Month 27): [*]

Subtask J3.5 (Month 30): [*]

Milestone (Month 33): [*]

Deliverables: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Subtask J3.6 (Month 30): [*]

Subtask J3.7 (Month 33): [*]

Milestone (Month 36): [*]

Deliverables: [*]

Subtask J3.8 (Month 33): [*]

Subtask J3.9 (Month 36): [*]

Task J.4 (Optional): [*] ( , Amyris)

Task Objective: [*]

Milestone (12 months): [*]

Deliverables: [*]

Subtask J4.1 (Month 3): [*]

Subtask J4.2 (Month 6): [*]

Subtask J4.3 (Month 6): [*]

Subtask J4.4 (Month 12): [*]

Milestone (18 months): [*]

Deliverables: [*]

Subtask J4.5 (Month 6): [*]

Subtask J4.6 (Month 12): [*]

Subtask J4.7 (Month 18): [*]

Milestone (24 months): [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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[*]

Deliverables: [*]

Subtask J4.8 (Month 21): [*]

Subtask J4.9 (Month 24): [*]

Subtask J4.10 (Month 24): [*]

MODULE K: [*]

Task K.1: [*] ( , Amyris)

Task Objective: [*]

Milestone (Month 6): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task K.2: [*] ( , Amyris)

Task objective: [*]

Milestone (Month 12): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task K.3[*] ( , Amyris)

Task objective: [*]

Milestone (Month 18): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task K.4: [*] ( , Amyris)

Task Objective: [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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Milestone (Month 24): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Milestone (Month 30): [*]

Metrics/Completion Criteria: [*]

Deliverables: [*]

Task L: Biosafety and Biosecurity Planning and Reporting

Task Objective:The research and engineering depicted in this Statement of Work seeks to make existing capabilities (e.g. genetic modification of microbes to produce commodity chemicals) more efficient with the intended purpose of speeding the development of Living Foundries. The goal of this research is to make better engineering tools, and not to produce microbes that may have dual-use potential. As noted in the Performer’s technical proposal, a review of the research activities identified within this Statement of Work determined that this project will not enable technologies that are related to human, animal, or plant health. The Performer’s choice of potential chassis or hosts will be made from amongst the list of microbes that, prior to genetic modification, are designated safely handled in a Biosafety Level 1 facility. Additionally, the resulting genetically modified organisms have no selective advantage in the environment. The Performer shall demonstrate throughout the program that all methods and demonstrations of capability comply with national guidance for manipulation of genes and organisms and follow all guidance for biological safety and biosecurity. Demonstrations and testbeds must meet any applicable regulations designed to protect human health and the environment promulgated by the Environmental Protection Agency, National Institutes of Health, or other relevant agencies of the Federal Government. The Performer shall use, store, and destroy biological material in accordance with all applicable regulations.

Deliverable: Include as part of the Monthly Technical Status Reports an on-going status of Performer efforts to develop and/or carry out Bio-Safety and Security requirements.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

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M2K project timelines and milestones

[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

Attachment 3

Total Agreement Funding Plan and Payable Milestones and Corresponding Payment Schedule

Revision 2

Total Agreement Funding Plan

(for informational purposes only)

	DARPA Payment Total	Performer Contribution $	Agreement Funding Grand Total	DARPA Share %	Performer Contribution %
Module A Total	$11,267,168	$1,238,563	$12,505,727	90.10%	9.90%
Module B Total	$4,517,217	$767,829	$5,285,046	85.47%	14.53%
Module C Total	$1,065,228	$565,813	$1,631,041	65.31%	34.69%
Module D Total	$2,532,939	$1,003,490	$3,536,429	71.62%	28.38%
Module E Total	$1,183,490	$1,939,053	$3,122,543	37.90%	62.10%
Module F Total	$1,054,407	$767,829	$1,822,236	57.86%	42.14%
Module G Total	DELETED
Module H Total	$5,895,752	$3,831,230	$9,726,982	60.61%	39.39%
Module I Total	$1,462,441	$1,775,450	$3,237,891	45.17%	54.83%
Module J Total	$3,000,887	$2,517,831	$5,518,718	54.38%	45.62%
Module K Total	$3,180,481	$1,154,251	$4,334,731	73.37%	26.63%
	$35,160,011	$15,561,338	$50,721,349	69.32%	30.68%

DARPA Payment Totals by Month
Month 3	Jan 31 2016	$1,194,797
Month 6	Apr 30 2016	$2,763,283
Month 9	Jul 31 2016	$852,072
Month 12	Oct 31 2016	$6,385,002
Month 15	Jan 31 2017	$100,567
Month 18	Apr 30 2017	$5,379,661
Month 21	Jul 31 2017	$350,130
Month 24	Oct 31 2017	$5,934,327
Month 30	Apr 30 2018	$5,262,210
Month 33	Jul 31 2018	$119,404
Month 36	Oct 31 2018	$3,429,005
Month 42	Apr 30 2019	$1,974,919
Month 42 Option	Apr 30 2019	$85,125
Month 45	Jul 31 2019	$391,210
Month 48	Oct 31 2019	$31,256
Month 48 Option	Oct 31 2019	$907,043
Baseline		$34,167,843
Option		$992,168
Grand Total		$35,160,011

HR0011-15-3-0001

Payable Milestones and Corresponding Payment Schedule

Revision 2

MS Month	Task	Metric	Technical MS	Payable MS Value	Technical MS Payment	CLIN/SLIN/ ACRN
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]		0001/01/AA

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA
[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA 0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]	[*]	0001/01/AA 0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

		[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

		[*]
[*]	[*]	[*]	[*]	[*]	[*]	0001/02/AB (partialy funded $431,041)
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]
[*]	[*]	[*]	[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

[*]	[*]	[*]	[*]	[*]	[*]
		Baseline Costs			$34,167,843
		Option Costs			$992,168
		TOTAL			$35,160,011

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

HR0011-15-3-0001

Attachment 5

List of Intellectual Property Assertions by the Performer

The Performer reserves the right to add to or modify this Attachment 5 (including Tables 1, 2, 3, 4, 5, 6, 7 and 8). Note that divisional patents and patent applications are not listed in this Attachment 5

Table 1 lists technical data and computer software of Amyris, Inc. that is intended to be generated, developed and/or delivered as a result of the work proposed for the Program, for which the Government will acquire Limited Rights.

Table 1.
Technical Data and Computer Software to be Furnished with Restrictions		Basis for Assertion	Name of Person Asserting Restrictions
[*]	Limited Rights	[*]	Amyris, Inc.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

1

HR0011-15-3-0001

[*]	Limited Rights	[*]	Amyris, Inc.
[*]	Limited Rights	[*]	Amyris, Inc.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

2

HR0011-15-3-0001

Table 2 provides an exemplary, non-limiting list of patents and patent applications, pending or issued as of September 11, 2015, of Amyris, Inc., the Inventions of which may be used in the performance of the Program but to which the Government shall have no rights because they existed prior to the Effective Date:

Table 2.

Title	Application No.	Patent No. (Publication No.)
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

3

HR0011-15-3-0001

[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

4

HR0011-15-3-0001

Table 3 lists technical data and computer software of Arzeda Corp. that is intended to be generated, developed and/or delivered as a result of the work proposed for the Program, for which the Government will acquire Limited Rights.

Table 3.
Technical Data and Computer Software to be Furnished with Restrictions		Basis for Assertion	Name of Person Asserting Restrictions
[*]	Limited Rights	[*]	Arzeda Corp.
[*]	Limited Rights	[*]	Arzeda Corp.
[*]	Limited Rights Government Purpose Rights (applicable during TIA Period of Performance)	[*]	Arzeda Corp.

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

5

HR0011-15-3-0001

[*]	Limited Rights	[*]	Arzeda Corp.
[*]	Limited Rights	[*]	Arzeda Corp.
[*]	Government Purpose Rights	[*]	Arzeda Corp.

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

6

HR0011-15-3-0001

[*] Limited Rights [*] Arzeda Corp.

Table 4 provides an exemplary, non-limiting list of patents and patent applications, pending or issued as of November 1, 2015, of Arzeda Corp., the Inventions of which may be used in the performance of the Program but to which the Government shall have no rights because they existed prior to the Effective Date:

Table 4.

Title	Application No.	Patent No. (Publication No.)
[*]	[*]	[*]
[*]		[*]
[*]		[*]
[*]	[*]	[*]
[*]	[*]	[*]
[*]	[*]
[*]	[*]
[*]	[*]	[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

7

HR0011-15-3-0001

Table 5 lists technical data and/or computer software of Agilent Technologies, Inc. that is intended to be used in the performance of the M2K Program, which was generated or developed at Agilent’s private expense for which the Government will acquire Government Purpose Rights.

Table 5
Technical Data and Computer Software to be Furnished with Restrictions	Restrictions	Basis for Assertion	Name of Person Asserting Restrictions
[*]	Government Purpose Rights	[*]	Agilent Technologies, Inc.
[*]	Government Purpose Rights	[*]	Agilent Technologies, Inc.

Table 6 provides an exemplary, non-limiting list of patents and patent applications, pending or issued as of September 11, 2015, of Agilent Technologies, Inc., the Inventions of which may be used in the performance of the Program but to which the Government shall have no rights because they existed prior to the Effective Date:

Table 6.

Title	Application No.	Patent No. (Publication No.)
[*]	[*]
[*]	[*]
[*]	[*]
[*]	[*]
[*]	[*]
[*]	[*]
[*]		[*]
[*]		[*]
[*]		[*]
[*]		[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

8

HR0011-15-3-0001

Table 7 lists technical data and computer software of Ruprecht-Karls-Universität Heidelberg, Professor Oliver Trapp, and/or Trapp ChemTech Inc. that is intended to be generated, developed and/or delivered as a result of the work proposed for the Program, for which the Government will acquire Limited Rights.

Table 7.
Technical Data and Computer Software to be Furnished with Restrictions	Restrictions	Basis for Assertion	Name of Person Asserting Restrictions
[*]	Limited Rights	[*]	Trapp ChemTech, Inc.

Table 8 provides an exemplary, non-limiting list of patents and patent applications, pending or issued as of September 11, 2015, of Ruprecht-Karls-Universität Heidelberg, Professor Oliver Trapp, and/or Trapp ChemTech Inc., the Inventions of which may be used in the performance of the Program but to which the Government shall have no rights because they existed prior to the Effective Date:

Title	Application No.	Patent No. (Publication No.)
[*]	[*]
[*]		[*]
[*]		[*]
[*]		[*]
[*]		[*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

9

HR0011-15-3-0001

Attachment 6

List of Property Greater than $5,000

Module	Material/Equipment	Units	Unit $	Total Cost
E	[*]	1	$237,177	$237,177
E	[*]	4	$4978	$19,912
E	[*]	1	$108,405	$108,405
E	[*]	1	$321,849	$321,849
E	[*]	2	$60,061	$120,122
E	[*]	1	$363,759	$363,759
H	[*]	2	$787,291.50	$1,574,583
H	[*]	1	$150,431	$150,431
H	[*]	1	$495,970	$495,970
H	[*]	1	$399,344	$399,344
H	[*]	1	$5,411	$5,411
H	[*]	1	$33,848	$33,848
H	[*]	1	$26,919	$26,919
H	[*]	1	$18,456	$18,456
H	[*]	1	$61,923	$61,923
H	[*]	1	$14,690	$14,690
H	[*]	2	$14,358	$28,716
I	[*]	1	$111,991	$111,991
I	[*]	1	$129,221	$129,221
I	[*]	1	$766,409	$766,409
I	[*]	1	$93,000	$93,000
I	[*]	2	$12,050	$24,100
J	[*]	1	$190,859	$190,859
J	[*]	1	$123,407	$123,407
J	[*]	3	$190,859	$572,577
J	[*]	3	$123,407	$370,221
J	[*]	1	$150,000	$150,000
K	[*]	1	$232,690	$232,690
K	[*]	1	$30,000	$30,000
K	[*]	1	$8,477	$8,477

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

This page contains proprietary information of Amyris, Inc. that is provided for purposes of review and evaluation only on a need-to-know basis within the Government. It should not be released to persons outside the Government.

10

EX-10.03

Execution Version  Exhibit 10.03

FIRST AMENDMENT TO THE AMENDED AND RESTATED JET FUEL LICENSE AGREEMENT

This First Amendment to the Amended and Restated Jet Fuel License Agreement (the “Amendment”) is entered as of February 14, 2017 by and between Amyris, Inc., a corporation organizing and existing under the laws of the state of Delaware, with its place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608 (“AMYRIS”) and Total-Amyris BioSolutions B.V., a private company with limited liability under the laws of the Netherlands (besloten vennootschap met bepekte aansprakelijkheid)(“Company”). AMYRIS and Company are sometimes referred to herein individually as a “Party” and collectively as the “Parties”.

RECITALS

WHEREAS, on December 2, 2013 the Parties entered into a License Agreement, which was amended and restated, effective March 21, 2016 (the “Agreement”); and

WHEREAS the Parties now desire to further amend a provision in the Agreement.

NOW THEREFORE, for good and valuable consideration the receipt of which is hereby acknowledged, the Parties, intending to be legally bound, agree to the following provisions and to amend the Agreement, as follows:

1.      Defined Terms; Construction. All capitalized terms used, but not defined, in this Amendment have the same meaning as in the Agreement. References herein to a “Section” of the Agreement include the corresponding “Article” of the Agreement.

2.      Formatting Errors. The Parties desire to amend certain formatting errors found in the Agreement:

a. The third WHEREAS clause in the Agreement is incorrectly formatted as subsection “a”. Such formatting is hereby deleted.

b. No Article was identified as Article 1 of the Agreement, with the first Article in the Agreement erroneously being identified as Article 2. Therefore, each Article number is hereby reduced by one digit, with Article 2 becoming Article 1, Article 3 becoming Article 2, Article 4 becoming Article 3, and so on.

All references hereinafter to a specific “Section” or an “Article” of the Agreement shall reflect the reformatting changes set forth in this Amendment.

3.      Amendment to Section 3.D(iii)(d). Pursuant to Section 10.B of the Agreement, Section 3.D(iii)(d) of the Agreement is hereby deleted in its entirety and replaced by the following:

Execution Version 

“(d) The Parties intend that each escrow agreement governing the Escrowed Materials is “an agreement supplementary to” this Agreement, as that phrase is used in section 365(n) of the Bankruptcy Code. Company will have the right to a permanent release of the Escrowed Materials from the Escrow Agent to Company upon the occurrence of any of the following:

(i) at such time as Company is entitled to exercise the license granted in Section 3.A(i)(b);

(ii) upon the filing of a case under the Bankruptcy Code by or against AMYRIS or any Co-Licensor (as such term is defined in Section 8.E.2.);

(iii) if the Bankrupt Entity rejects the Agreement in a case under the Bankruptcy Code and Company has made the 365(n) Election (as such term is defined in Section 2.B.(iii)); or

(iv) if AMYRIS or an AMYRIS Affiliate is a Bankrupt Entity, on the written request by Company to the trustee or debtor in possession in such bankruptcy case, and to Escrow Agent, to provide the Escrowed Materials as contemplated pursuant to Bankruptcy Code section 365(n)(4).”

4.      Amendment to Section 9.G. Company hereby designates the following address for purposes of receiving notice under the Agreement:

Total Amyris BioSolutions B.V.

Hoogoorddreef 15

Amsterdam,

The Netherlands

With a copy to (which shall not constitute notice):

c/o Total Raffinage Chimie

2, place Jean Millier – La Défense 6

92078 Paris La Défense Cedex

France
Attn:

Fax. No.:

Email:

With a copy to (which shall not constitute notice):

Legal Department

Total Energies Nouvelles Activités USA

24 Cours Michelet

92800 Courbevoie

France
Attn: Department Head

5.      No Other Changes. Except as specifically modified herein, all other terms of the Agreement shall remain in full force and effect. This Amendment and the Agreement shall be read together, as one document. All references to the Agreement or in any other document referencing the Agreement shall be deemed to be a reference to the Agreement as amended by this Amendment.

[Remainder of page intentionally left blank; signature page follows]

2 of 3

Execution Version 

This Amendment is executed by the authorized representatives of the Parties as of the date first above written.

AMYRIS, INC.		TOTAL-AMYRIS BIOSOLUTIONS BV.
By:	/s/ John Melo	By:	/s/ Phillipe Marchand
Name:	John Melo	Name:	Phillipe Marchand
Title:	President & CEO	Title:	General Manager
		By:	/s/ Xavier de Maupeou
		Name:	Xavier de Maupeou
		Title:	General Manager
		By:	/s/ Remi Bourgeois
		Name:	Remi Bourgeois
		Title:	General Manager

3 of 3

EX-10.04

Execution Version Exhibit 10.04

FIRST AMENDMENT TO LICENSE AGREEMENT REGARDING DIESEL FUEL IN THE EU

This First Amendment to License Agreement regarding Diesel Fuel in the EU (this “Amendment”) is entered as of February 14, 2017 by and between Amyris, Inc., a corporation organizing and existing under the laws of the state of Delaware, with its place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608 (“Amyris”) and Total Energies Nouvelles Activités USA SAS, a société par actions simplifiée organized and existing under the laws of France, having its head-office at 24 Cours Michelet, 92800 Puteaux, France (“TOTAL”). AMYRIS and TOTAL are sometimes referred to herein individually as a “Party” and collectively as the “Parties”.

RECITALS

WHEREAS, on March 21, 2016, Amyris and TOTAL entered into a License Agreement regarding Diesel Fuel in the EU (the “Agreement”); and

WHEREAS the Parties now desire to amend certain provisions of the Agreement by entering in this Amendment.

NOW THEREFORE, for good and valuable consideration the receipt of which is hereby acknowledged, the Parties, intending to be legally bound, agree as follows:

1.      Defined Terms; Construction. All capitalized terms used, but not defined in this Amendment have the same meaning as in the Agreement. References herein to a “Section” of the Agreement include the corresponding “Article” of the Agreement.

2.      Amendment to Section 2.A(i)(d). Pursuant to Section 9.B of the Agreement, Section 2.A(i)(d) of the Agreement is hereby deleted in its entirety and replaced by the following:

“(d)       a royalty-bearing (to be negotiated as described in the prior to last sentence below), right and license under the AMYRIS Licensed IP in each case that is necessary or, in the case of the AMYRIS Farnesene Production IP, useful to Manufacture Licensed Products (x) within the Territory and (y) outside the Territory (Subject to Section 2.E(iv) below), but, in each case, solely for the purposes of Manufacturing, importing, offering for sale, and selling such Licensed Products in the Territory for use in the Field. The license granted under subsection (x) shall be co-exclusive with AMYRIS while the license in (y) shall be non-exclusive. Prior to the Licensed Products first being Manufactured per the license in this Section 2.A(i)(d), TOTAL and AMYRIS will, in good faith, negotiate commercially reasonable terms on a “most favored nation basis” for royalties to be paid to AMYRIS by TOTAL on the sale of such Manufactured Licensed Product in the Territory. Notwithstanding the immediately preceding sentence, it is the intention of the Parties that the license granted under this Section 2.A(i)(d) shall be and hereby is effective immediately upon the Effective Date”

3.      Amendment to Section 2.D(iii)(d). Pursuant to Section 9.B of the Agreement, Section 2.D(iii)(d) of the Agreement is hereby deleted in its entirety and replaced by the following:

1 of 3

Execution Version Exhibit 10.04

“(d) The Parties intend that each escrow agreement governing the Escrowed Materials is “an agreement supplementary to” this Agreement, as that phrase is used in section 365(n) of the Bankruptcy Code. TOTAL will have the right to a permanent release of the Escrowed Materials from the Escrow Agent to TOTAL upon the occurrence of any of the following:

(i) at such time as TOTAL is entitled to exercise the license granted in Section 2.A(i)(b);

(ii) upon the filing of a case under the Bankruptcy Code by or against AMYRIS or any Co-Licensor (as such term is defined in Section 7.E.2.);

(iii) if the Bankrupt Entity rejects the Agreement in a case under the Bankruptcy Code and TOTAL has made the 365(n) Election (as such term is defined in Section 2.B.(iii)); or

(iv) if AMYRIS or an AMYRIS Affiliate is a Bankrupt Entity, on the written request by TOTAL to the trustee or debtor in possession in such bankruptcy case, and to Escrow Agent, to provide the Escrowed Materials as contemplated pursuant to Bankruptcy Code section 365(n)(4).”

4.      Amendment to Section 9.G. TOTAL hereby designates the following address for purposes of receiving notice under the Agreement:

c/o Total Raffinage Chimie

2, place Jean Millier – La Défense 6

92078 Paris La Défense Cedex

France
Attn:

Fax. No.:

Email:

With a copy to (which shall not constitute notice)

Legal Department

Total Energies Nouvelles Activités USA

24 Cours Michelet

92800 Courbevoie

France
Attn: Department Head

5.      No Other Changes. Except as specifically modified herein, all other terms of the Agreement shall remain in full force and effect. This Amendment and the Agreement shall be read together, as one document. All references to the Agreement or in any other document referencing the Agreement shall be deemed to be a reference to the Agreement as amended by this Amendment.

[Remainder of page intentionally left blank; signature page follows]

2 of 3

Execution Version

This Amendment is executed by the authorized representatives of the Parties as of the date first above written.

AMYRIS, INC.		TOTAL ENERGIES NOUVELLES
		ACTIVITÉS USA
/s/ John Melo		/s/ Christophe Vuillez
Name :	John Melo	Name :	Christophe Vuillez
Title	President +CEO	Title	Attorney in fact

The following AMYRIS Affiliates existing as of the effective date of this Amendment hereby acknowledge and approve the licenses granted to TOTAL in Section 2.A of the Agreement, as modified by this Amendment.

AMYRIS Fuels LLC		AB Technologies LLC
/s/ John Melo		/s/ John Melo
Name :	John Melo	Name :	John Melo
Title	President	Title	President
AMYRIS Brasil Ltda.
/s/ Eduardo Loosli Silveira		/s/ Erica Baumgarten
	Amyris Brasil Ltda
Name :	Eduardo Loosli Silveira	Name :	Erica Baumgarten
Title	Vice Presidente Amyris Brasil	Title	CFO

3 of 3

EX-10.05

Exhibit 10.05

AMENDMENT NUMBER ONE

TO THE

AMYRIS, INC. 2010 EMPLOYEE STOCK PURCHASE PLAN

WHEREAS, Amyris, Inc., a Delaware corporation (the “Company”), maintains the Amyris, Inc. 2010 Employee Stock Purchase Plan, effective as of September 27, 2010 (the “Plan”; capitalized terms used but not defined herein shall have the meanings given to such terms in the Plan);

WHEREAS, pursuant to Section 25 of the Plan, the Leadership Development and Compensation Committee of the Board of Directors of the Company (the “Committee”) has the authority to amend the Plan, subject to stockholder approval of any Plan amendment to (i) increase the number of shares that may be issued under the Plan or (ii) change the designation of the employees (or class of employees) eligible for participation in the Plan, and subject to the limitations of Section 423 of the Internal Revenue Code of 1986, as amended; and

WHEREAS, the Committee has authorized an amendment of the Plan (this “Amendment”) to increase the maximum number of shares which may be purchased by any Participant during any one Offering Period under the Plan.

NOW, THEREFORE, BE IT RESOLVED, that the Plan is hereby amended, effective as of February 15, 2017, as follows:

Section 10(b) of the Plan is hereby amended and restated as follows:

“(b)  The Committee may, in its sole discretion, set a lower maximum number of shares which may be purchased by any Participant during any Offering Period than that determined under Section 10(a) above, which shall then be the Maximum Share Amount for subsequent Offering Periods; provided, however, in no event shall a Participant be permitted to purchase more than 8,000 Shares during any one Offering Period, irrespective of the Maximum Share Amount set forth in (a) and (b) hereof. If a new Maximum Share Amount is set, then all Participants must be notified of such Maximum Share Amount prior to the commencement of the next Offering Period for which it is to be effective. The Maximum Share Amount shall continue to apply with respect to all succeeding Offering Periods unless revised by the Committee as set forth above.”

***

IN WITNESS WHEREOF, the Company has caused this Amendment to be executed by its duly authorized officer as of February 16, 2017.

AMYRIS, INC.
By:	/s/ John Melo
Name:	John Melo
Title:	President and Chief Executive Officer

EX-10.06

Exhibit 10.06

Execution Version

AMENDMENT #2 TO THE SECOND AMENDMENT

TO THE TECHNOLOGY, LICENSE, DEVELOPMENT, RESEARCH AND COLLABORATION AGREEMENT

This Amendment #2 to the Second Amendment to the Technology, License, Development, Research and Collaboration Agreement (the “Amendment #2”) is entered into to be effective as of February 28, 2017 (the “Amendment #2 Effective Date”), by and between Amyris, Inc., a Delaware corporation having its place of business at 5885 Hollis Street, Suite 100, Emeryville, California 94608 (“AMYRIS”) and Total Energies Nouvelles Activités USA SAS (formerly known as Total Gas & Power USA SAS), a company existing and organized under the French law having its head office located at 24, cours Michelet, 92800 Puteaux, France (“TOTAL”). AMYRIS and TOTAL are sometimes referred to herein individually as a “Party” and collectively as the “Parties”.

RECITALS

WHEREAS, on June 21, 2010, AMYRIS and TOTAL Gas & Power USA Biotech, Inc. entered into the Technology License, Development, Research and Collaboration Agreement, as amended by the First Amendment dated as of November 23, 2011 (the “Agreement”);

WHEREAS, TOTAL Gas & Power USA Biotech, Inc. assigned the Agreement to TOTAL as set forth in that certain letter dated January 11, 2011;

WHEREAS, on July 30, 2012, TOTAL and AMYRIS amended certain portions of the Agreement by entering into the Second Amendment to the Technology, License, Development, Research and Collaboration Agreement (as subsequently amended by the Amendment #1 to the Second Amendment to the Technology, License, Development, Research and Collaboration Agreement on April 1, 2015, collectively, the “Second Amendment”);

WHEREAS the Parties now desire to further amend a provision in the Second Amendment; and

NOW THEREFORE, for good and valuable consideration the receipt of which is hereby acknowledged, the Parties, intending to be legally bound, agree to the following provisions and to amend the Second Amendment, as follows:

1.Defined Terms. All capitalized terms used, but not defined, in this Amendment #2 have the same meaning as in the Agreement.

2.Amend Section 3.B to Extend the Term. Pursuant to Section 13.2 of the Agreement, the Parties hereby delete Section 3.B of the Second Amendment in its entirety and replace it with the following new Section 3.B:

“B. Term. Unless otherwise extended by the Parties via a signed written agreement, the Biofene Development Project shall continue until the earliest to occur of (i) the Parties terminate the Biofene Development Project by mutual written agreement signed by the Parties; or (ii) December 31, 2017.”

3.       No Other Changes. Except as specifically modified herein, all other terms of the Second Amendment and the Agreement shall remain in full force and effect.

This Amendment #2 is executed by the authorized representatives of the Parties as of the Amendment #2 Effective Date,

1 of 2

Execution Version

AMYRIS, INC.		TOTAL ENERGIES NOUVELLES ACTIVITES USA, SAS
	/s/ John Melo		/s/ Christophe Vuillez
Name	John Melo	Name	Christophe Vuillez
Title:	President & CEO	Title:	Attorney in Fact

2 of 2

EX-10.07

CONFIDENTIAL TREATMENT REQUESTED. CERTAIN PORTIONS OF THIS DOCUMENT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT AND, WHERE APPLICABLE, HAVE BEEN MARKED WITH AN ASTERISK TO DENOTE WHERE OMISSIONS HAVE BEEN MADE. THE CONFIDENTIAL MATERIAL HAS BEEN FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE COMMISSION.

Exhibit 10.07

Total Energies Nouvelles Activités USA SAS

24 Cours Michelet

92800 Puteaux

France

February 28, 2017

Amyris, Inc.

5885 Hollis Street, Suite 100

Emeryville, California 94608

USA
Attention: Mr. John Melo, President & CEO

Total New Energies, Inc.

1201 Louisiana Street, Suite 1600

Houston, Texas 77002

USA

Attention: Mrs Isabelle Kieffer, CEO

Total Amyris BioSolutions B.V.

Hoogoorddreef 15

1101 BA Amsterdam

Netherlands

Attention: Mr Philippe Marchand, General Manager

SIDE LETTER

Reference is made to (i) that certain Technology License, Development, Research and Collaboration Agreement between Amyris, Inc. (“Amyris”) and Total New Energies Inc. (“TNE”, formerly known as Total Gas & Power USA Biotech, Inc.), dated as of June 21, 2010 (as such agreement may be amended from time to time by the parties thereto, including by that certain Amendment # 2 to the Second Amendment to the Collaboration Agreement, effective as of February 28, 2017, the “Collaboration Agreement”), which Collaboration Agreement was assigned by TNE by letter agreement dated January 11, 2011 to Total Energies Nouvelles Activités USA SAS (“TENA”, formerly known as Total Gas & Power USA SAS); (ii) that certain Amended and Restated Secondment Agreement between TNE and Amyris, dated August 1, 2012 (as such agreement may be amended from time to time by the parties thereto, including by that certain Amendment #1 to the Secondment Agreement, effective as of May 1, 2016, the “Secondment Agreement”); (iii) that certain License Agreement between Amyris and Total Amyris BioSolutions B.V. (the “Company”), dated December 2, 2013, which was amended and restated on March 21, 2016 (as such agreement may be amended from time to time by the parties thereto, including by that certain First Amendment to the Amended and Restated Jet Fuel License Agreement, effective as of February 14, 2017, the “Amended and Restated Jet Fuel License Agreement”); and (iv) that certain License Agreement regarding Diesel Fuel in the EU between Amyris and TENA, dated March 21, 2016 (as such agreement may be amended from time to time by the parties thereto, including by that certain First Amendment to License Agreement regarding Diesel Fuel in the EU, effective as of February 14, 2017, the “Diesel Fuel License Agreement”, and together with the Collaboration Agreement, the Secondment Agreement and the Amended and Restated Jet Fuel License Agreement, collectively, the “Agreements”).

1

In addition to the rights and obligations of the parties hereto provided in the Agreements, we are writing to you to confirm our mutual agreement on the issues set out below.

1. Definitions.

Capitalized terms used herein but not otherwise defined shall have the meaning set forth in the applicable Agreement.

2. Extension of Biofene Development Project.

a. On July 29, 2016 the Management Committee decided to extend the term of the Biofene Development Project from July 31, 2016 to March 1, 2017. TENA and Amyris have further extended the term of the Biofene Development Project until December 31, 2017, as per that certain Amendment # 2 to the Second Amendment to the Collaboration Agreement, effective as of February 28, 2017 (“Amendment #2”).

b. The parties hereto agree that each of (i) the Management Committee’s decision on July 29, 2016 to extend the term of the Biofene Development Program to March 1, 2017, and (ii) Amendment #2, is a Biofene Development Project Extension Agreement, as such term is used in each of the Diesel Fuel License Agreement and the Jet Fuel License Agreement.

c. For purposes of clarification, the expiration of the Biofene Development Project Extension Agreement shall automatically occur on the date that Biofene Development Project terminates as per Amendment #2.

3. Outstanding Amount Owed by Amyris for Seconded Employees as of May 1, 2016.

a. The parties hereto agree that the aggregate unpaid Amyris Share owed by Amyris as per the Secondment Agreement, equals [*]. However, TNE agrees that Amyris may deduct from such outstanding amount the sum of [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

2

[*] as and for satisfaction of the rent payment obligation of TENA through December 31, 2017, under the Sublease between the Amyris and TENA, dated April 4, 2014. As a result of such deduction, the parties hereto agree that Amyris’ outstanding balance for the Amyris Share is [*] (the “Agreed Upon Secondee Payable”).

b. The Agreed Upon Secondee Payable will be paid by Amyris to TNE on or before June 30, 2017. Such payment shall satisfy all Amyris payment obligations related to Amyris Share, and claims related to any past-due payment thereof.

4. Biofene Development Project Milestones.

Amyris and TENA agree that the 2017 quarterly technical milestones of the Biofene Development Project are described in Appendix A, attached hereto and incorporated herein by reference.

5. Biofene Development Project Expenses.

Each of Amyris and TENA agrees to track (i) the hours that its employees (including, in the case of TENA, its Seconded Employees at the Amyris Facilities) spend working on the Biofene Development Project after April 30, 2016 and (ii) the expenses incurred for third-party services and/or equipment for the Biofene Development Project after April 30, 2016.

6. Out-of-Scope Expenses.

On the request of either Amyris or TENA, the other party shall consider on a case-by-case basis whether to share the cost of third-party expenses incurred outside the scope of the Biofene Development Project. Any agreement reached between Amyris and TENA in this respect must be evidenced in writing and signed by both parties.

7. Miscellaneous.

a. This Side Letter and any arbitration hereunder shall be governed by, interpreted and construed and enforced in accordance with, the laws of the State of New York, without giving effect to any conflicts of laws principles thereof. Each party irrevocably consents and agrees that any action for relief brought against it with respect to its obligations or liabilities under or arising out of or in connection with this Side Letter may be brought in the United States District Court for the Southern District of New York, unless no federal subject matter jurisdiction exists, in which case the action may be brought in the courts of the State of new York located in the Borough of Manhattan, and each party herby irrevocably accept and unconditionally submits to the non-exclusive jurisdiction of aforesaid courts in personam, with respect to any action for relieve. The language of any proceedings and of all submissions and written evidence shall be English; provided, however, that a party, at its expense, may provide for translation or simultaneous interpretation into a language other than English.

*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

3

b. Neither this Side Letter nor any right or obligations hereunder may be assigned or delegated by any of the parties hereto without the written consent of the other parties hereto, except that TENA may assign the Side Letter and its rights and obligations hereunder to its affiliate Total Raffinage Chimie, S.A., by giving written notice of such assignment to Amyris.

c. This Side Letter may be executed in multiple counterparts, each of which will be deemed to be an original and all of which will be deemed to be a single document.

Very truly yours,

Total Energies Nouvelles Activités USA SAS

By:	/s/ Christophe Vuillez
Name:	Christophe Vuillez
Title:	Attorney in Fact

4

Agreed and accepted by:

Amyris, Inc.
By:	/s/ John Melo
Name	John Melo
Title:	President & CEO
Total New Energies, Inc.
By:	/s/ Isabelle Kieffer
Name	Isabelle Kieffer
Title:	Chief Executive Officer
Total Amyris BioSolutions B. V.
By:	/s/ Xavier de Maupeou
Name	Jean-Marc Otereo del Val Xavier de Maupeou
Title:	General Manager
By:	/s/ Remi Bourgeois
Name	Remi Bourgeois
Title:	General Manager
By:	/s/ Philippe Marchand
Name	Philippe Marchand
Title:	General Manager

5

Exhibit A

2017 quarterly technical milestones for the Biofene Program

	YE 2016 ActualA	2017 Q1 GoalA	2017 Q2 GoalA	2017 Q3 GoalA	2017 Q4 GoalB
Fermentation yield (wt. %)	[*]	[*]	[*]	[*]	[*]
Productivity (g/L/h)	[*]	[*]	[*]	[*]	[*]
Recovery yield (wt. %)C	[*]	[*]	[*]	[*]	[*]

^A Fermentation yield and productivity to be measured at [*]

^B Fermentation yield and productivity to be measured at [*]

^C Recovery yield to be monitored at [*]

[*] Certain portions denoted with an asterisk have been omitted and filed separately with the Securities and Exchange Commission. Confidential treatment has been requested with respect to the omitted portions.

A-1

EX-10.08

Exhibit 10.08

March 6, 2017

Kathleen Valiasek

Dear Kathy:

This letter amends the offer letter between you and Amyris, Inc. (“Amyris” or the “Company”) dated November 23, 2016 (the “Original Offer Letter”). The Original Offer Letter shall be amended by amending and restating the section of the Original Offer Letter entitled “Termination and Change in Control Benefits” (including the related Exhibit A thereto) as follows (this “Amendment”):

Termination and Change in Control Benefits

As an executive of Amyris, you will be eligible to participate in the Company’s Executive Severance Plan (the “Severance Plan”), a copy of which is attached hereto as Exhibit A. In order to participate in the Severance Plan, you will be required to execute the “Participation Agreement” in the form attached to the Severance Plan and to comply with the other terms of the Severance Plan.

Please confirm your acceptance of this Amendment by signing and returning the enclosed copy of this letter.

Sincerely,

/s/ Christine Ofori

Christine Ofori

Chief Human Resources Officer

I HAVE READ AND ACCEPT THIS AMENDMENT:

/s/ Kathleen Valiasek	3/3/2017            , 2017
Kathleen Valiasek	Date

Enclosures:

Executive Severance Plan (Exhbit A)

1

EXHIBIT A

EXECUTIVE SEVERANCE PLAN

EX-31.01

Exhibit 31.01

CERTIFICATION OF CHIEF EXECUTIVE OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, John Melo, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Amyris, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: May 15, 2017	/s/  JOHN G. MELO
	John Melo
	President and Chief Executive Officer

EX-31.02

Exhibit 31.02

CERTIFICATION OF CHIEF FINANCIAL OFFICER

PURSUANT TO RULE 13a-14(c) and 15d-(14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

I, Kathleen Valiasek, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Amyris, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: May 15, 2017	/s/  KATHLEEN VALIASEK
	Kathleen Valiasek
	Chief Financial Officer

EX-32.01

Exhibit 32.01

Certification of CEO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended March 31, 2017, as filed with the Securities and Exchange Commission on the date hereof, I, John Melo, Chief Executive Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended March 31, 2017 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: March 15, 2017	/s/  JOHN G. MELO
	John Melo
	President and Chief Executive Officer
	(Principal Executive Officer)

EX-32.02

Exhibit 32.02

Certification of CFO Furnished Pursuant to 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act of 2002

In connection with the Quarterly Report of Amyris, Inc. (the “Company”) on Form 10-Q for the quarterly period ended March 31, 2017, as filed with the Securities and Exchange Commission on the date hereof, I, Kathleen Valiasek, Chief Financial Officer of the Company, certify for the purposes of section 1350 of chapter 63 of title 18 of the United States Code, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge,

(i) the Quarterly Report of the Company on Form 10-Q for the quarterly period ended March 31, 2017 (the “Report”), fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934, and

(ii) the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: May 15, 2017	/s/  KATHLEEN VALIASEK
	Kathleen Valiasek
	Chief Financial Officer
	(Principal Financial Officer)

XML

Document And Entity Information - shares	3 Months Ended
	Mar. 31, 2017	Apr. 30, 2017
Document Information [Line Items]
Entity Registrant Name	AMYRIS, INC.
Entity Central Index Key	0001365916
Trading Symbol	amrs
Current Fiscal Year End Date	--12-31
Entity Filer Category	Smaller Reporting Company
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Well-known Seasoned Issuer	No
Entity Common Stock, Shares Outstanding (in shares)		297,086,351
Document Type	10-Q
Document Period End Date	Mar. 31, 2017
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	Q1
Amendment Flag	false

XML

Condensed Consolidated Balance Sheets (Unaudited) - USD ($) $ in Thousands		Mar. 31, 2017	Dec. 31, 2016
Assets
Cash and cash equivalents		$ 1,297	$ 27,150
Restricted cash		301	4,326
Short-term investments		1,188	1,374
Accounts receivable, net of allowance of $478 and $478, respectively		8,122	13,105
Related party accounts receivable, net of allowance of $23 and $23, respectively		416	872
Inventories, net		7,077	6,213
Prepaid expenses and other current assets		5,652	6,083
Total current assets		24,053	59,123
Property, plant and equipment, net		53,045	53,735
Restricted Cash and Cash Equivalents, Noncurrent		958	957
Equity and loans in affiliates		34	34
Other assets		16,794	15,464
Goodwill and intangible assets		560	560
Total assets		95,444	129,873
Liabilities, Mezzanine Equity and Stockholders' Deficit
Accounts payable		16,453	15,315
Deferred revenue		3,487	5,288
Accrued and other current liabilities		31,806	29,188
Capital lease obligation, current portion		405	922
Debt, current portion		15,290	25,853
Related party debt		34,165	33,302
Total current liabilities		101,606	109,868
Capital lease obligation, net of current portion		405	334
Long-term debt, net of current portion		131,759	128,744
Related party debt		39,724	39,144
Deferred rent, net of current portion		8,691	8,906
Deferred revenue, net of current portion		6,650	6,650
Derivative liabilities		5,144	6,894
Other liabilities		7,716	7,841
Total liabilities		301,695	308,381
Commitments and contingencies (Note 6)
Contingently redeemable common stock (Note 8)	[1]	5,000	5,000
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding
Common stock - $0.0001 par value, 500,000,000 and 500,000,000 shares authorized as of March 31, 2017 and December 31, 2016, respectively; 287,973,020 and 274,108,808 shares issued and outstanding as of March 31, 2017 and December 31, 2016, respectively		28	27
Additional paid-in capital		1,000,174	990,870
Accumulated other comprehensive loss		(40,581)	(40,904)
Accumulated deficit		(1,171,809)	(1,134,438)
Total Amyris, Inc. stockholders’ deficit		(212,188)	(184,445)
Noncontrolling interest		937	937
Total stockholders' deficit		(211,251)	(183,508)
Total liabilities, mezzanine equity and stockholders' deficit		$ 95,444	$ 129,873

[1] See Note 8, "Significant Agreements" for details regarding the Bill & Melinda Gates Foundation Investment, classified as mezzanine equity.

XML

Condensed Consolidated Balance Sheets (Unaudited) (Parentheticals) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Allowance for doubtful accounts	$ 478	$ 478
Related party accounts receivable allowace	$ 23	$ 23
Preferred stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Preferred stock, shares authorized (in shares)	5,000,000	5,000,000
Preferred stock, shares issued (in shares)	0	0
Preferred stock, shares outstanding (in shares)	0	0
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized (in shares)	500,000,000	500,000,000
Common stock, shares issued (in shares)	287,973,020	274,108,808
Common stock, shares outstanding (in shares)	287,973,020	274,108,808

XML

Condensed Consolidated Statements of Operations (Unaudited) - USD ($)	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Renewable product sales	$ 8,292,000	$ 3,140,000
Grants and collaborations revenue	4,688,000	5,671,000
Total revenues	12,980,000	8,811,000
Cost and operating expenses
Cost of products sold	12,768,000	11,178,000
Research and development	14,778,000	11,906,000
Sales, general and administrative	12,778,000	12,266,000
Total cost and operating expenses	40,324,000	35,350,000
Loss from operations	(27,344,000)	(26,539,000)
Other income (expense):
Interest income	61,000	57,000
Interest expense	(12,184,000)	(8,359,000)
Gain from change in fair value of derivative instruments	2,339,000	21,678,000
Gain/(loss) upon extinguishment of debt	96,000	(216,000)
Other expense, net	(380,000)	(1,814,000)
Total other income (expense)	(10,068,000)	11,346,000
Loss before income taxes	(37,412,000)	(15,193,000)
(Benefit from)/provision for income taxes	41,000	(115,000)
Net loss	(37,371,000)	(15,308,000)
Net loss attributable to noncontrolling interest
Net loss attributable to Amyris, Inc. common stockholders	$ (37,371,000)	$ (15,308,000)
Net loss per share attributable to common stockholders:
Basic (in dollars per share)	$ (0.13)	$ (0.07)
Diluted (in dollars per share)	$ (0.13)	$ (0.12)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock:
Basic (in shares)	290,039,216	207,199,563
Diluted (in shares)	290,039,216	260,932.09

XML

Condensed Consolidated Statements of Comprehensive Loss (Unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Comprehensive loss:
Net loss	$ (37,371)	$ (15,308)
Foreign currency translation adjustment, net of tax	323	4,687
Total comprehensive loss	(37,048)	(10,621)
Loss attributable to noncontrolling interest	0	0
Comprehensive loss attributable to Amyris, Inc.	$ (37,048)	$ (10,621)

XML

Condensed Consolidated Statements of Stockholders' Deficit (Unaudited) - 3 months ended Mar. 31, 2017 - USD ($) $ in Thousands	Common Stock [Member]	Additional Paid-in Capital [Member]	Retained Earnings [Member]	AOCI Attributable to Parent [Member]	Noncontrolling Interest [Member]	Mezzanine Equity [Member]	Total
Balance (in shares) at Dec. 31, 2016	274,108,808
Balance at Dec. 31, 2016	$ 27	$ 990,870	$ (1,134,438)	$ (40,904)	$ 937	$ 5,000	$ (183,508)
Issuance of common stock upon exercise of stock options, net of restricted stock (in shares)	500						500
Issuance of common stock for settlement of debt principal payments (in shares)	13,546,448
Interest capitalized to debt	$ 1	7,680					$ 1,115
Shares issued from restricted stock settlement (in shares)	317,264
Shares issued from restricted stock settlement		(22)					(22)
Stock-based compensation		1,646					1,646
Foreign currency translation adjustment, net of tax				323			323
Net income (loss)			(37,371)				(37,371)
Balance (in shares) at Mar. 31, 2017	287,973,020
Balance at Mar. 31, 2017	$ 28	$ 1,000,174	$ (1,171,809)	$ (40,581)	$ 937	$ 5,000	$ (211,251)

XML

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($)	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Operating activities
Net loss	$ (37,371,000)	$ (15,308,000)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	2,715,000	2,869,000
Loss on disposal of property, plant and equipment	(55,000)	(37,000)
Stock-based compensation	1,646,000	2,051,000
Amortization of debt discount and issuance costs	4,473,000	2,994,000
(Gain)/loss upon extinguishment of debt	(96,000)	216,000
Gain from change in fair value of derivative instruments	(2,339,000)	(21,678,000)
(Gain)/loss on foreign currency exchange rates	(295,000)	1,117,000
Changes in assets and liabilities:
Accounts receivable	4,888,000	(1,484,000)
Related party accounts receivable	500,000	(300,000)
Inventories, net	(867,000)	3,870,000
Prepaid expenses and other assets	(713,000)	1,288,000
Accounts payable	450,000	(810,000)
Accrued and other liabilities	3,730,000	2,924,000
Deferred revenue	(1,844,000)	(1,292,000)
Deferred rent	(215,000)	(163,000)
Net cash used in operating activities	(25,393,000)	(23,743,000)
Investing activities
Purchase of short-term investments	(1,781,000)	(1,377,000)
Maturities of short-term investments	2,094,000	1,627,000
Change in restricted cash	4,040,000	13,000
Purchases of property, plant and equipment, net of disposals	(457,000)	(271,000)
Net cash provided by (used in) investing activities	3,896,000	(8,000)
Financing activities
Employees' taxes paid upon vesting of restricted stock units	(22,000)	(48,000)
Principal payments on capital leases	(627,000)	(160,000)
Proceeds from debt issued	1,500,000
Proceeds from debt issued to related party		20,000,000
Principal payments on debt	(4,273,000)	(729,000)
Net cash provided by (used in) financing activities	(3,762,000)	19,063,000
Effect of exchange rate changes on cash and cash equivalents	(83,000)	522,000
Net decrease in cash and cash equivalents	(25,853,000)	(4,166,000)
Cash and cash equivalents at beginning of period	27,150,000	11,992,000
Cash and cash equivalents at end of period	1,297,000	7,826,000
Supplemental disclosures of cash flow information:
Cash paid for interest	1,863,000	990,000
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	(821,000)	(521,000)
Financing of equipment	180,000	100,000
Financing of insurance premium under notes payable	(146,000)	(159,000)
Issuance of common stock for settlement of debt principal and interest payments	7,681,000
Interest capitalized to debt	1,115,000	1,010,000
Purchase of property, plant and equipment via deposit		24,000
Non-cash investment in joint venture		600,000
Cancellation of debt and accrued interest on disposal of interest in affiliate		$ 4,252,000

XML

Note 1 - The Company

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Nature of Operations [Text Block]

1.

The Company

Amyris, Inc. (or the Company) was incorporated in California on

July

17,

2003

and reincorporated in Delaware on

April

15,

2010

for the purpose of leveraging breakthroughs in bioscience technology to develop and provide renewable compounds for a variety of markets. The Company is currently applying its industrial synthetic biology platform to engineer, manufacture and sell high performance, low cost products into Health and Nutrition, Personal Care and Performance Material markets. The Company's

first

commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene (Biofene®), which forms the basis for a wide range of products including nutraceuticals, skin care, fragrances, solvents, polymers, and lubricants ingredients. In

2014,

the Company began manufacturing additional molecules for the flavors and fragrance (F&F) industry, in

2015

the Company began investing to expand its capabilities to other small molecule chemical classes beyond terpenes via its collaboration with the Defense Advanced Research Project Agency, as discussed below, and in

2016

the Company expanded into proteins. While the Company's platform is able to use a wide variety of feedstocks, the Company has initially focused on Brazilian sugarcane because of its renewability, low cost and relative price stability. The Company has established

one

principal operating subsidiary, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., or Amyris Brasil) which oversees the Company’s production operations in Brazil.

The Company's renewable products business strategy is to generally focus on direct commercialization of specialty products while moving established commodity products into joint venture arrangements with leading industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture its products at commercial scale and on an economically viable basis (i.e., low per unit production costs) and developing sufficient sales volume for those products to support its operations. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development.

Liquidity

The Company expects to fund its operations for the foreseeable future with cash and investments currently on hand, with cash inflows from collaborations and grants, with cash contributions from product sales, with new debt and equity financings and with proceeds from strategic asset divestments. The Company's planned

2017

and

2018

working capital needs and its planned operating and capital expenditures are dependent on significant inflows of cash from new and existing collaboration partners and from cash generated from renewable product sales and from strategic asset divestments, and will also require additional funding from debt or equity financings.

The Company has incurred significant operating losses since its inception and believes that it will continue to incur losses and negative cash flow from operations into at least

2018.

As of

March

 

31,

2017,

the Company had negative working capital of

$77.6

million, an accumulated deficit of

$1,171.8

million, and had cash, cash equivalents and short term investments of

$2.5

million. The Company will need additional financing as early as the

second

quarter of

2017

to support its liquidity needs. See Note

18,

“Subsequent Events” for details regarding financing transactions completed subsequent to

March

31,

2017.

These factors raise substantial doubt about the Company’s ability to continue as a going concern within

one

year after the date that the financial statements are issued. The financial statements do not include any adjustments that might result from the outcome of this uncertainty. If the Company is unable to continue as a going concern, it

may

be unable to meet its obligations under its existing debt facilities, which could result in an acceleration of its obligation to repay all amounts outstanding under those facilities, and it

may

be forced to liquidate its assets.

As of

March

 

31,

2017,

the Company's debt, net of discount and issuance costs of

$42.0

million, totaled

$220.9

million, of which

$49.5

million is classified as current. In addition to upcoming debt maturities, the Company's debt service obligations over the next

twelve

months are significant, including

$20.8

million of anticipated cash interest payments. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults such as restrictions on additional indebtedness, material adverse effect and cross default clauses. A failure to comply with the covenants and other provisions of the Company’s debt instruments, including any failure to make a payment when required would generally result in events of default under such instruments, which could permit acceleration of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of default under the Company’s other outstanding indebtedness, permitting acceleration of such other outstanding indebtedness. Any required repayment of such indebtedness as a result of acceleration or otherwise would consume current cash on hand such that the Company would not have those funds available for use in its business or for payment of other outstanding indebtedness. Please refer to Note

5,

“Debt and Mezzanine Equity”, Note

6,

“Commitments and Contingencies” and Note

18,

“Subsequent Events” for further details regarding the Company's debt service obligations and commitments. The Company also has a significant working capital deficit and contractual obligations related to capital and operating leases, as well as purchase commitments.

In addition to the need for financing described above, the Company

may

take the following actions as early as the

second

quarter of

2017

to support its liquidity needs through the remainder of

2017

and into

2018:

• Effect significant headcount reductions, particularly with respect to employees not connected to critical or contracted activities across all functions of the Company, including employees involved in general and administrative, research and development, and production activities.

• Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts.

• Reduce production activity at the Company’s Brotas manufacturing facility to levels only sufficient to satisfy volumes required for product revenues forecast from existing products and customers.

• Reduce expenditures for third party contractors, including consultants, professional advisors and other vendors.

• Reduce or delay uncommitted capital expenditures, including non-essential facility and lab equipment, and information technology projects.

• Closely monitor the Company’s working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on the Company's ability to continue its business as currently contemplated, including, without limitation, delays or failures in its ability to:

• Achieve planned production levels;

• Develop and commercialize products within planned timelines or at planned scales; and

• Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have an adverse effect on the Company's ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

XML

Note 2 - Summary of Significant Accounting Policies

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Significant Accounting Policies [Text Block]

2.

Summary of Significant Accounting Policies

Basis of Presentation

The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (or “GAAP”) and with the instructions for Form

10

-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form

10

-K for the fiscal year ended

December

31,

2016

as filed with the Securities and Exchange Commission (or the “SEC”) on

April

17,

2017.

The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

The Company uses the equity method to account for investments in companies, if its investments provide it with the ability to exercise significant influence over operating and financial policies of the investee. Consolidated net income or loss includes the Company’s proportionate share of the net income or loss of these companies. Judgments made by the Company regarding the level of influence over each equity method investment include considering key factors such as the Company’s ownership interest, representation on the board of directors, participation in policy-making decisions and material intercompany transactions.

Principles of Consolidation

The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and

two

consolidated variable interest entities (or “VIEs”), with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 

7,

"Joint Ventures and Noncontrolling Interest."

Variable Interest Entities

The Company has interests in joint venture entities that are VIEs. Determining whether to consolidate a VIE requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

Use of Estimates

In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements, except for the impact of adoption of certain accounting standards as described below, and in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented. In the quarter ended

March

31,

2017

the Company adopted Accounting Standards Update (“ASU”) No.

2015

-

11,

Simplifying the Measurement of Inventory

, ASU No.

2016

-

06,

Contingent Put and Call Options in Debt Instruments

, ASU No.

2016

-

09,

Compensation - Stock Compensation (Topic

718):

Improvements to Employee Share-Based Payment Accounting

. None of the ASU’s adopted had a material impact on the Company’s condensed consolidated financial statements.

The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.

Recent Accounting Pronouncements

In

November

2016,

the Financial Accounting Standards Board (FASB) issued ASU

2016

-

18

Statement of Cash Flows - Restricted Cash.

The amendments in this update require that a statement of cash flows explain the change during the period in the total of cash, cash equivalents, and amounts generally described as restricted cash or restricted cash equivalents. Therefore, amounts generally described as restricted cash and restricted cash equivalents should be included with cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. The amendments in this update are effective for public business entities for fiscal years beginning after

December

15,

2017,

and interim periods within those fiscal years. Early adoption is permitted, including adoption in an interim period. The amendments in this update should be applied using a retrospective transition method to each period presented. The Company has not adopted the update. Upon adoption this would result in a change in the presentation of restricted cash in the statement of cash flows.

In

October

2016,

FASB issued ASU

2016

-

16,

Intra-Entity Transfers of Assets Other Than Inventory

on simplifying the accounting for income taxes related to intra-entity asset transfers. The new guidance allows an entity to recognize the tax expense from the sale of an asset in the seller’s tax jurisdiction when the transfers occur, even though the pre-tax effects of that transaction are eliminated in consolidation. This guidance will be effective for fiscal years, and interim periods within those fiscal years, beginning after

December

15,

2017.

Early adoption is permitted only in the

first

quarter of

2017.

The Company does not expect a material impact on its financial statements upon adoption of this standard.

In

August

2016,

FASB issued ASU

2016

-

15

Classification of Certain Cash Receipts and Cash Payments

on the statement of cash flows. The new guidance clarifies classification of certain cash receipts and cash payments in the statement of cash flows. This guidance will be effective for fiscal years, and interim periods within those fiscal years, beginning after

December

15,

2017

and interim periods within those fiscal years. Early adoption is permitted. The Company is evaluating the impact of adopting this accounting standard update on the financial statements and related disclosures.

In

June

2016,

FASB issued ASU No.

2016

-

13,

Allowance for Loan and Lease Losses (Financial Instruments - Credit Losses Topic

326)

. New impairment guidance for certain financial instruments (including trade receivables) will replace the current “incurred loss” model for estimating credit losses with a forward looking “expected loss” model. The ASU is effective for the Company for fiscal years beginning after

December

15,

2019,

including interim periods within those fiscal years. Early application is permitted as of the fiscal years beginning after

December

15,

2018,

including interim periods within those fiscal years. The Company is evaluating the impact of this standard on its financial statements.

In

February

2016,

FASB issued Accounting Standards

Update2016

-

02

-

Leases

with fundamental changes to how entities account for leases. Lessees will need to recognize a right-of-use asset and a lease liability for virtually all of their leases (other than leases that meet the definition of a short-term lease). The liability will be equal to the present value of lease payments. The asset will be based on the liability, subject to adjustment, such as for initial direct costs. Additional disclosures for leases will also be required. The standard is effective for fiscal years, and interim periods within those fiscal years, beginning after

December

15,

2018.

Early adoption is permitted. The new standard must be adopted using a modified retrospective transition, and provides for certain practical expedients. The new standard

may

materially impact the Company’s financial statements.

In

January

2016,

FASB issued Accounting Standards Update

2016

-

01

Financial Instruments-Overall

, which address certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. The amendments in this update are effective for fiscal years beginning after

December

15,

2017,

including interim periods within those fiscal years. Earlier application is permitted under specific circumstances. The Company expects the new standard to impact the extent of its disclosures of financial instruments, particularly in relation to fair value disclosures, but otherwise does not expect a significant impact from the new standard.

In

May

2014,

FASB issued new guidance related to revenue recognition. In

March,

April,

May

and

December

2016,

the FASB issued additional amendments to the new revenue guidance relating to reporting revenue on a gross versus net basis, identifying performance obligations, licensing arrangements, collectability, noncash consideration, presentation of sales tax, and transition. This new standard will replace all current GAAP guidance on this topic and eliminate all industry-specific guidance. The new revenue recognition update guidance provides a unified model to determine how revenue is recognized. The core principle of the guidance is that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The FASB has issued several updates to the standard which i) clarify the application of the principal versus agent guidance (ASU

2016

-

08);

ii) clarify the guidance on inconsequential and perfunctory promises and licensing (ASU

2016

-

10)

and iii) narrow-scope improvements and practical expedients (ASU

2016

-

12).

On

July

9,

2015,

the FASB voted to defer the effective date by

one

year to

December

15,

2017

for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of

December

15,

2016.

Entities have the option of using either a full retrospective or a modified retrospective approach to adopt the new standard. Therefore, the new standard will be effective commencing with our quarter ending

March

31,

2018.

The Company is currently assessing the potential impact of this new standard on its financial statements and has not selected the transition method. While the Company continues to assess the impact of the new guidance on its revenue recognition policies, it is expected that a key area will be the assessment of contract modifications and collaboration contracts to determine if identification of performance obligations is impacted, which

may

impact the timing of revenue recognition. In addition, the Company expects additional disclosures related to revenue.

XML

Note 3 - Fair Value of Financial Instruments

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Financial Instruments Disclosure [Text Block]

3.

Fair Value of Financial Instruments

The inputs to the valuation techniques used to measure fair value are classified into the following categories:

Level

1:

Quoted market prices in active markets for identical assets or liabilities.

Level

2:

Observable market-based inputs or unobservable inputs that are corroborated by market data.

Level

3:

Unobservable inputs that are not corroborated by market data.

There were no transfers between the levels, and as of

March

 

31,

2017,

the Company’s financial assets and financial liabilities at fair value were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of March 31, 2017
Financial Assets
Money market funds	$	297	$	—	$	—	$	297
Certificates of deposit		1,188		—		—		1,188
Total financial assets	$	1,485	$	—	$	—	$	1,485
Financial Liabilities
Loans payable (1)	$	—	$	51,378	$	—	$	51,378
Credit facilities  (1)		—		50,891		—		50,891
Convertible notes (1)		—		—		115,268		115,268
Compound embedded derivative liabilities		—		—		2,728		2,728
Currency interest rate swap derivative liability		—		2,961		—		2,961
Total financial liabilities	$	—	$	105,230	$	117,996	$	223,226

________

(1)

These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.

The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds and certificates of deposit are based on fair values of identical assets. The fair values of the loans payable, convertible notes, credit facilities and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. The method of determining the fair value of the compound embedded derivative liabilities is described subsequently in this note. Market risk associated with the fixed and variable rate long-term loans payable, credit facilities and convertible notes relates to the potential reduction in fair value and negative impact to future earnings, from an increase in interest rates. Market risk associated with the compound embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable.

As of

December

 

31,

2016,

the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands):

	Level 1		Level 2		Level 3		Balance as of December 31, 2016
Financial Assets
Money market funds	$	1,549	$	—	$	—	$	1,549
Certificates of deposit		1,373		—		—		1,373
Total financial assets	$	2,922	$	—	$	—	$	2,922
Financial Liabilities
Loans payable (1)	$	—	$	53,579	$	—	$	53,579
Credit facilities  (1)		—		51,261		—		51,261
Convertible notes (1)		—		—		117,767		117,767
Compound embedded derivative liabilities		—		—		4,135		4,135
Currency interest rate swap derivative liability		—		3,343		—		3,343
Total financial liabilities	$	—	$	108,183	$	121,902	$	230,085

_______

(1)

These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis (noting that the Remaining Notes subject to the Maturity Treatment Agreement were revalued to fair value on

July

29,

2015,

see Note

5

“Debt and Mezzanine Equity” and Note

18,

“Subsequent Events” for details).

The following table provides a reconciliation of the beginning and ending balances for the convertible notes disclosed at fair value using significant unobservable inputs (Level

3)

(in thousands):

	2017
Balance at January 1	$	117,767
New instruments		15,049
Conversion/extinguishment of convertible notes		(21,077	)
Change in fair value of convertible notes		3,529
Balance at March 31	$	115,268

Derivative Instruments

The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liabilities measured at fair value using significant unobservable inputs (Level

3)

(in thousands):

	2017
Balance at January 1	$	4,135
Gain from change in fair value of derivative liabilities		(1,984	)
Additions		577
Balance at March 31	$	2,728

The compound embedded derivative liabilities represent the fair value of the equity conversion options and "make-whole" provisions, as well as the down round conversion price adjustment or conversion rate adjustment provisions of the R&D Notes, the Tranche I Notes, the Tranche II Notes, the

2014

144A

Notes and the

2015

144A

Notes (see Note

5,

“Debt and Mezzanine Equity”). There is no current observable market for these types of derivatives and, as such, the Company determined the fair value of the embedded derivatives using a Monte Carlo simulation valuation model for the R&D Notes and the binomial lattice model for the Tranche I Notes, the Tranche II Notes, the

2014

144A

Notes and the

2015

144A

Notes (or, collectively, Convertible Notes). A Monte Carlo simulation valuation model combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are or

may

be convertible. A binomial lattice model generates

two

probable outcomes -

one

up and another down - arising at each point in time, starting from the date of valuation until the maturity date. A lattice model was used to determine if the Convertible Notes would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the Convertible Notes will be converted early if the conversion value is greater than the holding value and (ii) the Convertible Notes will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the Convertible Notes are called, then the holder will maximize their value by finding the optimal decision between

(1)

redeeming at the redemption price and

(2)

converting the Convertible Notes. Using this lattice method, the Company valued the embedded derivatives using the "with-and-without method", where the fair value of the Convertible Notes including the embedded derivative is defined as the "with", and the fair value of the Convertible Notes excluding the embedded derivatives is defined as the "without". This method estimates the fair value of the embedded derivatives by looking at the difference in the values between the Convertible Notes with the embedded derivatives and the fair value of the Convertible Notes without the embedded derivatives. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company marks the compound embedded derivatives to market due to the conversion price not being indexed to the Company's own stock. As of

March

31,

2017

and

December

 

31,

2016,

included in "Derivative Liabilities" on the condensed consolidated balance sheet are the Company's compound embedded derivative liabilities of

$2.7

million and

$4.1

million, respectively.

The market-based assumptions and estimates used in valuing the compound embedded derivative liabilities include amounts in the following ranges/amounts:

	March 31, 2017			March 31, 2016
Risk-free interest rate	0.74%	-	1.30%	0.80%	-	0.89%
Risk-adjusted yields	12.50%	-	22.63%	35.00%	-	45.13%
Stock-price volatility		45%			45%
Probability of change in control		5%			5%
Stock price		$0.53			$1.11
Credit spread	11.28%	-	21.35%	34.16%	-	44.25%
Estimated conversion dates	2017	-	2019	2016	-	2019

Changes in valuation assumptions can have a significant impact on the valuation of the embedded derivative liabilities. For example, all other things being equal, a decrease/increase in the Company’s stock price, probability of change of control, credit spread, term to maturity/conversion or stock price volatility decreases/increases the valuation of the liabilities, whereas a decrease/increase in risk adjusted yields or risk-free interest rates increases/decreases the valuation of the liabilities. The conversion price of certain of the Convertible Notes also include conversion price adjustment features and for, example, issuances of common stock by the Company at prices lower than the conversion price result in a reset of the conversion price of such notes, which increases the value of the embedded derivative liabilities. See Note

5,

“Debt and Mezzanine Equity” for further details of conversion price adjustment features.

In

June

2012,

the Company entered into a loan agreement with Banco Pine S.A. (or "Banco Pine") under which Banco Pine provided the Company with a loan (or the "Banco Pine Bridge Loan") (see Note

5,

“Debt and Mezzanine Equity”). At the time of the Banco Pine Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of

R$22.0

million (approximately

US$6.9

million based on the exchange rate as of

March

 

31,

2017)

of the Banco Pine Bridge Loan. The swap arrangement exchanges the principal and interest payments under the Banco Pine Bridge Loan for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of

3.94%.

Changes in the fair value of the swap are recognized in “Gain (loss) from change in fair value of derivative instruments" in the condensed consolidated statements of operations are as follows (in thousands):

Type of Derivative Contract	Income Statement Classification	Three Months Ended March 31,
		2017		2016
Currency interest rate swap	Gain from change in fair value of derivative instruments	$	355	$	845

Derivative instruments measured at fair value as of

March

 

31,

2017

and

December

 

31,

2016,

and their classification on the condensed consolidated balance sheets are as follows (in thousands):

	March 31, 2017		December 31, 2016
Fair market value of compound embedded derivative liabilities	$	2,150	$	4,135
Non-current fair value of  swap obligations		2,979		3,343
Total derivative liabilities	$	5,129	$	7,478

XML

Note 4 - Balance Sheet Components

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Supplemental Balance Sheet Disclosures [Text Block]

4.

Balance Sheet Components

Inventories, net

Inventories, net are stated at the lower of cost or net realizable value and comprise of the following (in thousands):

	March 31,  2017		December 31,  2016
Raw materials	$	3,038	$	3,159
Work-in-process		1,343		1,848
Finished goods		2,696		1,206
Inventories, net	$	7,077	$	6,213

Property, Plant and Equipment, net

Property, plant and equipment, net is comprised of the following (in thousands):

	March 31, 2017			December 31, 2016
Machinery and equipment	$	84,853		$	82,688
Leasehold improvements		38,828			38,785
Computers and software		9,658			9,585
Buildings		4,834			4,699
Furniture and office equipment		2,350			2,333
Vehicles		136			164
Land		460			460
Construction in progress		2,465			2,216
		143,584			140,930
Less: accumulated depreciation and amortization		(90,539	)		(87,195	)
Property, plant and equipment, net	$	53,045		$	53,735

The Company's

first,

purpose-built, large-scale Biofene production plant in southeastern Brazil commenced operations in

December

2012.

This plant is located at Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Tonon Bioenergia S.A. (or “Tonon”) (formerly Paraíso Bioenergia) with which the Company has an agreement to purchase a certain number of tons of sugarcane per year, along with specified water and vapor volumes.

Property, plant and equipment, net includes

$3.1

million and

$3.1

million of machinery and equipment under capital leases as of

March

 

31,

2017

and

December

 

31,

2016,

respectively. Accumulated amortization of assets under capital leases totaled

$0.1

million and

$0.6

million as of

March

 

31,

2017

and

December

 

31,

2016,

respectively.

Depreciation and amortization expense, including amortization of assets under capital leases was

$2.7

million and

$2.9

million for the

three

months ended

March

 

31,

2017

and

2016,

respectively.

Other Assets (non-current)

Other assets are comprised of the following (in thousands):

	March 31, 2017		December 31, 2016
Recoverable taxes from Brazilian government entities	$	14,894	$	13,723
Deposits on property and equipment, including taxes		499		291
Other		1,401		1,450
Total other assets	$	16,794	$	15,464

Accrued and Other Current Liabilities

Accrued and other current liabilities are comprised of the following (in thousands):

	March 31, 2017		December 31, 2016
Withholding tax related to conversion of related party notes	$	1,370	$	1,370
Professional services		5,358		6,876
SMA relocation accrual		3,746		3,641
Accrued interest		8,259		4,847
Tax-related liabilities		2,480		2,610
Accrued vacation		2,228		2,034
Payroll and related expenses		2,761		4,310
Deferred rent, current portion		1,111		1,111
Contractual obligations to contract manufacturers		381		—
Other		1,960		2,389
Total accrued and other current liabilities	$	29,654	$	29,188

XML

Note 5 - Debt and Mezzanine Equity

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Debt Disclosure [Text Block]

5.

Debt and Mezzanine Equity

Debt is comprised of the following (in thousands):

	March 31, 2017			December 31, 2016
Senior secured loan facility	$	27,844		$	27,658
BNDES credit facility		904			1,172
FINEP credit facility		637			696
Guanfu credit facility		19,858			19,564
Total credit facilities		49,243			49,090
Convertible notes		75,218			78,981
Related party convertible notes		43,335			42,754
Related party loan payable		30,554			29,691
Loans payable		22,588			26,527
Total debt		220,938			227,043
Less: current portion		(49,455	)		(59,155	)
Long-term debt	$	171,483		$	167,888
Mezzanine equity	$	5,000		$	5,000

Senior Secured Loan Facility

In

March

2014,

the Company entered into a Loan and Security Agreement (or the LSA) with Hercules Technology Growth Capital, Inc. (or Hercules) to make available to Amyris a collateralized loan facility (or the Senior Secured Loan Facility) in the aggregate principal amount of up to

$25.0

million, which loan facility was fully drawn at the closing. The initial loan of

$25.0

million under the Senior Secured Loan Facility accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus

6.25%

or

9.50%.

The Company

may

repay the outstanding amounts under the Senior Secured Loan Facility before the maturity date

(October

15,

2018)

if it pays an additional fee of

1%

of the outstanding loans. The Company was also required to pay a

1%

facility charge at the closing of the Senior Secured Loan Facility, and is required to pay a

10%

end of term charge with respect to the initial loan of

$25.0

million. In connection with the entry into the LSA, Amyris agreed to certain customary representations and warranties and covenants, as well as certain covenants that were subsequently amended (as described below).

In

June

2014,

the Company and Hercules entered into a

first

amendment of the LSA. Pursuant to the

first

amendment, the parties agreed to extend the maturity date of the loans under the Senior Secured Loan Facility from

May

31,

2015

to

February

 

1,

2017

and remove (i) a requirement for the Company to pay a forbearance fee of

$10.0

million in the event certain covenants were not satisfied, (ii) a covenant that the Company maintain positive cash flow commencing with the fiscal quarter beginning

October

1,

2014,

(iii) a covenant that, commencing with the fiscal quarter beginning

July

1,

2014,

the Company and its subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for the Company to file a registration statement on Form S-

3

with the SEC by no later than

June

30,

2014

and complete an equity financing of more than

$50.0

million by no later than

September

30,

2014.

The Company further agreed to include a new covenant in the LSA requiring the Company to maintain unrestricted, unencumbered cash in defined U.S. bank accounts in an amount equal to at least

50%

of the principal amount of the loans then outstanding under the Senior Secured Loan Facility (or the “Minimum Cash Covenant”) and borrow an additional

$5.0

million. The additional

$5.0

million borrowing under the Senior Secured Loan Facility was completed in

June

2014,

and accrues interest at a rate per annum equal to the greater of (i) the prime rate reported in the Wall Street Journal plus

5.25%

and (ii)

8.5%.

In

March

2015,

the Company and Hercules entered into a

second

amendment of the LSA. Pursuant to the

second

amendment, the parties agreed to, among other things, establish an additional credit facility in the principal amount of up to

$15.0

million, which would be available to be drawn by the Company through the earlier of

March

31,

2016

or such time as the Company raised an aggregate of at least

$20.0

million through the sale of new equity securities. Under the terms of the

second

amendment, the Company agreed to pay Hercules a

3.0%

facility availability fee on

April

1,

2015.

The Company had the ability to cancel the additional facility at any time prior to

June

30,

2015

at its own option, and the additional facility would terminate upon the Company securing a new equity financing of at least

$20.0

million. If the facility was not canceled, and any outstanding borrowings were not repaid, before

June

30,

2015,

an additional

5.0%

facility fee would become payable on

June

30,

2015.

The Company did not cancel the facility prior to

June

30,

2015,

and the

5.0%

facility fee became payable as of

June

30,

2015.

The Company did not pay the additional facility fee and thereafter received a waiver from Hercules with respect thereto. The additional facility was cancelled undrawn upon the completion of the Company’s private offering of common stock and warrants in

July

2015.

In

November

2015,

the Company and Hercules entered into a

third

amendment of the LSA. Pursuant to the

third

amendment, the Company borrowed

$10,960,000

(or the Third Amendment Borrowed Amount) from Hercules on

November

30,

2015.

As of

December

1,

2015,

after the funding of the Third Amendment Borrowed Amount (and including repayment of

$9.1

million of principal that had occurred prior to the

third

amendment), the aggregate principal amount outstanding under the Senior Secured Loan Facility was approximately

$31.7

million. The Third Amendment Borrowed Amount accrues interest at a rate per annum equal to the greater of (i)

9.5%

and (ii) the prime rate reported in the Wall Street Journal plus

6.25%,.

Upon the earlier of the maturity date, prepayment in full or such obligations otherwise becoming due and payable, in addition to repaying the outstanding Third Amendment Borrowed Amount (and all other amounts owed under the Senior Secured Loan Facility, as amended), the Company is also required to pay an end-of-term charge of

$767,200.

Pursuant to the

third

amendment, the Company also paid Hercules fees of

$1.0

million,

$750,000

of which was owed in connection with the expired

$15.0

million facility under the

second

amendment and

$250,000

of which was related to the Third Amendment Borrowed Amount. Under the

third

amendment, the parties agreed that the Company would, commencing on

December

1,

2015,

be required to pay only the interest accruing on all outstanding loans under the Senior Secured Loan Facility until

February

29,

2016.

Commencing on

March

1,

2016,

the Company would have been required to begin repaying principal of all loans under the Senior Secured Loan Facility, in addition to the applicable interest. However, pursuant to the

third

amendment, the Company could, by achieving certain cash inflow targets in

2016,

extend the interest-only period to

December

1,

2016.

Upon the issuance and sale by the Company of

$20.0

million of unsecured promissory notes and warrants in a private placement in

February

2016

for aggregate cash proceeds of

$20.0

million, the Company satisfied the conditions for extending the interest-only period to

May

31,

2016.

On

June

1,

2016,

the Company commenced the repayment of outstanding principal under the Senior Secured Loan Facility. In

June

2016,

the Company was notified by Hercules that it had transferred and assigned its rights and obligations under the Senior Secured Loan Facility to Stegodon Corporation (Stegodon), an affiliate of Ginkgo Bioworks, Inc. (Ginkgo). On

June

29,

2016,

in connection with the execution by the Company and Ginkgo of an initial strategic partnership agreement, the Company received a deferment from Stegodon of all scheduled principal repayments under the Senior Secured Loan Facility, as well as a waiver of the Minimum Cash Covenant, through

October

31,

2016.

Refer to Note

8,

“Significant Agreements” for additional details. On

October

6,

2016,

in connection with the execution by the Company and Ginkgo of a definitive collaboration agreement (or the Ginkgo Collaboration Agreement), the Company and Stegodon entered into a

fourth

amendment of the LSA, pursuant to which the parties agreed to (i) subject to the Company extending the maturity of certain of its other outstanding indebtedness (or the Extension Condition), extend the maturity date of the Senior Secured Loan Facility, (ii) make the Senior Secured Loan Facility interest-only until maturity, subject to the requirement that the Company apply certain monies received by it under the Ginkgo Collaboration Agreement to repay the amounts outstanding under the Senior Secured Loan Facility, up to a maximum amount of

$1

million per month and (iii) waive the Minimum Cash Covenant until the maturity date of the Senior Secured Loan Facility. On

January

11,

2017,

the maturity date of the Senior Secured Loan Facility was extended to

October

15,

2018

due to the Extension Condition being met as a result of the Fidelity Exchange (as defined below). See below under “Fidelity” for additional details. This modification of the Senior Secured Loan Facility was accounted for as a troubled debt restructuring with the future undiscounted cash flows being greater than the carrying value of the debt prior to extension. No gain was recorded and a new effective interest rate was established based on the carrying value of the debt and the revised cash flows. In

December

2016,

in connection with Stegodon granting certain waivers and releases under the LSA in connection with the Company’s formation of its Neossance joint venture with Nikko, as described in more detail in Note 

7,

“Joint Ventures and Noncontrolling Interest”, the Company agreed to pay to Stegodon (i) a fee of

$425,000

on or prior to

December

31,

2017

and (ii) a fee of

$450,000

on or prior to the maturity date of the loans under the Senior Secured Loan Facility. Subsequently, in

January

2017,

in connection with Stegodon granting certain waivers of the debt and transfer covenants under the LSA, the Company, certain of its subsidiaries and Stegodon entered into a

fifth

amendment of the LSA. Pursuant to the

fifth

amendment, the Company agreed to apply additional monies received by the Company under the Ginkgo Collaboration Agreement towards repayment of the outstanding loans under the Senior Secured Loan Facility, up to a maximum amount of

$3

million, to the extent any such monies are received by the Company.

As of

March

 

31,

2017,

$27.8

million was outstanding under the Senior Secured Loan Facility, net of discount and issuance costs of

$0.7

million. The Senior Secured Loan Facility is collateralized by liens on the Company's assets, including on certain Company intellectual property. The Senior Secured Loan Facility includes customary events of default, including failure to pay amounts due, breaches of covenants and warranties, material adverse effect events, certain cross defaults and judgments, and insolvency. If an event of default occurs, Stegodon

may

require immediate repayment of all amounts outstanding under the Senior Secured Loan Facility.

BNDES Credit Facility

In

December

2011,

the Company entered into a credit facility with the Brazilian Development Bank (or “BNDES” and such credit facility is the “BNDES Credit Facility”) in the amount of

R$22.4

million (approximately

US$7.1

million based on the exchange rate as of

March

 

31,

2017).

This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line was divided into an initial tranche of up to approximately

R$19.1

million and an additional tranche of approximately

R$3.3

million that would become available upon delivery of additional guarantees. The credit line was cancelled in

2013.

The principal of the loans under the BNDES Credit Facility is required to be repaid in

60

monthly installments, with the

first

installment paid in

January

2013

and the last due in

December

2017.

Interest was due initially on a quarterly basis with the

first

installment due in

March

2012.

From and after

January

2013,

interest payments are due on a monthly basis together with principal payments. The loaned amounts carry interest of

7%

per annum. Additionally, there is a credit reserve charge of

0.1%

on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid.

The BNDES Credit Facility is collateralized by a

first

priority security interest in certain of the Company's equipment and other tangible assets totaling

R$24.9

million (approximately

$7.9

million based on the exchange rate as of

March

 

31,

2017).

The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company was required to provide a bank guarantee equal to

10%

of the total approved amount

(R$22.4

million in total debt) available under the BNDES Credit Facility. For advances of the

second

tranche (above

R$19.1

million), the Company is required to provide additional bank guarantees equal to

90%

of each such advance, plus additional Company guarantees equal to at least

130%

of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, BNDES

may

terminate its commitments and declare immediately due all borrowings under the facility. As of

March

 

31,

2017

and

December

 

31,

2016,

the Company had

R$2.9

million (approximately

US$0.9

million based on the exchange rate as of

March

 

31,

2017)

and

R$3.8

million (approximately

US$1.2

million based on the exchange rate as of

December

 

31,

2016),

respectively, in outstanding advances under the BNDES Credit Facility.

FINEP Credit Facility

In

November

 

2010,

the Company entered into a credit facility with Financiadora de Estudos e Projetos (or the “FINEP Credit Facility”). The FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (or the “FINEP Project”) and provided for loans of up to an aggregate principal amount of

R$6.4

million (approximately

US$2.0

million based on the exchange rate as of

March

 

31,

2017),

which is secured by a chattel mortgage on certain equipment of Amyris Brasil as well as by bank letters of guarantee. All available credit under this facility is fully drawn.

Interest on loans drawn under the FINEP Credit Facility is fixed at

5%

 per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the “TJLP”). If the TJLP at the time of default is greater than

6%,

then the interest will be

5%

plus a TJLP adjustment factor, otherwise the interest will be

11%

 per annum. In addition, a fine of up to

10%

shall apply to the amount of any obligation in default. Interest on late balances will be

1%

per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in

81

monthly installments, which commenced in

July

2012

and extends through

March

2019.

Interest on loans drawn and other charges are paid on a monthly basis and commenced in

March

2011.

As of

March

 

31,

2017

and

December

 

31,

2016,

the total outstanding loan balance under this credit facility was

R$2.0

million (approximately

US$0.7

million based on the exchange rate as of

March

 

31,

2017)

and

R$2.3

million (approximately

US$0.7

million based on exchange rate as of

December

 

31,

2016),

respectively.

Guanfu Credit Facility

On 

October

26,

2016,

the Company and Guanfu Holding Co., Ltd. (or, together with its subsidiaries, Guanfu), an existing commercial partner of the Company, entered into a credit agreement (or the Guanfu Credit Agreement) to make available to the Company an unsecured credit facility (or the Guanfu Credit Facility) with an aggregate principal amount of up to 

$25.0

million, which the Company could borrow from time to time in up to

three

closings. The effectiveness of the Guanfu Credit Agreement was subject to the parties obtaining certain required approvals, which occurred on

November

16,

2016,

and upon the effectiveness of the Guanfu Credit Agreement, the Company granted to Guanfu the global exclusive purchase right with respect to the Company products subject to the parties’ pre-existing commercial relationship. The initial funding of the Guanfu Credit Facility was scheduled to occur on

December

1,

2016,

subject to Guanfu’s right to extend such initial funding to a date no later than

December

31,

2016.

Guanfu exercised its right to extend the initial funding to

December

31,

2016,

and on such date the Company borrowed the full amount under the Guanfu Credit Facility and issued to Guanfu a note in the principal amount of

$25.0

million (or the Guanfu Note). The Guanfu Note has a term of

five

years and will accrue interest at a rate of

10%

per annum, payable quarterly beginning

March

31,

2017.

The Company

may,

at its option, repay the Guanfu Note before its maturity date, in whole or in part, at a price equal to

100%

of the amount being repaid plus accrued and unpaid interest on such amount to the date of repayment.

Upon the occurrence of certain specified events of default under the Guanfu Credit Facility, the Company will grant to Guanfu an exclusive, royalty-free, global license to certain intellectual property useful in connection with Guanfu’s existing commercial relationship with the Company. In addition, in the event the Company fails to pay interest or principal under the Guanfu Note within

ten

days of when due, the Company will also be required, subject to applicable laws and regulations, to repay the outstanding principal amount under the Guanfu Note, together with accrued and unpaid interest, in the form of shares of the Company’s common stock at a per share price equal to

90%

of the volume weighted average closing sale price of the Company’s common stock for the

90

trading days ending on and including the trading day that is

two

trading days preceding such default.

Convertible Notes

Fidelity

In

February

2012,

the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of

$25.0

million pursuant to a securities purchase agreement between the Company and certain investment funds affiliated with FMR LLC (or the Fidelity Securities Purchase Agreement). The offering consisted of the sale of

3%

senior unsecured convertible promissory notes with a

March

1,

2017

maturity date and an initial conversion price equal to

$7.0682

per share of the Company's common stock, subject to proportional adjustment for adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions (or the Fidelity Notes). In

October

2015,

the Company issued and sold

$57.6

million of convertible senior notes and used approximately

$8.8

million of the proceeds therefrom to repurchase

$9.7

million aggregate principal amount of outstanding Fidelity Notes. As of

March

31,

2017,

the Fidelity Notes were convertible into an aggregate of up to

2,165,898

shares of the Company's common stock. The holders of the Fidelity Notes have a right to require repayment of

101%

of the principal amount of the Fidelity Notes in an acquisition of the Company, and the Fidelity Notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment. The Fidelity Securities Purchase Agreement and Fidelity Notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of corporate existence, and timely filing of SEC reports. The Fidelity Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults and breaches of the covenants in the Fidelity Securities Purchase Agreement and Fidelity Notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the Fidelity Notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the Fidelity Notes provide that the Company's total outstanding debt at any time cannot exceed the greater of

$200.0

million or

50%

of its consolidated total assets and its secured debt cannot exceed the greater of

$125.0

million or

30%

of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for

$35.0

million in

October

2013

(or the Temasek Bridge Note), holders of the Fidelity Notes waived compliance with the debt limitations outlined above as to the Temasek Bridge Note and the

August

2013

Financing (as defined below). In consideration for such waiver, the Company granted to holders of the Fidelity Notes or their affiliates the right to purchase up to an aggregate of

$7.6

million worth of convertible promissory notes in the

first

tranche of the

August

2013

Financing (as defined below). See "Related Party Convertible Notes" in this Note

5,

"Debt and Mezzanine Equity" for additional details. On

December

28,

2016,

the Company entered into an Exchange Agreement (or the Fidelity Exchange Agreement) with the holders of the outstanding Fidelity Notes. Pursuant to the Fidelity Exchange Agreement, the Company and the holders agreed to exchange (or the Fidelity Exchange) all outstanding Fidelity Notes, together with accrued and unpaid interest thereon, for approximately

$19.1

million in aggregate principal amount of additional

2015

144A

Notes (as defined below), representing an exchange ratio of approximately

1:1.25

(

i.e

., each

$1.00

of Fidelity Notes was exchanged for approximately

$1.25

of additional

2015

144A

Notes), in a private placement exempt from registration under the Securities Act of

1933,

as amended (or the Securities Act). The closing of the Fidelity Exchange occurred on

January

11,

2017.

At the closing, the Company issued approximately

$19.1

million in aggregate principal amount of its

2015

144A

Notes (or the Additional

2015

144A

Notes) to the holders in exchange for the cancellation of the outstanding Fidelity Notes. The Company did not receive any cash proceeds from the Fidelity Exchange. The exchange has been accounted for as an extinguishment of the Fidelity Notes and issuance of the Additional

2015

144A

Notes. A gain of approximately

$0.1

million was recognized in the

first

quarter to recognize the deficit of the fair value of the Additional

2015

144A

Notes (including related embedded derivatives) compared to the carrying value of the Fidelity Notes at the time of extinguishment. Pursuant to the Fidelity Exchange Agreement, upon the closing of the Fidelity Exchange, the Fidelity Securities Purchase Agreement terminated. In addition, upon the closing of the Fidelity Exchange, in accordance with the terms of the

fourth

amendment to the LSA, the maturity date of all outstanding loans under the LSA was extended to

October

15,

2018.

See above under “Senior Secured Loan Facility” for details regarding the

fourth

amendment to the LSA.

2014

Rule

144A

Convertible Note Offering

In

May

2014,

the Company entered into a Purchase Agreement with Morgan Stanley & Co. LLC, as the initial purchaser (or the Initial Purchaser), relating to the sale of

$75.0

million aggregate in principal amount of

6.50%

Convertible Senior Notes due

2019

(or the

2014

144A

Notes) to the Initial Purchaser in a private placement, and for initial resale by the Initial Purchaser to certain qualified institutional buyers (or the

2014

144A

Convertible Note Offering). In addition, the Company granted the Initial Purchaser an option to purchase up to an additional

$15.0

million aggregate principal amount of

2014

144A

Notes, which option expired unexercised according to its terms. Under the terms of the purchase agreement for the

2014

144A

Notes, the Company agreed to customary indemnification of the Initial Purchaser against certain liabilities. The Notes were issued pursuant to an Indenture, dated as of

May

29,

2014

(or the

2014

Indenture), between the Company and Wells Fargo Bank, National Association, as trustee. The net proceeds from the offering of the

2014

144A

Notes were approximately

$72.0

million after payment of the Initial Purchaser’s discounts and offering expenses. In addition, in connection with obtaining a waiver from Total of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by the Company for new notes issued in the

2014

144A

Convertible Note Offering, the Company used approximately

$9.7

million of the net proceeds to repay previously issued notes (representing the amount of

2014

144A

Notes purchased by Total from the Initial Purchaser). Certain of the Company's affiliated entities purchased

$24.7

million in aggregate principal amount of

2014

144A

Notes from the Initial Purchaser (described further below under "Related Party Convertible Notes"). In

October

2015,

as discussed below, the Company issued

$57.6

million of convertible senior notes and used approximately

$18.3

million of the net proceeds therefrom to repurchase

$22.9

million aggregate principal amount of outstanding

2014

144A

Notes. The

2014

144A

Notes bear interest at a rate of

6.50%

per year, payable semiannually in arrears on

May

15

and

November

15

of each year, beginning

November

 

15,

2014.

The

2014

144A

Notes mature on

May

 

15,

2019,

unless earlier converted or repurchased. The

2014

144A

Notes are convertible into shares of the Company's common stock at any time prior to the close of business on the business day immediately preceding the maturity date of the

2014

144A

Notes, at the initial conversion rate of

267.037

shares of Common Stock per

$1,000

principal amount of

2014

144A

Notes (subject to adjustment in certain circumstances). This represents an effective conversion price of approximately

$3.74

per share of common stock. For any conversion on or after

May

 

15,

2015,

in the event that the last reported sale price of the Company’s common stock for

20

or more trading days (whether or not consecutive) in a period of

30

consecutive trading days ending within

five

trading days immediately prior to the date the Company receives a notice of conversion exceeds the then-applicable conversion price per share on each such trading day, the holders, in addition to the shares deliverable upon conversion, noteholders will be entitled to receive a cash payment equal to the present value of the remaining scheduled payments of interest that would have been made on the

2014

144A

Notes being converted from the conversion date to the earlier of the date that is

three

years after the date the Company receives such notice of conversion and maturity

(May

 

15,

2019),

which will be computed using a discount rate of

0.75%.

In the event of a fundamental change, as defined in the

2014

Indenture, holders of the

2014

144A

Notes

may

require the Company to purchase all or a portion of the

2014

144A

Notes at a price equal to

100%

of the principal amount of the

2014

144A

Notes, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. In addition, holders of the

2014

144A

Notes who convert their

2014

144A

Notes in connection with a make-whole fundamental change will, under certain circumstances, be entitled to an increase in the conversion rate of such notes. Refer to the “Exchange” and “Maturity Treatment Agreement” sections of this Note

5,

"Debt and Mezzanine Equity", as well as Note

18,

“Subsequent Events”, for details of the impact of the Maturity Treatment and Exchange Agreements on the

2014

144A

Notes.

2015

Rule

144A

Convertible Note Offering

In

October

2015,

the Company entered into a purchase agreement with certain qualified institutional buyers relating to the sale of

$57.6

million aggregate principal amount of

9.50%

Convertible Senior Notes due

2019

(or the

2015

144A

Notes) to the purchasers in a private placement (or the

2015

144A

Offering). The

2015

144A

Notes were issued pursuant to an Indenture, dated as of

October

20,

2015

(or the

2015

Indenture), between the Company and Wells Fargo Bank, National Association, as trustee. The net proceeds from the offering of the

2015

144A

Notes were approximately

$54.4

million after payment of the offering expenses and placement agent fees. The Company used approximately

$18.3

million of the net proceeds to repurchase

$22.9

million aggregate principal amount of outstanding

2014

144A

Notes and approximately

$8.8

million to repurchase

$9.7

million aggregate principal amount of outstanding Fidelity Notes, in each case held by purchasers of the

2015

144A

Notes. The

2015

144A

Notes bear interest at a rate of

9.50%

per year, payable semiannually in arrears on

April

15

and

October

15

of each year, beginning

April

15,

2016.

Interest on the

2015

144A

Notes is payable, at the Company’s option, entirely in cash or entirely in common stock. The Company elected to make the

April

15,

2016

interest payment in shares of common stock, the

October

15,

2016

interest payment in cash and the

April

15,

2017

interest payment in shares of common stock. The

2015

144A

Notes will mature on

April

15,

2019

unless earlier converted or repurchased.

The

2015

144A

Notes are convertible into shares of the Company's common stock at any time prior to the close of business on

April

15,

2019.

The

2015

144A

Notes had an initial conversion rate of

443.6557

shares of Common Stock per

$1,000

principal amount of

2015

144A

Notes (subject to adjustment in certain circumstances). This represented an initial effective conversion price of approximately

$2.25

per share of common stock. Following the issuance by the Company of warrants to purchase common stock in a private placement transaction in

February

2016

and the issuance by the Company of convertible notes in

May,

September

and

October

2016,

as described below, the conversion rate of the

2015

144A

Notes was

446.8707

shares of Common Stock per

$1,000

principal amount of

2015

144A

Notes as of

December

31,

2016.

Furthermore, following the issuance by the Company of shares of convertible preferred stock and warrants to purchase common stock in

May

2017,

the conversion rate of the

2015

144A

Notes is

711.1209

shares of Common Stock per

$1,000

principal amount of

2015

144A

Notes as of

May

11,

2017,

representing an effective conversion price of approximately

$1.41

per share of common stock. For any conversion on or after

November

27,

2015,

in addition to the shares deliverable upon conversion, noteholders will be entitled to receive a payment equal to the present value of the remaining scheduled payments of interest that would have been made on the

2015

144A

Notes being converted from the conversion date to the earlier of the date that is

three

years after the date the Company receives such notice of conversion and maturity

(April

15,

2019),

which will be computed using a discount rate of

0.75%.

The Company

may

make such payment (the “Early Conversion Payment”) either in cash or in common stock, at its election, provided that it

may

only make such payment in common stock if such common stock is not subject to restrictions on transfer under the Securities Act by persons other than the Company’s affiliates. If the Company elects to pay an Early Conversion Payment in common stock, then the stock will be valued at

92.5%

of the simple average of the daily volume-weighted average price per share for the

10

trading days ending on and including the trading day immediately preceding the conversion date. Through

March

31,

2017,

the Company has elected to make each Early Conversion Payment in shares of common stock. In the event of a fundamental change, as defined in the

2015

Indenture, holders of the

2015

144A

Notes

may

require the Company to purchase all or a portion of the

2015

144A

Notes at a price equal to

100%

of the principal amount of the

2015

144A

Notes, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. In addition, holders of the

2015

144A

Notes who convert their

2015

144A

Notes in connection with a make-whole fundamental change will, under certain circumstances, be entitled to an increase in the conversion rate. The issuance of shares of common stock upon conversion of the

2015

144A

Notes, upon the Company’s election to pay interest on the

2015

144A

Notes in shares of common stock and upon the Company’s election to pay the Early Conversion Payment in shares of common stock in an aggregate amount in excess of

38,415,626

shares of the Company’s common stock was subject to stockholder approval, which was obtained on

May

17,

2016.

With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the

2015

144A

Notes provide that, as long as the aggregate outstanding principal amount of the

2015

144A

Notes exceeds

$25.0

million, the Company's outstanding unsecured debt at any time cannot exceed

$200.0

million and its secured debt cannot exceed the greater of

$65.0

million or

30%

of its consolidated total assets. In

January

2017,

the Company issued an additional

$19.1

million in aggregate principal amount of

2015

144A

Notes (or the Additional

2015

144A

Notes) in exchange for the cancellation of

$15.3

million in aggregate principal amount of outstanding Fidelity Notes. The Additional

2015

144A

Notes were issued pursuant to the

2015

Indenture, as amended by the First Supplemental Indenture thereto, dated as of

January

11,

2017,

which amended the

2015

Indenture to clarify the Exchange Cap (as defined below) for the Additional

2015

144A

Notes. Unless and until the Company obtains stockholder approval to issue a number of shares of the Company’s common Stock in excess of the Exchange Cap (as defined below), holders of the Additional

2015

144A

Notes will not have the right to receive shares of the Company’s common stock upon conversion of the Additional

2015

144A

Notes, and the Company will not have the right to issue shares of common stock as payment of interest on the Additional

2015

144A

Notes, including any Early Conversion Payment, if the aggregate number of shares issued with respect to the Additional

2015

144A

Notes (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed

19.99%

of the number of shares of the Company’s common stock outstanding as of

December

28,

2016

(or the Exchange Cap). The Company will pay cash in lieu of any shares that would otherwise be deliverable in excess of the Exchange Cap.

May

2016

Convertible Note Offering

In

May

2016,

the Company entered into a securities purchase agreement (or the

May

2016

Purchase Agreement) between the Company and a private investor relating to the sale of up to

$15.0

million aggregate principal amount of convertible notes (or the

May

2016

Convertible Notes) that are convertible into shares of the Company’s common stock at an initial conversion price of

$1.90

per share. The conversion price will be subject to adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar transaction. The

May

2016

Purchase Agreement includes customary representations, warranties and covenants by the Company. The

May

2016

Purchase Agreement also provides the purchaser with a right of

first

refusal with respect to any variable rate transaction on the same terms and conditions as are offered to a

third

-party purchaser for as long as the purchaser holds any

May

2016

Convertible Notes or shares of the Company’s common stock underlying the

May

2016

Convertible Notes.

Pursuant to the

May

2016

Purchase Agreement, the

May

2016

Convertible Notes were to be issued and sold in

two

separate closings. The initial closing occurred on

May

10,

2016.

At the initial closing, the Company issued and sold a

May

2016

Convertible Note in a principal amount of

$10.0

million to the purchaser, resulting in net proceeds to the Company of approximately

$9.9

million. The

second

closing was to occur on the

first

trading day following the completion of the

first

three

installment periods under the

May

2016

Convertible Notes and the satisfaction or waiver of certain other closing conditions, including certain equity conditions, such as that no Triggering Event (as defined below) had occurred. At the

second

closing, the Company was to issue and sell a

May

2016

Convertible Note in a principal amount of

$5.0

million to the purchaser, resulting in expected net proceeds to the Company of approximately

$5.0

million. On

September

2,

2016,

in connection with the Company and the purchaser waiving certain conditions to the

second

closing under the

May

2016

Purchase Agreement, the Company issued and sold an additional

May

2016

Convertible Note in the principal amount of

$3.0

million to the purchaser, for proceeds to the Company of approximately

$3.0

million, and granted the purchaser the option to purchase a further

May

2016

Convertible Note in the principal amount of

$2.0

million (or the Remaining

May

2016

Note), representing the remaining

May

2016

Convertible Notes provided for in the

May

2016

Purchase Agreement, on or before

December

31,

2016.

On

October

13,

2016,

the Company issued and sold the Remaining

May

2016

Note to the purchaser for proceeds to the Company of

$2.0

million.

The

May

2016

Convertible Notes are general unsecured obligations of the Company. Unless earlier converted or redeemed, the

May

2016

Convertible Notes will mature on the

18

-month anniversary of their respective issuance, subject to the rights of the holders to extend the maturity date in certain circumstances.

The

May

2016

Convertible Notes are payable in monthly installments, in either cash at

118%

of such installment amount or, at the Company’s option, subject to the satisfaction of certain equity conditions, shares of common stock at a discount to the then-current market price, subject to a price floor. In addition, in the event that the Company elects to pay all or any portion of a monthly installment in common stock, the holders of the

May

2016

Convertible Notes shall have the right to require that the Company repay in common stock an additional amount of the

May

2016

Convertible Notes not to exceed

50%

of the cumulative sum of the aggregate amounts by which the dollar-weighted trading volume of the Company’s common stock for all trading days during the applicable installment period exceeds

$200,000.

The Company elected to make the

May,

June,

July,

August,

September

and

October

2016

installment payments on the

May

2016

Convertible Notes in shares of common stock. As of

October

31,

2016,

all

May

2016

Convertible Notes had been repaid in full.

The

May

2016

Convertible Notes contain customary terms and covenants, including certain events of default, including failure to pay amounts due, breaches of warranties, material adverse effect events, certain cross defaults and judgments, and insolvency, after which the holders

may

require the Company to redeem all or any portion of their

May

2016

Convertible Notes in cash at a price equal to the greater of (i) 

118%

of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

In the event of a Fundamental Transaction (as defined in the

May

2016

Convertible Notes), holders of the

May

2016

Convertible Notes

may

require the Company to redeem all or any portion of their

May

2016

Convertible Notes at a price equal to the greater of (i) 

118%

of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

The Company has the right to redeem the

May

2016

Convertible Notes for cash, in whole, at any time, or in part, from time to time, at a redemption price equal to

118%

of the principal amount of the

May

2016

Convertible Notes being redeemed. In addition, if the volume-weighted average price of the Company’s common stock is (i) less than

$1.00

for

30

consecutive trading days or (ii) less than

$0.50

for

five

consecutive trading days (each, a “Triggering Event”) within

four

months of the issuance of any

2016

Convertible Notes, the Company will have the option to redeem such

May

2016

Convertible Notes in whole for cash at a redemption price equal to

112%

of the principal amount of such

May

2016

Convertible Notes.

Notwithstanding the foregoing, the holders will not have the right to convert any portion of a

May

2016

Convertible Note, and the Company

may

not issue shares of common stock upon conversion or repayment of the

May

2016

Convertible Notes, if (a) the holder, together with its affiliates, would beneficially own in excess of

4.99%

(or such other percentage as determined by the holder and notified to the Company in writing, not to exceed

9.99%,

provided that any increase of such percentage will not be effective until

61

days after notice thereof) of the number of shares of the Company’s common stock outstanding immediately after giving effect to such conversion or payment, as applicable, or (b) the aggregate number of shares issued with respect to the

May

2016

Convertible Notes after giving effect to such conversion or payment, as applicable, would exceed

19.99%

of the number of shares of the Company’s common stock outstanding as of

May

10,

2016.

In the event that the Company is prohibited from issuing any shares of common stock in respect of the

May

2016

Convertible Notes as a result of such limits, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess thereof.

For as long as they hold the

May

2016

Convertible Notes or shares of common stock issued under the

May

2016

Convertible Notes, the holders

may

not sell any shares of the Company’s common stock at a price less than

$1.05

per share; provided, that with respect to any shares of common stock issued under the

May

2016

Convertible Notes at a price less than

$1.00,

the holders

may

sell such shares at a price not less than the price floor applicable to the installment period with respect to which such shares were issued.

The

May

2016

Convertible Notes had been fully repaid as of

March

31,

2017.

December

2016

Convertible Note Offering

On

December

1,

2016,

the Company entered into a securities purchase agreement (or the

December

2016

Purchase Agreement) with a private investor relating to the sale of a convertible note in the original principal amount

$10.0

million (or the

December

2016

Convertible Note) that is convertible into shares of the Company’s common stock at an initial conversion price of

$1.90

per share. The conversion price will be subject to adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar transaction. The

December

2016

Purchase Agreement includes customary representations, warranties and covenants by the Company. The Purchase Agreement also provides the purchaser with a right of

first

refusal with respect to any variable rate transaction, subject to certain exceptions, on the same terms and conditions as are offered to a

third

-party purchaser for as long as the purchaser holds the

December

2016

Convertible Note or shares of common stock underlying the

December

2016

Convertible Note.

The

December

2016

Convertible Note was issued on

December

2,

2016,

resulting in net proceeds to the Company of approximately

$9.9

million.

The

December

2016

Convertible Note is a general unsecured obligation of the Company. Unless earlier converted or redeemed, the

December

2016

Convertible Note will mature on

May

1,

2018,

subject to the rights of the holder to extend the maturity date in certain circumstances.

The

December

2016

Convertible Note is payable in monthly installments, beginning

January

1,

2017,

in either cash at

118%

of such installment amount or, at the Company’s option, subject to the satisfaction of certain equity conditions, shares of common stock at a discount to the then-current market price, subject to a price floor. In addition, between

December

1,

2016

and

December

31,

2016,

 or in the event that the Company elects to pay all or any portion of a monthly installment in common stock, the holder of the

December

2016

Convertible Note shall have the right to require that the Company repay in common stock an additional amount of the

December

2016

Convertible Note not to exceed

50%

of the cumulative sum of the aggregate amounts by which the dollar-weighted trading volume of the Company’s common stock for all trading days during the applicable period exceeds

$200,000.

The

December

2016

Convertible Note contains customary terms and covenants, including certain events of default, including failure to pay amounts due, breaches of warranties, material adverse effect events, certain cross defaults and judgments, and insolvency, after which the holders

may

require the Company to redeem all or any portion of their

December

2016

Convertible Note in cash at a price equal to the greater of (i)

118%

of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

In the event of a Fundamental Transaction (as defined in the

December

2016

Convertible Note), the holder of the

December

2016

Convertible Note

may

require the Company to purchase all or any portion of its

December

2016

Convertible Note at a price equal to the greater of (i) 

118%

of the amount being redeemed and (ii) the intrinsic value of the shares of Common Stock issuable upon an installment payment of the amount being redeemed in shares.

The Company has the right to redeem the

December

2016

Convertible Note for cash, in whole, at any time, or in part, from time to time, at a redemption price equal to

118%

of the principal amount of the

December

2016

Convertible Note to be redeemed.

Notwithstanding the foregoing, the holder will not have the right to convert any portion of the

December

2016

Convertible Note, and the Company will not have the option to pay any amount in shares of common stock, if (a) the holder, together with its affiliates, would beneficially own in excess of

4.99%

(or such other percentage as determined by the holder and notified to the Company in writing, not to exceed

9.99%,

provided that any increase of such percentage will not be effective until

61

days after notice thereof) of the number of shares of the Company’s common stock outstanding immediately after giving effect to such conversion or payment, as applicable, or (b) the aggregate number of shares issued with respect to the

December

2016

Convertible Note (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed

19.99%

of the number of shares of the Company’s common stock outstanding as of

December

1,

2016.

In the event that the Company is prohibited from issuing any shares of common stock in respect of the

December

2016

Convertible Note as a result of such limits, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess thereof.

For as long as it holds the

December

2016

Convertible Note or shares of common stock issued under the

December

2016

Convertible Note, the holder

may

not sell any shares of the Company’s common stock at a price less than

$1.05

per share; provided, that with respect to any shares of common stock issued under the

December

2016

Convertible Note at a price less than

$1.00,

the holder

may

sell such shares at a price not less than the price floor applicable to the period with respect to which such shares were issued. The embedded derivative features in this instrument are separately accounted for and the fair value of such features was not material at

March

31,

2017

and

December

31,

2016.

In

May

2017,

the Company agreed to amend the

December

2016

Convertible Note, as described in more detail in Note

18,

“Subsequent Events.”

See Note

18,

“Subsequent Events” for details regarding financing transactions completed subsequent to

March

31,

2017.

Related Party Convertible Notes

Total R&D Convertible Notes

In

July

 

2012

and

December

2013,

the Company entered into a series of agreements (or the Total Fuel Agreements) with Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, and referred to as Total) to establish a research and development program (or the Program) and form a joint venture (or the Fuels JV) with Total to produce and commercialize farnesene- or farnesane-based diesel and jet fuels, and established a convertible debt structure for the collaboration funding from Total.

The purchase agreement for the notes related to the funding from Total (or the Total Purchase Agreement) provided for the sale of an aggregate of

$105.0

million in

1.5%

Senior Unsecured Convertible Notes due

March

2017

(or the Unsecured R&D Notes) as follows:

• As part of an initial closing under the purchase agreement (which was completed in two installments), (i) on July   30, 2012, the Company sold an Unsecured R&D Note with a principal amount of $38.3 million, including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September   14, 2012, the Company sold another Unsecured R&D Note for $15.0 million in new funds from Total. These Unsecured R&D Notes had an initial conversion price of $7.0682 per share.

• At a second closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional Unsecured R&D Notes for an aggregate of $30.0 million in new funds from Total ($10.0 million in June 2013 and $20.0 million in July 2013). These Unsecured R&D Notes had an initial conversion price of $3.08 per share, as described below.

• At a third closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional Unsecured R&D Notes for an aggregate of $21.7 million in new funds from Total ($10.85 million in July 2014 and $10.85 million in January 2015). These Unsecured R&D Notes had an initial conversion price of $4.11 per share, as described below.

In

March

 

2013,

the Company entered into a letter agreement with Total (or the

March

2013

Letter Agreement) under which Total agreed to waive its right to cease its participation in the parties' fuels collaboration at the

July

2013

decision point and committed to proceed with the

July

2013

funding tranche of

$30.0

million (subject to the Company's satisfaction of the relevant closing conditions for such funding in the Total Purchase Agreement). As consideration for this waiver and commitment, the Company agreed to:

• Reduce the conversion price for the $30.0 million in principal amount of Unsecured R&D Notes to be issued in connection with the second closing of the Unsecured R&D Notes (as described above) from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the March 2013 Letter Agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price would not be reduced by more than the maximum possible amount permitted under the rules of The NASDAQ Stock Market (or NASDAQ) such that the new conversion price would require the Company to obtain stockholder consent; and

• Grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV.

In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the

second

closing.

In

June

 

2013,

the Company sold and issued

$10.0

million in principal amount of Unsecured R&D Notes to Total pursuant to the

second

closing of the Unsecured R&D Notes as discussed above. In accordance with the

March

2013

Letter Agreement, this Unsecured R&D Note had an initial conversion price equal to

$3.08

per share of the Company's common stock.

In

July

 

2013,

the Company sold and issued

$20.0

million in principal amount of Unsecured R&D Notes to Total pursuant to the Total

second

closing of the Unsecured R&D Notes as discussed above. This purchase and sale completed Total's commitment to purchase

$30.0

million of the Unsecured R&D Notes in the

second

closing by

July

2013.

In accordance with the

March

2013

Letter Agreement, this Unsecured R&D Note has an initial conversion price equal to

$3.08

per share of the Company's common stock.

In

December

2013,

in connection with the Company's entry into a Shareholders Agreement dated

December

2,

2013

and License Agreement dated

December

2,

2013

(or, collectively, the JV Documents) with Total and Total Amyris BioSolutions B.V. (or TAB) relating to the establishment of TAB (see Note

7,

"Joint Ventures and Noncontrolling Interest"), the Company (i) exchanged the

$69.0

million of the then-outstanding Unsecured R&D Notes issued pursuant to the Total Purchase Agreement for replacement

1.5%

Senior Secured Convertible Notes due

March

2017

(or the Secured R&D Notes, and together with the Unsecured R&D Notes, the R&D Notes), in principal amounts equal to the principal amount of each cancelled note and with substantially similar terms except that such replacement notes were secured, (ii) in connection therewith, granted to Total a security interest in and lien on all of the Company’s rights, title and interest in and to the Company’s shares in the capital of TAB as security for such Secured R&D Notes and (iii) agreed that any securities to be purchased and sold at the

third

closing under the Total Purchase Agreement by Total would be Secured R&D Notes instead of Unsecured R&D Notes. As a consequence of executing the JV Documents and forming TAB, the security interest in all of the Company's intellectual property, granted by the Company in favor of Total, Maxwell (Mauritius) Pte Ltd (or Temasek), and certain entities affiliated with FMR LLC (or the Fidelity Entities) pursuant to the Restated Intellectual Property Security Agreement dated as of

October

16,

2013,

was automatically terminated effective as of

December

2,

2013

upon Total’s and the Company’s joint written notice to Temasek and the Fidelity Entities.

In

April

2014,

the Company and Total entered into a letter agreement dated as of

March

29,

2014

(or the

March

2014

Total Letter Agreement) to amend the Amended and Restated Master Framework Agreement entered into as of

December

2,

2013

(included as part of JV Documents) and the Total Purchase Agreement. Under the

March

2014

Total Letter Agreement, the Company agreed to (i) amend the conversion price of the Secured R&D Notes to be issued in the

third

closing under the Total Purchase Agreement from

$7.0682

per share to

$4.11

per share subject to stockholder approval at the Company's

2014

annual meeting (which was obtained in

May

2014),

(ii) extend the period during which Total

may

exchange for other Company securities Secured R&D Notes issued under the Total Fuel Agreements from

June

30,

2014

to the later of

December

 

31,

2014

and the date on which the Company shall have raised

$75.0

million of equity and/or convertible debt financing (excluding any convertible promissory notes issued pursuant to the Total Purchase Agreement), (iii) eliminate the Company’s ability to qualify, in a disclosure letter to Total, certain of the representations and warranties that the Company must make at the closing of any

third

closing sale, and (iv) beginning on

March

31,

2014,

provide Total with monthly reporting on the Company’s cash, cash equivalents and short-term investments. In consideration of these agreements, Total agreed to waive its right not to consummate the

third

closing under the Total Purchase Agreement if it had decided not to proceed with the collaboration and had made a "No-Go" decision with respect thereto.

In

July

 

2014,

the Company sold and issued a Secured R&D Note to Total with a principal amount of

$10.85

million with a

March

 

1,

2017

maturity date pursuant to the Total Purchase Agreement. This purchase and sale constituted the initial installment of the

$21.7

million

third

closing described above. In accordance with the

March

2014

Total Letter Agreement, this Secured R&D Note had an initial conversion price equal to

$4.11

per share of the Company's common stock.

In

January

2015,

the Company sold and issued a Secured R&D Note to Total with a principal amount of

$10.85

million with a

March

 

1,

2017

maturity date pursuant to the Total Purchase Agreement. This purchase and sale constituted the final installment of the

$21.7

million

third

closing described above. In accordance with the

March

2014

Total Letter Agreement, this Secured R&D Note had an initial conversion price equal to

$4.11

per share of the Company's common stock.

In

July

2015,

Total exchanged all but

$5.0

million of Secured R&D Notes then held by Total, such cancelled notes having an aggregate principal amount of

$70

million, in exchange for approximately

30.4

million shares of the Company’s common stock in connection with the Exchange. Refer to the “Exchange” section of this Note

5,

"Debt and Mezzanine Equity", for additional details of the impact of the Exchange on the R&D Notes.

In

March

2016,

in connection with the restructuring of TAB (see Note

7,

"Joint Ventures and Noncontrolling Interest"), the Company sold to Total

one

half of the Company’s ownership stake in TAB (giving Total an aggregate ownership stake of

75%

of TAB and giving the Company an aggregate ownership stake of

25%

of TAB) in exchange for Total cancelling (i) approximately

$1.3

million of Secured R&D Notes, plus all paid-in-kind and accrued interest under all outstanding Secured R&D Notes

($2.8

million, including all such interest that was outstanding as of

July

29,

2015)

and (ii) a note in the principal amount of Euro

50,000,

plus accrued interest, issued to Total in connection with the original capitalization of TAB. To satisfy its purchase obligation above, Total surrendered to the Company the remaining Secured R&D Note of approximately

$5.0

million in principal amount, and the Company executed and delivered to Total a new Unsecured R&D Note in the principal amount of

$3.7

million. The disposal of the

25%

ownership stake in the Fuels JV resulted in a gain to the Company of

$4.2

million, which was recognized as a capital contribution from Total within equity.

As of

March

 

31,

2017

and

December

31,

2016,

$3.7

million and

$3.7

million, respectively, of R&D Notes were outstanding. In

February

2017,

the Company and Total agreed to extend the maturity of the outstanding R&D Notes from

March

1,

2017

to

May

15,

2017.

The R&D Notes bear interest of

1.5%

per annum (with a default rate of

2.5%),

accruing from the date of issuance and payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes, as described below.

The R&D Notes become convertible into the Company's common stock (i) within

10

trading days prior to maturity, (ii) on a change of control of the Company, and (iii) on a default by the Company. The conversion price of the R&D Notes are subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of

101%

of the principal amount of the R&D Notes in the event of a change of control of the Company and the R&D Notes provide for payment of unpaid future interest through the maturity date on conversion following such a change of control, subject to a cap, if Total does not require such repayment. The Total Purchase Agreement and R&D Notes include covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The R&D Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the Total Purchase Agreement and R&D Notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, with exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the R&D Notes provide that the Company's total outstanding debt at any time

may

not exceed the greater of

$200.0

million or

50%

of its consolidated total assets and its secured debt

may

not exceed the greater of

$125.0

million or

30%

of its consolidated total assets.

August

2013

Financing Convertible Notes and Temasek Bridge Note

In

August

2013,

the Company entered into a Securities Purchase Agreement (or the

August

2013

SPA) with Total and Temasek to sell up to

$73.0

million in convertible promissory notes in private placements (or the

August

2013

Financing), with such notes to be sold and issued over a period of up to

24

months from the date of signing. The

August

2013

SPA provided for the

August

2013

Financing to be divided into

two

tranches (the

first

tranche for

$42.6

million and the

second

tranche for

$30.4

million), each with differing closing conditions. Of the total possible purchase price in the financing,

$25.0

million was to be paid in the form of cash by Temasek

($25.0

million in the

second

tranche),

$35.0

million was to be paid by the exchange and cancellation of the Temasek Bridge Note, as described below, and

$13.0

million was to be paid by the exchange and cancellation of outstanding R&D Notes held by Total in connection with its exercise of pro rata rights

($7.6

million in the

first

tranche and

$5.4

million in the

second

tranche). The

August

2013

SPA included requirements that the Company meet certain production milestones before the

second

tranche would become available, obtain stockholder approval prior to completing any closing of the transaction, and issue a warrant to Temasek to purchase

1,000,000

shares of the Company's common stock at an exercise price of

$0.01

per share, initially exercisable only if Total converted R&D Notes previously issued to Total in the

second

closing under the Total Purchase Agreement. In

September

2013,

prior to the initial closing of the

August

2013

Financing, the Company's stockholders approved the issuance in a private placement of up to

$110.0

million aggregate principal amount of senior convertible promissory notes, the issuance of a warrant to purchase

1,000,000

shares of the Company's common stock and the issuance of the common stock issuable upon conversion or exercise of such notes and warrant, which approval included the transactions contemplated by the

August

2013

Financing.

In

October

2013,

the Company sold and issued a senior secured promissory note to Temasek (or the Temasek Bridge Note) in exchange for a bridge loan of

$35.0

million. The Temasek Bridge Note was due on

February

2,

2014

and accrued interest at a rate of

5.5%

quarterly from the

October

4,

2013

date of issuance. The Temasek Bridge Note was cancelled on

October

16,

2013

as payment for Temasek’s purchase of Tranche I Notes in the

first

tranche of the

August

2013

Financing, as further described below.

In

October

2013,

the Company amended the

August

2013

SPA to include the investment by the Fidelity Entities in the

first

tranche of the

August

2013

Financing of

$7.6

million, and to proportionally increase the amount of

first

tranche notes acquired by exchange and cancellation of outstanding R&D Notes held by Total in connection with its exercise of pro rata rights up to

$9.2

million in the

first

tranche. Also in

October

2013,

the Company completed the closing of the

first

tranche of senior convertible notes provided for in the

August

2013

Financing (or the Tranche I Notes), issuing a total of

$51.8

million in Tranche I Notes for cash proceeds of

$7.6

million and exchange and cancellation of outstanding convertible promissory notes of

$44.2

million, of which

$35.0

million resulted from the exchange and cancellation of the Temasek Bridge Note and the remaining

$9.2

million from the exchange and cancellation of an outstanding R&D Note held by Total. As a result of the exchange and cancellation of the

$35.0

million Temasek Bridge Note and the

$9.2

million R&D Note held by Total for the Tranche I Notes, the Company recorded a loss from extinguishment of debt of

$19.9

million. The Tranche I Notes are due

sixty

months from the date of issuance and were initially convertible into the Company’s common stock at a conversion price equal to

$2.44

per share, which represents a

15%

discount to the trailing

60

-day weighted-average closing price of the common stock on The NASDAQ Stock Market (or NASDAQ) through

August

7,

2013,

subject to certain adjustments as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after

18

months from the date of the

August

2013

SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues on the Tranche I Notes at a rate of

5%

per

six

months, compounded semiannually (with graduated interest rates of

6.5%

applicable to the

first

180

days and

8%

applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or of

6.5%

for all other defaults). Interest for the

first

30

months is payable in kind and added to the principal every

six

months and thereafter, the Company

may

continue to pay interest in kind by adding to the principal every

six

months or

may

elect to pay interest in cash. Through

March

31,

2017,

the Company has elected to pay interest on the Tranche I Notes in kind. The Tranche I Notes

may

be prepaid by the Company on the

30

-month anniversary of the issuance date, and thereafter every

six

months at the date of payment of the semi-annual coupon.

In

December

2013,

the Company further amended the

August

2013

SPA to sell

$3.0

million of senior convertible notes under the

second

tranche of the

August

2013

Financing (or the Tranche II Notes) to funds affiliated with Wolverine Asset Management, LLC (or Wolverine) and the Company elected to call

$25.0

million in additional funds from Temasek pursuant to its previous commitment to purchase such amount of Tranche II Notes. In

January

2014,

the Company sold and issued, for face value, approximately

$34.0

million of Tranche II Notes in the

second

tranche of the

August

2013

Financing. At the closing, Temasek purchased

$25.0

million of the Tranche II Notes and funds affiliated with Wolverine purchased

$3.0

million of the Tranche II Notes, each for cash. Total purchased approximately

$6.0

million of the Tranche II Notes through exchange and cancellation of the same amount of principal of previously outstanding R&D Notes held by Total. As a result of the exchange and cancellation of the

$6.0

million R&D Note held by Total for the Tranche II Notes, the Company recorded a loss from extinguishment of debt of

$9.4

million. The Tranche II Notes will be due

sixty

months from the date of issuance and were initially convertible into shares of common stock at a conversion price equal to

$2.87

per share, which represents the trailing

60

-day weighted-average closing price of the common stock on NASDAQ through

August

7,

2013,

subject to certain adjustments as described below. The Tranche II Notes are convertible at the option of the holder (i) at any time after the

12

month anniversary of the issue date, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. Each Tranche II Note will accrue interest from the date of issuance until the earlier of the date that such Tranche II Note is converted into common stock or repaid in full. Interest will accrue on the Tranche II Notes at a rate per annum equal to

10%,

compounded annually (with graduated interest rates of

13%

applicable to the

first

180

days and

16%

applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or of

12%

for all other defaults). Interest for the

first

36

months shall be payable in kind and added to principal every year following the issue date and thereafter, the Company

may

continue to pay interest in kind by adding to the principal on every year anniversary of the issue date or

may

elect to pay interest in cash.

The conversion prices of the Tranche I Notes and Tranche II Notes are subject to adjustment (i) according to proportional adjustments to outstanding common stock of the Company in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the Company in connection with future financing transactions in excess of its pro rata amount. The holders have a right to require repayment of

101%

of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment. The

August

2013

SPA, Tranche I Notes and Tranche II Notes include covenants regarding payment of interest, maintenance of the Company’s listing status, limitations on debt and on certain liens, maintenance of corporate existence, and filing of SEC reports. The Tranche I Notes and Tranche II Notes include standard events of default including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the

August

2013

SPA, Tranche I Notes and Tranche II Notes, after which such notes

may

be due and payable immediately, as well as associated default interest rates as set forth above.

In

July

2015,

Temasek exchanged all of the Tranche I and Tranche II Notes then held by Temasek, such notes having an aggregate principal amount of approximately

$71.0

million, in exchange for approximately

30.86

million shares of the Company’s common stock in connection with the Exchange. Refer to the “Exchange” section of this Note

5,

"Debt and Mezzanine Equity", for additional details of the impact of the Exchange on the Tranche I Notes and Tranche II Notes.

The conversion price of the Tranche I Notes and Tranche II Notes was reduced to approximately

$1.42

per share upon the completion of a private placement of common stock and warrants to purchase common stock in

July

2015,

as described below. Following the issuance by the Company of warrants to purchase common stock in a private placement transaction in

February

2016,

the conversion price of the Tranche I Notes and Tranche II Notes was further adjusted to

$1.40

per share, and following the sale by the Company of shares of common stock to the Bill & Melinda Gates Foundation in

May

2016,

as described below, the conversion price of the Tranche I Notes and Tranche II Notes was further adjusted to

$1.14

per share. Furthermore, following the issuance by the Company of shares of convertible preferred stock and warrants to purchase common stock in

May

2017,

as described in Note

18,

“Subsequent Events,” the conversion price of the Tranche I Notes and Tranche II Notes was further adjusted to approximately

$0.50

per share.

As of

March

31,

2017

and

December

31,

2016,

the related party convertible notes outstanding under the Tranche I Notes and Tranche II Notes were

$22.1

million and

$21.8

million, respectively, net of debt discount of

$0.0

million and

$0.0

million, respectively. Refer to the “Exchange” and “Maturity Treatment Agreement” sections of this Note

5,

"Debt and Mezzanine Equity", for details of the impact of the Maturity Treatment and Exchange agreements on the Tranche I and II Notes.

2014

144A

Notes Sold to Related Parties

As of

March

 

31,

2017

and

December

31,

2016,

the related party convertible notes outstanding under the

2014

Rule

144A

Convertible Note Offering were

$17.6

million and

$17.3

million, respectively, net of discount and issuance costs of

$7.1

million and

$7.4

million, respectively.

As of

March

 

31,

2017

and

December

 

31,

2016,

the total related party convertible notes outstanding were

$43.3

million and

$42.8

million, respectively, net of discount and issuance costs of

$5.6

million and

$5.4

million, respectively.

Loans Payable

In

July

2012,

the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods Agreement (together, the

"July

2012

Bank Agreements") with each of Nossa Caixa Desenvolvimento (or “Nossa Caixa”) and Banco Pine S.A. (or “Banco Pine”). Under the

July

2012

Bank Agreements, the Company pledged certain farnesene production assets as collateral for the loans of

R$52.0

million. The Company's total acquisition cost for such pledged assets was approximately

R$68.0

million (approximately

US$21.5

million based on the exchange rate as of

March

 

31,

2017).

The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. Under the

July

2012

Bank Agreements, the Company could borrow an aggregate of

R$52.0

million (approximately

US$16.4

million based on the exchange rate as of

March

 

31,

2017)

as financing for capital expenditures relating to the Company's manufacturing facility located in Brotas, Brazil. Specifically, Banco Pine, agreed to lend

R$22.0

million and Nossa Caixa agreed to lend

R$30.0

million. The funds for the loans are provided by BNDES, but are guaranteed by the lenders. The loans have a final maturity date of

July

 

15,

2022

and bear a fixed interest rate of

5.5%

per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at the Company's manufacturing facility in Brotas, Brazil for more than

30

days, except during the sugarcane off-season. For the

first

two

years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis. Since

August

 

15,

2014,

the Company has been required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. As of

March

 

31,

2017

and

December

 

31,

2016,

a principal amount of

$10.9

million and

$11.1

million, respectively, was outstanding under these loan agreements.

Exchange (Debt Conversion - Related Party Transaction)

On

July

29,

2015,

the Company closed the "Exchange" pursuant to that certain Exchange Agreement, dated as of

July

26,

2015

(or the Exchange Agreement), among the Company, Temasek and Total.

Under the Exchange Agreement, at the closing of the Exchange, Temasek exchanged

$71.0

million in principal amount of outstanding Tranche I and Tranche II Notes (including paid-in-kind and accrued interest through

July

29,

2015)

and Total exchanged

$70.0

million in principal amount of outstanding R&D Notes for shares of the Company’s common stock. The exchange price was

$2.30

per share (or the Exchange Price) and was paid by the exchange and cancellation of such outstanding convertible promissory notes, and Temasek and Total received

30,860,633

and

30,434,782

shares of the Company’s common stock, respectively, in the Exchange. As a result of the Exchange, accretion of debt discount was accelerated based on the Company’s estimate of the expected conversion date, resulting in an additional interest expense of

$39.2

million for the year ended

December

31,

2015.

Under the Exchange Agreement, Total also received the following warrants, each with a

five

-year term, at the closing of the Exchange:

• A warrant to purchase 18,924,191 shares of the Company’s Common Stock (or the Total Funding Warrant).

• A warrant to purchase 2,000,000 shares of the Company’s common stock that would only be exercisable if the Company failed, as of March 1, 2017, to achieve a target cost per liter to manufacture farnesene (or the Total R&D Warrant). The Total Funding Warrant and the Total R&D Warrant are collectively referred to as the “Total Warrants.”

Additionally, under the Exchange Agreement, Temasek received the following warrants:

• A warrant to purchase 14,677,861 shares of the Company’s common stock (or the Temasek Exchange Warrant).

• A warrant exercisable for that number of shares of the Company’s common stock equal to (1) (A) the number of shares for which Total exercises the Total Funding Warrant plus (B) the number of additional shares for which the certain convertible notes remaining outstanding following the completion of the Exchange may become exercisable as a result of a reduction in the conversion price of such remaining notes as of a result of and/or subsequent to the date of the Exchange plus (C) that number of additional shares in excess of 2,000,000, if any, for which the Total R&D Warrant becomes exercisable multiplied by a fraction equal to 30.6% divided by 69.4% plus (2) (A) the number of any additional shares for which certain other outstanding convertible promissory notes may become exercisable as a result of a reduction to the conversion price of such notes multiplied by (B) a fraction equal to 13.3% divided by 86.7% (or the Temasek Funding Warrant).

• A warrant exercisable for that number of shares of the Company’s common stock equal to 880,339 multiplied by a fraction equal to the number of shares for which Total exercises the Total R&D Warrant divided by 2,000,000 (or the Temasek R&D Warrant). If Total is entitled to, and does, exercise the Total R&D Warrant in full, the Temasek R&D Warrant would be exercisable for 880,339 shares.

The Temasek Exchange Warrant, the Temasek Funding Warrant and the Temasek R&D Warrant each have

ten

-year terms and are referred to herein as the “Temasek Warrants” and, the Temasek Warrants and Total Warrants are hereinafter collectively referred to as the “Exchange Warrants”. All of the Exchange Warrants have an exercise price of

$0.01

per share.

In addition to the grant of the Exchange Warrants, a warrant issued by the Company to Temasek in

October

2013

in conjunction with a prior convertible debt financing (or the

2013

Warrant) became exercisable in full upon the completion of the Exchange. There were

1,000,000

shares underlying the

2013

Warrant, with an exercise price of

$0.01

per share.

The exercisability of all of the Exchange Warrants was subject to stockholder approval, which was obtained on

September

17,

2015.

In

February

and

May

2016,

as a result of adjustments to the conversion price of the Tranche Notes discussed above, the Temasek Funding Warrant became exercisable for an additional

127,194

and

2,335,342

shares of common stock, respectively. Following the issuance by the Company of shares of convertible preferred stock and warrants to purchase common stock in

May

2017,

as described in Note

18,

“Subsequent Events,” and a corresponding adjustment to the conversion price of the Tranche I Notes and Tranche II Notes, as described above, the Temasek Funding Warrant became exercisable for an additional

16,886,320

shares of common stock.

As of

March

1,

2017,

the Company had not achieved the target cost per liter to manufacture farnesene provided in the Total R&D Warrant, and as a result, on

March

1,

2017

the Total R&D Warrant became exercisable in accordance with its terms. In addition, upon any exercise by Total of the Total R&D Warrant, the Temasek R&D Warrant will become exercisable for that number of shares of the Company's common stock equal to

880,339

multiplied by a fraction equal to the number of shares for which Total exercises the Total R&D Warrant divided by

2,000,000.

As of

March

31,

2017,

the Total Funding Warrant, the Temasek Exchange Warrant, and the

2013

Warrant had been fully exercised and Temasek had exercised the Temasek Funding Warrant with respect to

12,700,244

shares of common stock. Neither the Total R&D Warrant nor the Temasek R&D Warrant had been exercised as of

March

31,

2017.

Warrants to purchase

2,462,536

shares of common stock under the Temasek Funding Warrant were unexercised as of

March

31,

2017

Maturity Treatment Agreement

At the closing of the Exchange, the Company, Total and Temasek also entered into a Maturity Treatment Agreement, dated as of

July

29,

2015,

pursuant to which Total and Temasek agreed to convert any Tranche I Notes, Tranche II Notes or

2014

144A

Notes held by them that were not cancelled in the Exchange (or the Remaining Notes) into shares of the Company’s common stock in accordance with the terms of such Remaining Notes upon maturity, provided that certain events of default had not occurred with respect to the applicable Remaining Notes prior to such maturity. As of immediately following the closing of the Exchange, Temasek held

$10.0

million in aggregate principal amount of Remaining Notes (consisting of

2014

144A

Notes) and Total held approximately

$25.0

million in aggregate principal amount of Remaining Notes (consisting of

$9.7

million of

2014

144A

Notes and

$15.3

million of Tranche I and II Notes). See Note

18,

“Subsequent Events” for additional details regarding the Remaining Notes.

February

2016

Private Placement - Related Party Transaction

On

February

12,

2016,

the Company entered into a Note and Warrant Purchase Agreement (or the

February

2016

Purchase Agreement) with the purchasers named therein for the sale of

$18.0

million in aggregate principal amount of unsecured promissory notes (or the

February

2016

Notes) to the purchasers, as well as warrants to purchase

2,571,428

shares of the Company’s common stock at an exercise price of

$0.01

per share, representing aggregate proceeds to the Company of

$18

million (or the Initial Sale). On

February

15,

2016,

an additional purchaser joined the

February

2016

Purchase Agreement and purchased

$2.0

million in aggregate principal amount of the

February

2016

Notes, as well as warrants to purchase

285,714

shares of the Company’s common stock at an exercise price of

$0.01

per share, representing aggregate proceeds to the Company of

$2

million (or the Subsequent Sale and together with the Initial Sale, the

February

2016

Private Placement). The

February

2016

Notes and the warrants were issued in a private placement exempt from registration under the Securities Act. The purchasers are existing stockholders of the Company and affiliated with certain members of the Company’s Board of Directors: Foris Ventures, LLC (or Foris, an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder), which purchased

$16.0

million aggregate principal amount of the

February

2016

Notes and warrants to purchase

2,285,714

shares of the Company’s common stock; Naxyris S.A. (an investment vehicle owned by Naxos Capital Partners SCA Sicar; director Carole Piwnica is Director of NAXOS UK, which is affiliated with Naxos Capital Partners SCA Sicar), which purchased

$2.0

million aggregate principal amount of the

February

2016

Notes and warrants to purchase

285,714

shares of the Company’s common stock; and Biolding Investment SA, a fund affiliated with director HH Sheikh Abdullah bin Khalifa Al Thani, which purchased

$2.0

million aggregate principal amount of the

February

2016

Notes and warrants to purchase

285,714

shares of the Company’s common stock. The Initial Sale closed on

February

12,

2016,

and the Subsequent Sale closed on

February

15,

2016.

The

February

2016

Notes are unsecured obligations of the Company and are subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to a Subordination Agreement, dated as of

February

12,

2016,

by and among the Company, the purchasers and the administrative agent under the Senior Secured Loan Facility. Interest will accrue on the

February

2016

Notes from and including, with respect to the Initial Sale,

February

12,

2016,

and with respect to the Subsequent Sale,

February

15,

2016,

at a rate of

13.50%

per annum and is payable on

May

15,

2017,

the maturity date of the

February

2016

Notes, unless the

February

2016

Notes are prepaid in accordance with their terms prior to such date. The

February

2016

Purchase Agreement and the

February

2016

Notes contain customary terms, provisions, representations and warranties, including certain events of default after which the

February

2016

Notes

may

be due and payable immediately, as set forth in the

February

2016

Notes.

The exercisability of the warrants issued in the

February

2016

Private Placement, which each have a term of

five

years, was subject to stockholder approval, which was obtained on

May

17,

2016.

As of

March

31,

2017,

the carrying amount of the

February

2016

Notes was

$19.6

million.

In

May

2017,

in connection with the issuance and sale of convertible preferred stock and warrants to purchase common stock, as described in more detail below in Note

18,

“Subsequent Events,”

$18.0

million of the

February

2016

Notes were exchanged for shares of convertible preferred stock and warrants to purchase common stock in the offering.

June

2016

Private Placement - Related Party Transaction

On

June

24,

2016,

the Company entered into a Note Purchase Agreement (or the

June

2016

Purchase Agreement) with Foris for the sale of

$5.0

million in aggregate principal amount of secured promissory notes (or the

June

2016

Notes) to Foris in exchange for aggregate proceeds to the Company of

$5.0

million (or the

June

2016

Private Placement). The

June

2016

Notes were issued in a private placement exempt from registration under the Securities Act. The

June

2016

Private Placement closed on

June

24,

2016.

The

June

2016

Notes are collateralized by a

second

priority lien on the assets securing the Company’s obligations under the Senior Secured Loan Facility, and are subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to a Subordination Agreement, dated as of

June

24,

2016,

by and among the Company, Foris and the administrative agent under the Company’s Senior Secured Loan Facility. Interest will accrue on the

June

2016

Notes from and including

June

24,

2016

at a rate of

13.50%

per annum and is payable in full on

May

15,

2017,

the maturity date of the

June

2016

Notes, unless the

June

2016

Notes are prepaid in accordance with their terms prior to such date. The

June

2016

Purchase Agreement and the

June

2016

Notes contain customary terms, provisions, representations and warranties, including certain events of default after which the

June

2016

Notes

may

be due and payable immediately, as set forth in the

June

2016

Notes.

In

May

2017,

in connection with the issuance and sale of convertible preferred stock and warrants to purchase common stock, as described in more detail below in Note

18,

“Subsequent Events,” the

June

2016

Notes were exchanged for shares of convertible preferred stock and warrants to purchase common stock in the offering.

October

2016

Private Placements

On

October

21

and

October

27,

2016,

the Company entered into separate Note Purchase Agreements (or the

October

2016

Purchase Agreements) with Foris and Ginkgo, respectively, for the sale of

$6.0

million and

$8.5

million, respectively, in aggregate principal amount of secured promissory notes (or the

October

2016

Notes) in exchange for aggregate proceeds to the Company of

$6.0

million and

$8.5

million, respectively (or the

October

2016

Private Placements). The

October

2016

Notes were issued in private placements exempt from registration under the Securities Act. The

October

2016

Private Placements closed on

October

21

and

October

27,

2016,

respectively.

The

October

2016

Notes are collateralized by a

second

priority lien on the assets securing the Company’s obligations under the Senior Secured Loan Facility, and are subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to Subordination Agreements, dated as of the respective dates of the

October

2016

Purchase Agreements, by and among the Company, the applicable purchaser and the administrative agent under the Company’s Senior Secured Loan Facility. Interest will accrue on the

October

2016

Notes from and including

October

21

and

27,

2016,

respectively, at a rate of

13.50%

per annum and is payable in full on

May

15,

2017,

the maturity date of the

October

2016

Notes, unless the

October

2016

Notes are prepaid in accordance with their terms prior to such date. The

October

2016

Purchase Agreements and the

October

2016

Notes contain customary terms, provisions, representations and warranties, including certain events of default after which the

October

2016

Notes

may

be due and payable immediately, as set forth in the

October

2016

Notes.

In

May

2017,

in connection with the issuance and sale of convertible preferred stock and warrants to purchase common stock, as described in more detail below in Note

18,

“Subsequent Events,” the

October

2016

Notes purchased by Foris in the

October

2016

Private Placements were exchanged for shares of convertible preferred stock and warrants to purchase common stock in the offering.

Salisbury Note

In

December

2016,

in connection with the Company’s purchase of a manufacturing facility in Leland, North Carolina and related assets (Glycotech Assets), as discussed in more detail in Note

7,

“Joint Venture and Noncontrolling Interests,” the Company issued a purchase money promissory note in the principal amount of

$3.5

million (Salisbury Note) in favor of Salisbury Partners, LLC (Salisbury). The Salisbury Note (i) bears interest at a rate of

5%

per year, (ii) has a term of

13

years, (iii) is payable in equal monthly installments of principal and interest beginning on

January

1,

2017

(which payments are subject to a penalty of

5%

if delinquent more than

5

days) and (iv) is secured by a purchase money lien on the Glycotech Assets. The Salisbury Note contains customary terms and provisions, including certain events of default after which the Salisbury Note

may

become immediately due and payable. In addition, the Salisbury Note

may

be prepaid in full or in part at any time without penalty or premium. In

January

2017,

the Salisbury Note was repaid with proceeds from the Nikko Note (as defined below).

Nikko Note

In

December

2016,

in connection with the Company’s formation of its cosmetics joint venture (or the Aprinnova JV) with Nikko Chemicals Co., Ltd. (or Nikko), an existing commercial partner of the Company, and Nippon Surfactant Industries Co., Ltd., an affiliate of Nikko, as discussed in more detail in Note

7,

“Joint Venture and Noncontrolling Interests,” Nikko made a loan to the Company in the principal amount of

$3.9

million, and the Company in consideration therefor issued a promissory note (or the Nikko Note) to Nikko in an equal principal amount. The proceeds of the Nikko Note were used to satisfy the Company’s remaining liabilities relating to the Company’s purchase of the Glycotech Assets, including liabilities under the Salisbury Note. The Nikko Note (i) bears interest at a rate of

5%

per year, (ii) has a term of

13

years, (iii) is payable in equal monthly installments of principal and interest beginning on

January

1,

2017

(which payments are subject to a penalty of

5%

if delinquent more than

5

days) and (iv) is collateralized by a

first

-priority lien on

10%

of the Aprinnova JV interests owned by the Company. In addition to the payments under the Nikko Note set forth in the preceding sentence, the Company is required to (i) repay

$400,000

of the Nikko Note in equal monthly installments of

$100,000

on

January

1,

2017,

February

1,

2017,

March

1,

2017

and

April

1,

2017

and (ii) commencing with the distributions from the Aprinnova JV to its members relating to the

fourth

fiscal year of the Aprinnova JV and continuing for each fiscal year thereafter until the Nikko Note is fully repaid, repay the Nikko Note in an amount equal to the profits, if any, distributed to the Company by the Aprinnova JV. The Note contains customary terms and provisions, including certain events of default after which the Note

may

become immediately due and payable. In addition, the Nikko Note

may

be prepaid in full or in part at any time without penalty or premium.

In

February

2017,

in connection with the Aprinnova JV, Nikko made an unsecured loan to Aprinnova JV in the principal amount of

$1.5

million and the Aprinnova issued a promissory note (Aprinnova Note) to Nikko in an equal principal amount. The proceeds of the Aprinnova Note will be used as working capital for Aprinnova JV and are repayable in

$375,000

instalments on the following dates:

May

1,

2017,

August,

2017,

November

1,

2018

and

February

1,

2018.

The Aprinnova Note bears interest at

2.75%

annually payable on the principal installment dates.

Letters of Credit

In

June

2012,

the Company entered into a letter of credit agreement for

$1.0

million under which it provided a letter of credit to the landlord of its headquarters in Emeryville, California, in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has

$1.0

million as restricted cash under this arrangement as of

March

 

31,

2017

and

December

 

31,

2016.

Future minimum payments under the debt agreements as of

March

 

31,

2017

are as follows (in thousands):

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Related Party Loans payable			Credit Facility			Total
2017 (remaining nine months)	$	4,537		$	12,677		$	11,899		$	31,511		$	5,271		$	65,895
2018		16,290			21,803			2,878			—			33,710			74,681
2019		34,913			93,287			2,766			—			2,580			133,546
2020		—			—			2,656			—			2,500			5,156
2021		—			—			2,543			—			27,396			29,939
Thereafter		—			—			1,442			—			—			1,442
Total future minimum payments (1)		55,740			127,767			24,184			31,511			71,457			310,659
Less: amount representing interest (2)		(12,405	)		(52,549	)		(1,596	)		(957	)		(22,214	)		(89,721	)
Present value of minimum debt payments		43,335			75,218			22,588			30,554			49,243			220,938
Less: current portion		(3,611	)		(2,288	)		(11,780	)		(30,554	)		(1,222	)		(49,455	)
Noncurrent portion of debt	$	39,724		$	72,930		$	10,808		$	—		$	48,021		$	171,483

______________

(1)

Including

$3.9

million in

2017

related to Nomis Bay convertible note which, at the Company’s election,

may

be settled in shares or cash, and

$46.8

million between

2018

and

2019

subject to the Maturity Treatment Agreement, which will be converted to common stock at maturity, subject to there being no default under the terms of the debt. See Note

18,

“Subsequent Events” for additional details regarding the notes subject to the Maturity Treatment Agreement.

(2)

Including debt discount and issuance cost of

$42.0

million associated with the related party and non-related party debt which will be accreted to interest expense under the effective interest method over the term of the debt.

XML

Note 6 - Commitments and Contingencies

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Commitments Contingencies and Guarantees [Text Block]

6.

Commitments and Contingencies

Lease Obligations

The Company leases certain facilities and finances certain equipment under operating and capital leases, respectively. Operating leases include leased facilities and capital leases include leased equipment (see Note

4,

"Balance Sheet Components"). The Company recognizes rent expense on a straight-line basis over the non-cancellable lease term and records the difference between rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or

tenant

incentives or allowances, the Company applies them as a straight-line rent expense over the lease term. The Company has non-cancellable operating lease agreements for office, research and development, and manufacturing space that expire at various dates, with the latest expiration in

February

2031.

Rent expense under operating leases was

$1.3

million for each of the

three

months ended

March

 

31,

2017

and

2016,

respectively.

Future minimum payments under the Company's lease obligations as of

March

 

31,

2017,

are as follows (in thousands):

Years ending December 31:	Capital Leases			Operating Leases		Total Lease Obligations
2017 (remaining nine months)	$	734		$	5,194	$	5,928
2018		106			6,909		7,015
2019		9			6,782		6,791
2020		—			7,012		7,012
2021		—			7,248		7,248
Thereafter		—			10,993		10,993
Total future minimum lease payments		849		$	44,138	$	44,987
Less: amount representing interest		(39	)
Present value of minimum lease payments		810
Less: current portion		(405	)
Long-term portion	$	405

Guarantor Arrangements

The Company has agreements whereby it indemnifies its officers and directors for certain events or occurrences while the officer or director is serving in his or her official capacity. The indemnification period remains enforceable for the officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future payments. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of

March

 

31,

2017

and

December

 

31,

2016.

The Company entered into the FINEP Credit Facility to finance a research and development project on sugarcane-based biodiesel (see Note

5,

"Debt and Mezzanine Equity"). The FINEP Credit Facility is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately

R$6.0

million (approximately

US$1.9

million based on the exchange rate as of

March

 

31,

2017).

The Company entered into the BNDES Credit Facility to finance a production site in Brazil (see Note

5,

"Debt and Mezzanine Equity").The BNDES Credit Facility is collateralized by a

first

priority security interest in certain of the Company's equipment and other tangible assets with a total acquisition cost of

R$24.9

million (approximately

US$7.9

million based on the exchange rate as of

March

 

31,

2017).

The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide certain bank guarantees under the BNDES Credit Facility.

The Company entered into loan agreements and security agreements whereby the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Nossa Caixa and Banco Pine (see Note

5,

"Debt and Mezzanine Equity"). The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately

R$68.0

million (approximately

US$21.5

million based on the exchange rate as of

March

 

31,

2017).

The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. 

In

December

2013,

in connection with the execution of the JV Documents entered into by and among the Company, Total and TAB relating to the establishment of TAB (see Note

5,

"Debt and Mezzanine Equity" and Note

7,

“Joint Venture and Noncontrolling Interests”), the Company agreed to exchange the

$69.0

million of outstanding Unsecured R&D Notes issued pursuant to the Total Purchase Agreement for replacement

1.5%

Senior Secured Convertible Notes due

March

2017,

and grant a security interest to Total in and lien on all the Company’s rights, title and interest in and to the Company’s shares in the capital of TAB. Following execution of the JV Documents, all Unsecured R&D Notes that had been issued were exchanged for Secured R&D Notes. Further, the

$10.85

million in principal amount of such notes issued in the initial tranche of the

third

closing under the Total Purchase Agreement in

July

2014

and the

$10.85

million in principal amount of such notes issued in the

second

tranche of the

third

closing in

January

2015

were Secured R&D Notes instead of Unsecured R&D Notes. See Note

5,"Debt

and Mezzanine Equity" for details regarding the impact of the Exchange and Maturity Treatment Agreement on the R&D Notes. In

March

2016,

as a result of the restructuring of TAB discussed under Note

5,

“Debt and Mezzanine Equity” and Note

7,

“Joint Venture and Noncontrolling Interests,” the remaining Secured R&D Notes were exchanged for an Unsecured R&D Note in the principal amount of

$3.7

million. Further, in

February

2017,

the Company and Total agreed to extend the maturity of the outstanding R&D Notes from

March

1,

2017

to

May

15,

2017.

The Senior Secured Loan Facility and the

June

2016

Notes and

October

2016

Notes (see Note

5,

"Debt and Mezzanine Equity") are collateralized by

first

- and

second

- priority liens, respectively, on substantially all of the Company's assets, including Company intellectual property. In addition, as discussed above, the Nikko Note is collateralized by a

first

-priority lien on

10%

of the Aprinnova JV interests owned by the Company.

Purchase Obligations

As of

March

31,

2017

and

December

31,

2016,

the Company had

$3.7

million and

$0.8

million, respectively, in purchase obligations which included

zero

and

$0.6

million, respectively, of non-cancellable contractual obligations and construction commitments.

Production Cost Commitment

As of

March

31,

2017,

the Company committed to manufacture Squalane and Hemisqualane supplied to our Aprinnova JV at specified cost targets. The Company is obligated to pay all manufacturing costs above the production cost target but is not obligated to produce squalane and hemisqualane at a loss. The Company’s obligations under this arrangement for the quarter ended

March

31,

2017

were offset by its entitlement to all of the profits of Aprinnova for the same period, which entitlement continues for the

three

year period following the date of the Joint Venture Agreement, up to a maximum of

$10

million.

Other Matters

Certain conditions

may

exist as of the date the financial statements are issued, which

may

result in a loss to the Company but will only be recorded when

one

or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that

may

result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought.

If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be reasonably estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed. The Company has levied indirect taxes on sugarcane-based biodiesel sales by Amyris Brasil to customers in Brazil based on advice from external legal counsel. In the absence of definitive rulings from the Brazilian tax authorities on the appropriate indirect tax rate to be applied to such product sales, the actual indirect rate to be applied to such sales could differ from the rate we levied.

In

April

2017,

a securities class action complaint was filed against Amyris and our CEO, John G. Melo, and CFO, Kathleen Valiasek, in the U.S. District Court for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported class that would comprise all individuals who acquired our common stock between

March

2,

2017

and

April

17,

2017.

The complaint alleges securities law violations based on statements made by the Company in its earnings press release issued on

March

2,

2017

and Form

12b

-

25

filed with the SEC on

April

3,

2017.

The Company believes that the complaint lacks merit, and intends to defend itself vigorously.

The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that

may

arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with reasonable assurance and therefore an estimate of all the reasonably possible losses cannot be determined at this time. Therefore, if

one

or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s condensed consolidated financial statements for the relevant reporting period could be materially adversely affected.

XML

Note 7 - Joint Ventures and Noncontrolling Interest

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Equity Method Investments and Joint Ventures Disclosure [Text Block]

7.

Joint Ventures and Noncontrolling Interests

Novvi LLC

In

September

2011,

the Company and Cosan US, Inc. (Cosan U.S.) formed Novvi LLC (or Novvi), a U.S. entity that was initially jointly owned by the Company and Cosan U.S. In

March

 

2013,

the Company and Cosan U.S. entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi (or the Novvi Operating Agreement), which sets forth the governance procedures for Novvi and the parties' initial contribution. The Company also entered into an IP License Agreement with Novvi (as amended, the Novvi IP License Agreement) under which the Company granted Novvi (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in automotive, commercial, and industrial lubricants markets, and (ii) a non-exclusive, royalty free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan U.S. granted Novvi certain rights of

first

refusal with respect to alternative base oil and additive technologies that

may

be acquired by the Company or Cosan U.S. during the term of the IP License Agreement. Under these agreements, through

December

31,

2015

the Company and Cosan U.S. each owned

50%

of Novvi and each party shared equally in any costs and any profits ultimately realized by the joint venture. Novvi is governed by a

six

member Board of Managers (or the Board of Managers). The Board of Managers appoints the officers of Novvi, who are responsible for carrying out the daily operating activities of Novvi as directed by the Board of Managers. The Novvi IP License Agreement has an initial term of

20

years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency. Under the terms of the Novvi Operating Agreement, Cosan U.S. was obligated to fund its initial

50%

ownership share of Novvi in cash in the amount of

$10.0

million and the Company was obligated to fund its initial

50%

ownership share of Novvi through the granting of an intellectual property license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets, which Cosan U.S. and Amyris agreed was valued at

$10.0

million. In

March

 

2013,

the Company measured its initial contribution of intellectual property to Novvi at the Company's carrying value of the licenses granted under the Novvi IP License Agreement, which was

zero.

In

April

2014,

the Company, via its forgiveness of existing receivables due from Novvi related to rent and other services performed by the Company, purchased additional membership units of Novvi for a purchase price of

$0.2

million. Concurrently, Cosan U.S. purchased an equal amount of additional membership units of Novvi. Also in

April

2014,

the Company and Cosan U.S. each contributed

$2.1

million in cash in exchange for receiving additional membership units in Novvi. Following such transactions, the Company and Cosan U.S. continued to each own

50%

of Novvi's issued and outstanding membership units.

In

September

2014,

the Company and Cosan U.S. entered into a member senior loan agreement to grant Novvi a loan amounting to approximately

$3.7

million. The loan is due on

September

1,

2017

and bears interest at a rate of

0.36%

per annum. Interest accrues daily and is due and payable in arrears on

September

1,

2017.

The Company and Cosan U.S. each agreed to provide

50%

of the loan. The Company's share of approximately

$1.8

million was disbursed in

two

installments. The

first

installment of

$1.2

million was made in

September

2014

and the

second

installment of

$0.6

million was made in

October

2014.

In

November

2014,

the Company and Cosan U.S. entered into a

second

member senior loan agreement to grant Novvi a loan of approximately

$1.9

million on the same terms as the loan issued in

September

2014,

except that the due date is

November

10,

2017.

The Company and Cosan U.S. each agreed to provide

50%

of the loan. The Company disbursed its share of the loan (i.e., approximately

$1.0

million) in

November

2014.

In

May

2015,

the Company and Cosan U.S. entered into a

third

member senior loan agreement to grant Novvi a loan of approximately

$1.1

million on the same terms as the loan issued in

September

2014,

except that the due date is

May

14,

2018.

The Company and Cosan U.S. each agreed to provide

50%

of the loan.

In the

fourth

quarter of

2015,

the Company and Cosan U.S. entered into

four

additional member senior loan agreements to grant Novvi an aggregate loan of approximately

$1.6

million on the same terms as the loan issued in

September

2014,

except that the respective due dates are

August

19,

2018,

October

15,

2018,

November

12,

2018

and

December

17,

2018.

The Company and Cosan U.S. each agreed to provide

50%

of each of these

four

loans. In

July

2016,

the Company contributed all outstanding amounts owing by Novvi to the Company under the

seven

member senior loan agreements in exchange for receiving additional membership units in Novvi.

In

February

2016,

the Company purchased additional membership units of Novvi for an aggregate purchase price of approximately

$0.6

million in the form of forgiveness of existing receivables due from Novvi related to rent and other services performed by the Company, and Cosan U.S. purchased an equal number of additional membership units in Novvi for approximately

$0.6

million in cash. Following such transactions, each member continued to own

50%

of Novvi's issued and outstanding membership units.

On

July

19,

2016,

American Refining Group, Inc. (ARG) agreed to make a capital contribution of up to

$10.0

million in cash to Novvi, subject to certain conditions, in exchange for a

one

third

ownership stake in Novvi. In connection with such investment, the Company agreed to contribute all outstanding amounts owed by Novvi to the Company under the

seven

existing member senior loan agreements between the Company and Novvi, as well as certain existing receivables due from Novvi to the Company related to rent and other services performed by the Company, in exchange for receiving additional membership units in Novvi. Likewise, Cosan U.S. contributed an equal amount to Novvi as the Company in exchange for receiving an equal amount of additional membership interests in Novvi. Following the ARG investment, assuming it is made in full, and the capital contributions of the Company and Cosan U.S., each of Novvi’s

three

members (i.e., ARG, the Company and Cosan U.S.) would own

one

third

of Novvi’s issued and outstanding membership units and would each be represented by

two

members of the Board of Managers. In order to reflect the ARG investment in Novvi and related transactions, the Novvi Operating Agreement was amended and restated on

July

19,

2016.

In addition, the Novvi IP License Agreement was also amended on

July

19,

2016.

As of

March

31,

2017,

all of the

$10.0

million of ARG's capital contribution to Novvi had been funded.

In

November

2016,

Chevron U.S.A. Inc. (Chevron) made a capital contribution of

$1.0

million in cash to Novvi in exchange for

20,000

membership units, representing an approximately

3%

ownership stake in Novvi, which reduced the ownership interests of the Company, Cosan U.S. and ARG pro rata. In connection with its investment in Novvi, for so long as Chevron or its affiliates owns any membership units in Novvi, Chevron shall have the right to purchase up to such additional membership units as would result in Chevron owning the greater of (i)

25%

of the aggregate membership units then outstanding held by Chevron, the Company, Cosan U.S. and ARG (including their affiliates and successors-in-interest) following such purchase and (ii) the highest percentage of such membership units held by the Company, Cosan U.S. and ARG (including their affiliates and successors-in-interest) following such purchase. In addition, Chevron shall have the right to purchase up to its pro rata share (as determined by the then issued and outstanding membership units, excluding any such units beneficially owned by Novvi) of all additional membership units that Novvi

may,

from time to time, propose to sell or issue.

Additional funding requirements to finance the ongoing operations of Novvi are expected to happen through revolving credit or other loan facilities provided by unrelated parties (i.e., such as financial institutions); cash advances or other credit or loan facilities provided by Novvi’s members or their affiliates; or additional capital contributions by the existing Novvi members or new investors.

The Company has identified Novvi as a VIE and determined that the power to direct activities which most significantly impact the economic success of the joint venture (i.e., continuing research and development, marketing, sales, distribution and manufacturing of Novvi products) are shared among the Company, Cosan U.S. and ARG. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi under the equity method of accounting. The Company will continue to reassess its primary beneficiary analysis of Novvi if there are changes in events and circumstances impacting the power to direct activities that most significantly affect Novvi's economic success. Under the equity method, the Company's share of profits and losses and impairment charges on investments in affiliates (nil for both periods presented) are included in “Loss from investments in affiliates” in the condensed consolidated statements of operations. The carrying amount of the Company's equity investment in Novvi was

zero

as of each of

March

31,

2017

and

2016.

Total Amyris BioSolutions B.V.

In

November

2013,

the Company and Total formed Total Amyris BioSolutions B.V. (TAB), a joint venture to produce and commercialize farnesene- or farnesane-based jet and diesel fuels. Prior to the restructuring of TAB in

March

2016

as described below, the common equity of TAB was owned equally by the Company and Total, and TAB’s purpose was limited to executing the License Agreement dated

December

2,

2013

between the Company, Total and TAB and maintaining such licenses under it, unless and until either (i) Total elected to go forward with either the full (diesel and jet fuel) TAB commercialization program (R&D Program) or the jet fuel component of the R&D Program (or a Go Decision), (ii) Total elected to not continue its participation in the R&D Program and TAB (or a No-Go Decision), or (iii) Total exercised any of its rights to buy out the Company’s interest in TAB. Following a Go Decision, the articles and shareholders’ agreement of TAB would be amended and restated to be consistent with the shareholders’ agreement contemplated by the Total Fuel Agreements (see Note

5,

"Debt and Mezzanine Equity" and Note

8,

"Significant Agreements").

In

July

2015,

the Company and Total entered into a Letter Agreement (or, as amended in

February

2016,

the TAB Letter Agreement) regarding the restructuring of the ownership and rights of TAB (Restructuring), pursuant to which the parties agreed to, among other things, enter into an Amended & Restated Jet Fuel License Agreement between the Company and TAB (Jet Fuel Agreement), a License Agreement regarding Diesel Fuel in the European Union (EU) between the Company and Total (EU Diesel Fuel Agreement), and an Amended and Restated Shareholders’ Agreement among the Company, Total and TAB, and file a Deed of Amendment of Articles of Association of TAB, all in order to reflect certain changes to the ownership structure of TAB and license grants and related rights pertaining to TAB.

On

February

12,

2016,

the Company and Total entered into an amendment to the TAB Letter Agreement, pursuant to which the parties agreed that, upon the closing of the Restructuring, Total would cancel R&D Notes in an aggregate principal amount of approximately

$1.3

million, plus all paid-in-kind and accrued interest as of the closing of the Restructuring under all outstanding R&D Notes (including all such interest that was outstanding as of

July

29,

2015),

and a note in the principal amount of Euro

50,000,

plus accrued interest, issued by the Company to Total in connection with the existing TAB capitalization, in exchange for an additional

25%

ownership interest of TAB (giving Total an aggregate ownership stake of

75%

of TAB and giving the Company an aggregate ownership stake of

25%

of TAB). In connection therewith, Total would surrender to the Company the remaining R&D Notes and the Company would provide to Total a new R&D Note containing substantially similar terms and conditions to the outstanding R&D Notes other than it would be unsecured and its payment terms would be severed from TAB’s business performance, in the principal amount of

$3.7

million (collectively, the “TAB Share Purchase”).

On

March

21,

2016,

the Company, Total and TAB closed the Restructuring and the TAB Share Purchase. See Note

5,

“Debt and Mezzanine Equity” for further details of these transactions and the impact of these transaction on the Company’s condensed consolidated financial statements.

Under the Jet Fuel Agreement, (a) the Company granted exclusive (co-exclusive in Brazil), world-wide, royalty-free rights to TAB for the production and commercialization of farnesene- or farnesane-based jet fuel, (b) the Company granted TAB the option, until

March

1,

2018,

to purchase the Company’s Brazil jet fuel business at a price based on the fair value of the commercial assets and on the Company’s investment in other related assets, (c) the Company granted TAB the right to purchase farnesene or farnesane for its jet fuel business from us on a “most-favored” pricing basis and (d) all rights to farnesene- or farnesane-based diesel fuel the Company previously granted to TAB reverted back to the Company. As a result of the Jet Fuel Agreement, the Company generally no longer has an independent right to make or sell, without the approval of TAB, farnesene- or farnesane-based jet fuels outside of Brazil.

Upon all farnesene-or farnesane-based diesel fuel rights reverting back to the Company, the Company granted to Total, pursuant to the EU Diesel Fuel Agreement, (a) an exclusive, royalty-free license to offer for sale and sell farnesene- or farnesane-based diesel fuel in the EU, (b) the non-exclusive right to make farnesene or farnesane anywhere in the world, but Total must (i) use such farnesene or farnesane to produce only diesel fuel to offer for sale or sell in the EU and (ii) pay the Company a to-be-negotiated, commercially reasonable, “most-favored” basis royalty and (c) the right to purchase farnesene or farnesane for its EU diesel fuel business from the Company on a “most-favored” pricing basis. As a result of the EU Diesel Fuel Agreement, the Company generally no longer has an independent right to make or sell, without the approval of Total, farnesene- or farnesane-based diesel fuels in the EU.

As a result of, and in order to reflect, the changes to the ownership structure of TAB described above, on

March

21,

2016,

(a) the Company, Total and TAB entered into an Amended and Restated Shareholders’ Agreement and filed a Deed of Amendment of Articles of Association of TAB and (b) the Company and Total terminated the Amended and Restated Master Framework Agreement, dated

December

2,

2013

and amended on

April

1,

2015,

between the Company and Total.

As of

March

31,

2017,

the common equity of TAB was owned

25%

by the Company and

75%

by Total. TAB has a capitalization as of

March

31,

2017

of

€0.1

million (approximately

US$0.1

million based on the exchange rate as of

March

31,

2017).

The Company has identified TAB as a VIE and determined that the Company is not the primary beneficiary and therefore accounts for its investment in TAB under the equity method of accounting. Under the equity method, the Company's share of profits and losses (nil for both periods presented) are included in “Loss from investment in affiliate” in the condensed consolidated statements of operations.

SMA Indústria Química S.A.

In

April

 

2010,

the Company established SMA Indústria Química (or SMA), a joint venture with São Martinho S.A. (or SMSA), to build a production facility in Brazil. SMA is located at the SMSA mill in Pradópolis, São Paulo state. The joint venture agreements establishing SMA had a

20

year initial term.

SMA was initially managed by a

three

member executive committee, of which the Company appointed

two

members,

one

of whom is the plant manager who is the most senior executive responsible for managing the construction and operation of the facility. SMA was initially governed by a

four

member board of directors, of which the Company and SMSA each appointed

two

members. The board of directors had certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee.

The joint venture agreements required the Company to fund the construction costs of the new facility and SMSA would reimburse the Company up to

R$61.8

million (approximately

US$19.5

million based on the exchange rate as of

March

 

31,

2017)

of the construction costs after SMA commences production. After commercialization, the Company would market and distribute Amyris renewable products produced by SMA and SMSA would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that SMSA could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the

first

four

years at a price that guarantees the return of SMSA’s investment plus a fixed interest rate. After this

four

year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return.

Under the terms of the joint venture agreements, if the Company became controlled, directly or indirectly, by a competitor of SMSA, then SMSA would have the right to acquire the Company’s interest in SMA. If SMSA became controlled, directly or indirectly, by a competitor of the Company, then the Company would have the right to sell its interest in SMA to SMSA. In either case, the purchase price would be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management.

The Company initially had a

50%

ownership interest in SMA. The Company had identified SMA as a VIE pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk was not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, the Company directed the design and construction activities, as well as production and distribution. In addition, the Company had the obligation to fund the design and construction activities until commercialization was achieved. Subsequent to the construction phase, both parties equally would fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. As of

March

31,

2017,

the Company indirectly owned

100%

of the equity interest in SMA and as a wholly owned subsidiary its financial results are included in the Company’s condensed consolidated financial statements.

The Company completed a significant portion of the construction of the new facility in

2012.

The Company suspended construction of the facility in

2013

in order to focus on completing and operating the Company's smaller production facility in Brotas, Brazil. In

February

2014,

the Company entered into an amendment to the joint venture agreement with SMSA which updated and documented certain preexisting business plan requirements related to the recommencement of construction at the joint venture operated plant and sets forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than

18

months following the construction of the plant no later than

March

31,

2017,

and (ii) the extension of an option held by SMSA to build a

second

large-scale farnesene production facility to no later than

December

31,

2018

with the commencement of operations at such

second

facility to occur no later than

April

1,

2019.

On

July

1,

2015

SMSA filed a material fact document with CVM, the Brazilian securities regulator, that announced that certain contractual targets undertaken by the Company have not been achieved, which affects the feasibility of the project. Therefore, SMSA decided not to approve continuing construction of the plant for the joint venture with the Company and its Brazilian subsidiary Amyris Brasil. In

July

2015,

the Company announced that it was in discussions with SMSA regarding the continuation of the joint venture. In

December

2015,

the Company and SMSA entered into a Termination Agreement and a Share Purchase and Sale Agreement relating to the termination of the joint venture. Under the Termination Agreement, the parties agreed that the joint venture would be terminated effective upon the closing of a purchase by Amyris Brasil of SMSA’s shares of SMA. Under the Share Purchase and Sale Agreement, Amyris Brasil agreed to purchase, for

R$50,000

(approximately

US$15,780

based on the exchange rate as of

March

 

31,

2017),

50,000

shares of SMA (representing all the outstanding shares of SMA held by SMSA), which purchase and sale was consummated on

January

11,

2016.

The Share Purchase and Sale Agreement also provided that the Company and Amyris Brasil would have

12

months following the closing of the share purchase to remove assets from SMSA’s site, and enter into an extension of the lease for such

12

month period for monthly rental payments of

R$9,853

(approximately

US$3,110

based on the exchange rate as of

March

 

31,

2017).

The Share Purchase and Sale Agreement also clarified that the Company and Amyris Brasil would not be required to demolish or remove the foundations of the plant at the SMSA site. On

September

1,

2016,

the parties entered into an addendum to the Share Purchase and Sale Agreement (and a corresponding amendment to the lease) which extended the deadline for the Company and Amyris Brasil to remove assets from SMSA’s site until

December

31,

2017.

Salisbury transaction

In

January

2011,

the Company entered into a production service agreement (Glycotech Agreement) with Glycotech, Inc. (or Glycotech), under which Glycotech provides process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina (Glycotech Facility). The Company products manufactured by Glycotech are owned and distributed by the Company. Pursuant to the terms of the Glycotech Agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility, which is dedicated solely to the manufacture of Amyris products. The initial term of the Glycotech Agreement was for a

two

year period commencing on

February

 

1,

2011

and the Glycotech Agreement renews automatically for successive

one

-year terms, unless terminated by the Company. Concurrent with the Glycotech Agreement, the Company also entered into a Right of First Refusal Agreement with Salisbury Partners, LLC (or Salisbury), the lessor of the facility and site leased by Glycotech (ROFR Agreement). Per conditions of the ROFR Agreement, Salisbury agreed not to sell the facility and site leased by Glycotech during the term of the Glycotech Agreement. In the event that Salisbury was presented with an offer to sell or decides to sell an adjacent parcel, the Company had the right of

first

refusal to acquire it.

On

November

10,

2016,

the Company, Glycotech and Salisbury entered into a Purchase and Sale Agreement (PSA) for the purchase and sale of the Glycotech Facility, the real property on which the Glycotech Facility is located and the fixtures, equipment, materials and supplies and other tangible assets located at or used in connection with the Facility (collectively, the Glycotech Assets). Pursuant to the PSA, on

December

5,

2016,

the Company purchased the Glycotech Assets from Glycotech and Salisbury for an aggregate purchase price of

$4.35

million, of which

$3.5

million was paid in the form of a purchase money promissory note in favor of Salisbury, as described in more detail in Note

5,

“Debt.” In connection with the closing of the purchase and sale of the Glycotech Assets under the PSA, the Company, Glycotech and Salisbury terminated the current lease of the Glycotech Facility and the Glycotech Agreement and modified the ROFR Agreement such that the Company’s right of

first

refusal with respect to certain parcels of real property owned by Salisbury adjacent to the Glycotech Facility would be an appurtenant right running with the ownership of the real property on which the Glycotech Facility is located. The Glycotech Assets were subsequently transferred to the Company’s cosmetics joint venture with Nikko Chemicals Co., Ltd. and Nippon Surfactant Industries Co., Ltd. in connection with the formation of such joint venture, as described below under “Aprinnova JV.”

Aprinnova JV

On

December

12,

2016,

the Company, Nikko Chemicals Co., Ltd. an existing commercial partner of the Company, and Nippon Surfactant Industries Co., Ltd., an affiliate of Nikko (collectively, Nikko) entered into a Joint Venture Agreement (Aprinnova JV Agreement), pursuant to which the Company and Nikko agreed to form a joint venture under the name Neossance, LLC, a Delaware limited liability company (Aprinnova JV). Pursuant to the Aprinnova JV Agreement, the Company agreed to initially form the Aprinnova JV and contribute certain assets of the Company, including certain intellectual property and other commercial assets relating to its Neossance cosmetic ingredients business (Aprinnova JV Business), as well as the Glycotech Assets. The Company also agreed to provide the Aprinnova JV with exclusive (to the extent not already granted to a

third

party), royalty-free licenses to certain intellectual property of the Company necessary to make and sell products associated with the Aprinnova JV Business (Aprinnova JV Products), and, in the event the Company is unable to meet its supply commitments under the Aprinnova JV Supply Agreement (as defined below), or Nikko terminates the Aprinnova JV Supply Agreement due to a material breach or default thereunder by the Company, the Company would be required to grant to the Aprinnova JV and Nikko additional non-exclusive, royalty-free licenses to certain intellectual property rights of the Company related to the production of farnesene in connection with the manufacture, production and sale of the Aprinnova JV Products. In

March

2017,

the name of the Aprinnova JV was changed to Aprinnova, LLC.

At the closing of the formation of the Neossance JV, which occurred on

December

19,

2016,

Nikko purchased a

50%

interest in the Aprinnova JV in exchange for the following payments to the Company: (i) an initial payment of

$10

million and (ii) the profits, if any, distributed to Nikko in cash as members of the Aprinnova JV during the

three

year period following the date of the Joint Venture Agreement, up to a maximum of

$10

million.

Pursuant to the Joint Venture Agreement, the Company and Nikko agreed to make working capital loans to the Aprinnova JV in the amounts of

$500,000

and

$1,500,000,

respectively. In addition, the Company agreed to execute, and cause Amyris Brasil to execute, a supply agreement (Aprinnova JV Supply Agreement) to supply farnesene to the Aprinnova JV, and further agreed to conduct its business in the Aprinnova JV Products through the Aprinnova JV, to purchase all of its requirements for the Aprinnova JV Products from the Neossance JV and to transfer all of its customers for the Aprinnova JV Products to the Aprinnova JV. In addition, the Company agreed to guarantee a maximum production cost for certain Aprinnova JV Products to be produced by the Aprinnova JV and to bear any cost of production above such guaranteed costs.

Under the Aprinnova JV Agreement, in the event of a merger, acquisition, sale or other similar reorganization, or a bankruptcy, dissolution, insolvency or other similar event, of the Company, on the

one

hand, or Nikko, on the other hand, the other member will have a right of

first

purchase with respect to such member’s interest in the Aprinnova JV, at the fair market value of such interest, in the case of a merger, acquisition, sale or other similar reorganization, and at the lower of the fair market value or book value of such interest, in the case of a bankruptcy, dissolution, insolvency or other similar event.

In connection with the formation of the Aprinnova JV, the members entered into a First Amended and Restated LLC Operating Agreement of the Aprinnova JV (Operating Agreement). Pursuant to the Operating Agreement, the Aprinnova JV will be managed by a Board of Directors, which shall initially consist of

four

directors,

two

of which will be appointed by the Company and

two

of which will be appointed by Nikko. In addition, Nikko will have the right to designate the Chief Executive Officer of the Aprinnova JV from among the directors and the Company will have the right to designate the Chief Financial Officer. Pursuant to the Joint Venture Agreement, Nikko designated John Melo, the President and CEO of the Company, to serve as the initial CEO of the Aprinnova JV for a period of

one

year and the Company designated Shizuo Ukaji, the President and CEO of Nikko, to serve as the initial CFO of the Aprinnova JV for a period of

one

year. The Company has determined that it controls the Aprinnova JV because of its significant ongoing involvement in operational decision making and its guarantee of production costs for squalane/hemisqualane.

Under the Operating Agreement, profits from the operations of the Aprinnova JV, if any, will be distributed as follows: (i)

first,

to the members in proportion to their respective unreturned capital contribution balances, until each member’s unreturned capital contribution balance equals

zero

and (ii)

second,

to the members in proportion to their respective interests. In addition, future capital contributions will be made from time to time as the members shall determine, in each case on an equal

(50%/50%)

basis between the Company, on the

one

hand, and Nikko, on the other hand, unless otherwise mutually agreed by the members.

In connection with the contribution of the Glycotech Assets by the Company to the Aprinnova JV, at the closing of the formation of the Aprinnova JV, Nikko made a loan to the Company in the principal amount of

$3.9

million, and the Company in consideration therefor issued a promissory note to Nikko in an equal principal amount, as described in more detail in Note

5,

“Debt.”

The table below reflects the carrying amount of the assets and liabilities of the consolidated VIE for which the Company is the primary beneficiary at

March

31,

2017.

 The creditors of each consolidated VIE have recourse only to the assets of that VIE.

(In thousands)	March 31, 2017		December 31, 2016
Assets	$	2,306	$	2,277
Liabilities	$	158	$	135

The change in noncontrolling interest for the

three

months ended

March

 

31,

2017

and

2016,

is summarized below (in thousands):

	2017		2016
Balance at January 1	$	937	$	391
Acquisition of noncontrolling interest		—		(277	)
Balance at March 31	$	937	$	114

XML

Note 8 - Significant Agreements

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Collaborative Arrangement Disclosure [Text Block]

8.

Significant Agreements

Research and Development Activities

Firmenich Collaboration Agreement

In

March

 

2013,

the Company entered into a Collaboration Agreement (or, as amended, the Firmenich Collaboration Agreement) with Firmenich SA (or Firmenich), a global flavors and fragrances company, to establish a collaboration arrangement for the development and commercialization of multiple renewable flavors and fragrances compounds. Under the Firmenich Collaboration Agreement, except for rights granted under pre-existing collaboration relationships, the Company granted Firmenich exclusive access to specified Company intellectual property for the development and commercialization of flavors and fragrances compounds in exchange for research and development funding and a profit sharing arrangement. The Firmenich Collaboration Agreement superseded and expanded the

November

2010

Master Collaboration and Joint Development Agreement between the Company and Firmenich. Unless sooner terminated in accordance with its terms, the Firmenich Collaboration Agreement has an initial term of

10

years and will automatically renew at the end of such term (and at the end of any extension) for an additional

3

-year term unless and until a party provides the other party written notice, at least

twelve

months before the end of the then-current term, of its desire to terminate the agreement at the end of the then-current term.

The Firmenich Collaboration Agreement provided for annual, up-front funding to the Company by Firmenich of

$10.0

million for each of the

first

three

years of the collaboration. Payments of

$10.0

million were received by the Company in each of

March

2013,

2014

and

2015.

The Firmenich Collaboration Agreement contemplates additional funding by Firmenich of up to

$5.0

million under

four

potential milestone payments, as well as additional funding by the collaboration partner on a discretionary basis. Through

March

2017,

the Company had achieved the

third

performance milestone under the Firmenich Collaboration Agreement and recognized collaboration revenues of

$1.1

million and

$3.0

million for the

three

months ended

March

31,

2017

and

2016,

respectively. The Firmenich Collaboration Agreement does not impose any specific research and development obligations on either party after year

six,

but provides that if the parties mutually agree to perform research and development activities after year

six,

the parties will fund such activities equally.

Under the Firmenich Collaboration Agreement, the parties agreed to jointly select target compounds, subject to final approval of compound specifications by Firmenich. During the development phase, the Company would be required to provide labor, intellectual property and technology infrastructure and Firmenich would be required to contribute downstream polishing expertise and market access. The Firmenich Collaboration Agreement provides that the Company will own research and development and strain engineering intellectual property, and Firmenich will own blending and, if applicable, chemical conversion intellectual property. Under certain circumstances, such as the Company’s insolvency, Firmenich would gain expanded access to the Company’s intellectual property. The Firmenich Collaboration Agreement contemplates that, following development of flavors and fragrances compounds, the Company will manufacture the initial target molecules for the compounds and Firmenich will perform any required downstream polishing and distribution, sales and marketing. The Firmenich Collaboration Agreement provides that the parties will mutually agree on a supply price for each compound developed under the agreement and, subject to certain exceptions, will share product margins from sales of each such compound on a

70/30

basis

(70%

for Firmenich) until Firmenich receives

$15.0

million more than the Company in the aggregate from such sales, after which time the parties will share the product margins

50/50.

The Company also agreed to pay a

one

-time success bonus to Firmenich of up to

$2.5

million if certain commercialization targets are met.

In

September

2014,

the Company entered into a supply agreement with Firmenich for compounds developed under the Firmenich Collaboration Agreement. The Company recognized

$1.2

million and

$2.0

million of revenues from product sales under this supply agreement for the

three

months ended

March

31,

2017

and

2016,

respectively.

In

December

2016,

the Company and Firmenich entered into an amendment of the Firmenich Collaboration Agreement, pursuant to which the parties agreed to exclude certain compounds from the scope of the agreement and to permit the Company to engage in certain activities relating to such excluded compounds with a

third

party, in exchange for a

ten

percent royalty on net sales by the Company to such

third

party of products related to such excluded compounds, as well as (i) the transfer of certain technical materials relating to the Firmenich Collaboration Agreement, previously held in escrow, to Firmenich, (ii) a credit to Firmenich against products previously ordered from the Company under the parties’ existing supply agreement, (iii) a reduced price for the sale of additional products to Firmenich under such supply agreement, and (iv) training for the employees of Firmenich at the Company’s manufacturing plant located in Brotas, Brazil.

Kuraray Collaboration Agreement

In

July

2011,

the Company entered into a collaboration agreement with Kuraray Co., Ltd (or Kuraray), with an initial focus on using farnesene-based polymers to replace petroleum-derived additives in tires. In

March

2014,

the Company entered into the Second Amended and Restated Collaboration Agreement with Kuraray in order to extend the term of the original collaboration agreement between the Company and Kuraray for an additional

two

years and add additional fields and products to the scope of development. In consideration for the Company’s agreement to extend the term of the original collaboration agreement and add additional fields and products, Kuraray agreed to pay the Company

$4.0

million in

two

equal installments of

$2.0

million. The

first

installment was paid on

April

 

30,

2014

and the

second

installment was due on

April

 

30,

2015.

In

March

2015,

the Company and Kuraray entered into the First Amendment to the Second Amended and Restated Collaboration Agreement to extend the term of the collaboration agreement until

December

31,

2016

and to accelerate payment to the Company of the

second

installment of

$2.0

million due from Kuraray under the Second Amended and Restated Collaboration Agreement to

March

31,

2015.

Subsequently, in

November

2016

the Company and Kuraray entered into Amendment

#3

to the Second Amended and Restated Collaboration Agreement to, among other things, extend the term of the collaboration agreement to

December

31,

2018

as well as extend certain exclusive rights granted to Kuraray under the collaboration agreement. In connection with such extensions, Kuraray agreed to pay the Company

$1.0

million in

two

equal installments of

$500,000

on or before

January

15,

2017

and

January

15,

2018,

respectively.

The Company recognized (i) collaboration revenues of

$0.1

million and

$0.4

million for the

three

months ended

March

 

31,

2017

and

2016,

respectively, and (ii)

$1.6

million and

zero

of revenues from product sales for the

three

months ended

March

31,

2017

and

2016,

respectively, under this agreement.

DARPA Technology Investment Agreement

In

September

2015,

the Company entered into a Technology Investment Agreement (or, as amended, the

2015

TIA) with The Defense Advanced Research Projects Agency (or DARPA), under which the Company, with the assistance of

five

specialized subcontractors, will work to create new research and development tools and technologies for strain engineering and scale-up activities. The program that is the subject of the

2015

TIA will be performed and funded on a milestone basis, where DARPA, upon the Company’s successful completion of each milestone event in the

2015

TIA, will pay the Company the amount set forth in the

2015

TIA corresponding to such milestone event. Under the

2015

TIA, the Company and its subcontractors could collectively receive DARPA funding of up to

$35.0

million over the program’s

4

-year term if all of the program’s milestones are achieved. In conjunction with DARPA’s funding, the Company and its subcontractors are obligated to collectively contribute approximately

$15.5

million toward the program over its

four

year term (primarily by providing specified labor and/or purchasing certain equipment). The Company can elect to retain title to the patentable inventions it produces under the program, but DARPA receives certain data rights as well as a government purposes license to certain of such inventions. Either party

may,

upon written notice and subject to certain consultation obligations, terminate the

2015

TIA upon a reasonable determination that the program will not produce beneficial results commensurate with the expenditure of resources.

The Company recognized collaboration revenues of

$1.0

million and

$0.4

million under this agreement for the

three

months ended

March

31,

2017

and

2016,

respectively.

Nenter Supply Agreement

In

April

2016,

the Company entered into a Renewable Farnesene Supply Agreement (or the Nenter Supply Agreement) with Nenter & Co., Inc. (or Nenter) to establish the terms of a supply and value-share arrangement between the Company and Nenter related to farnesene. Under the Nenter Supply Agreement and related agreements, the Company has agreed to supply Nenter with farnesene at prices and on delivery terms set forth in the Nenter Supply Agreement and to provide Nenter with certain exclusive purchase rights, and Nenter has agreed to annual minimum purchase volume requirements and to provide the Company with quarterly value-share payments representing a portion of Nenter’s profit on the sale of products produced using farnesene purchased under the Nenter Supply Agreement. Unless earlier terminated in accordance with its terms, the Nenter Supply Agreement will remain in effect until

December

31,

2020

and will automatically renew at the end of such initial term for an additional

5

-year term unless a party provides the other party written notice, no later than

July

1,

2020,

of its desire to terminate the agreement at the end of the initial term.

The Company recognized

$2.3

million of revenues from product sales under the Nenter Supply Agreement for the

three

months ended

March

31,

2017.

Givaudan Agreements

In

February

2011,

the Company entered into an Amended and Restated Research Agreement with Givaudan International, SA (or Givaudan), a global flavors and fragrances company, relating to the development of a fragrance ingredient. In

October

2015,

the Company and Givaudan entered into a Farnesene Supply Agreement (or the Givaudan Supply Agreement) related to the supply of farnesene by the Company to Givaudan for use in the production of such ingredient, on such terms and at such prices set forth in the Givaudan Supply Agreement. The Company recognized

$0.6

million and

zero

of revenues from product sales under the Givaudan Supply Agreement for the

three

months ended

March

31,

2017

and

2016,

respectively. The Givaudan Supply Agreement has an initial term of

5

years, which term shall be automatically extended for additional periods of

2

years each, up to a maximum of

three

such extensions, unless sooner terminated in accordance with its terms.

In

June

2016,

the Company entered into a Collaboration Agreement with Givaudan to establish a collaboration for the development and commercialization of certain renewable compounds for use in the fields of active cosmetics and flavors (or the Givuadan Collaboration Agreement). Under the Givaudan Collaboration Agreement, the Company agreed to use its labor, intellectual property and technology infrastructure to develop and commercialize certain compounds for Givaudan. In exchange, Givaudan agreed to pay to the Company

$12.0

million in semi-annual installments of

$3.0

million each, beginning on

June

30,

2016.

The Company received installments of

$3.0

million on

June

30,

2016

and

December

29,

2016,

and these amounts were recognized in deferred revenue as of such dates.

Pursuant to the Givaudan Collaboration Agreement, the Company agreed to grant to Givaudan an exclusive license to the intellectual property that the Company generates under the agreement. Such license will include the rights to make, use and sell compounds in the active cosmetics and flavors fields, and is subject to certain ‘claw back’ rights by the Company if a compound is not commercialized by Givaudan during the term of the agreement. The Company also agreed to grant Givaudan non-exclusive rights to certain portions of the Company’s existing intellectual property in order to facilitate activities under the Givaudan Collaboration Agreement. Givaudan, on the other hand, agreed to grant the Company a non-exclusive license to the intellectual property that is generated under the Givaudan Collaboration Agreement. Such non-exclusive license will include the rights to make, use and sell compounds in all fields except active cosmetics and flavors.

Subject to certain rights granted to a

third

party, Givaudan will have the exclusive right to commercialize the compounds in the active cosmetics and flavors markets during the term of the agreement. Further, the Company has agreed that it will not assist any

third

party in the development or commercialization of other compounds for sale or use in the active cosmetics or flavors markets during the term of the Givaudan Collaboration Agreement. In addition, the Givaudan Collaboration Agreement contemplates that the Company will be the primary supplier of commercial quantities of the compounds to Givaudan pursuant to supply agreements to be mutually negotiated by the parties. Unless sooner terminated in accordance with its terms, the Givaudan Collaboration Agreement has an initial term of

2

years and, prior to the expiration of the initial term, the parties will meet and discuss in good faith the extension of the agreement beyond the initial term.

The Company recognized collaboration revenues of

$1.5

million under the Givaudan Collaboration Agreement for the

three

months ended

March

31,

2017.

Ginkgo Initial Strategic Partnership Agreement and Collaboration Agreement

In

June

2016,

the Company entered into an Initial Strategic Partnership Agreement (Initial Ginkgo Agreement) with Ginkgo Bioworks, Inc. (or Ginkgo), pursuant to which the Company licensed certain intellectual property to Ginkgo in exchange for a fee of

$20.0

million, to be paid by Ginkgo to the Company in

two

installments, and a

ten

percent royalty on net revenue, including without limitation net sales, royalties, fees and any other amounts received by Ginkgo related directly to such license. The

first

installment of

$15.0

million was received on

July

25,

2016.

The

second

installment, in the amount of

$5.0

million, has not been received as of

March

31,

2017.

In addition, pursuant to the Initial Ginkgo Agreement, (i) the Company and Ginkgo agreed to pursue the negotiation and execution of a detailed definitive partnership and license agreement setting forth the terms of a commercial partnership and collaboration arrangement between the parties (Ginkgo Collaboration), (ii) the Company agreed to issue to Ginkgo an option to purchase

five

million shares of the Company’s common stock at an exercise price of

$0.50,

exercisable for

one

year from the date of issuance, in connection with the execution of such definitive agreement for the Ginkgo Collaboration, (iii) the Company received a deferment of all scheduled principal repayments under the Senior Secured Loan Facility, the lender and administrative agent under which is an affiliate of Ginkgo, as well as a waiver of the Minimum Cash Covenant, through

October

31,

2016

and (iv) in connection with the execution of the definitive agreement for the Ginkgo Collaboration, the parties would effect an amendment of the LSA to (x) extend the maturity date of all outstanding loans under the Senior Secured Loan Facility, (y) waive any required amortization payments under the Senior Secured Loan Facility until maturity and (z) eliminate the Minimum Cash Covenant under the Senior Secured Loan Facility. See Note

5,

“Debt and Mezzanine Equity” for details regarding the amendments to the LSA entered into in connection with the Initial Ginkgo Agreement and Ginkgo Collaboration Agreement (as defined below).

On

August

6,

2016,

the Company issued to Ginkgo a warrant to purchase

five

million shares of the Company’s common stock at an exercise price of

$0.50

per share, exercisable for

one

year from the date of issuance. The warrant was issued prior to the execution of the definitive agreement for the Ginkgo Collaboration in connection with the transfer of certain information technology from Ginkgo to the Company.

On

September

30,

2016,

the Company and Ginkgo entered into a Collaboration Agreement (Ginkgo Collaboration Agreement) setting forth the terms of the Ginkgo Collaboration, under which the parties will collaborate to develop, manufacture and sell commercial products and will share in the value created thereby. The Ginkgo Collaboration Agreement provides that, subject to certain exceptions, all

third

party contracts for the development of chemical small molecule compounds whose manufacture is enabled by the use of microbial strains and fermentation technologies that are entered into by the Company or Ginkgo during the term of the Ginkgo Collaboration Agreement will be subject to the Ginkgo Collaboration and the approval of the other party (not to be unreasonably withheld). Responsibility for the engineering and small-scale process development of the newly developed products will be allocated between the parties on a project-by-project basis, and the Company will be principally responsible for the commercial scale-up and production of such products, with each party generally bearing their own respective costs and expenses relating to the Ginkgo Collaboration, including capital expenditures. Notwithstanding the foregoing, subject to the Company sourcing funding and breaking ground on a new production facility by

March

30,

2017,

Ginkgo will pay the Company a fee of

$5.0

million on or before

March

31,

2017.

The

$5.0

million fee has not been received as of

March

31,

2017.

Under the Ginkgo Collaboration Agreement, subject to certain exceptions, including excluded or refused products and cost savings initiatives, the profit on the sale of products subject to the Ginkgo Collaboration Agreement as well as cost-sharing, milestone and “value-creation” payments associated with the development and production of such products will be shared equally between the parties. The parties also agreed to provide each other with a license and other rights to certain intellectual property necessary to support the development and manufacture of the products under the Ginkgo Collaboration, and also to provide each other with access to certain other intellectual property useful in connection with the activities to be undertaken under the Ginkgo Collaboration Agreement, subject to certain carve-outs.

The initial term of the Ginkgo Collaboration Agreement is

three

years, and will automatically renew for successive

one

-year terms unless either party provides written notice of termination not less than

90

days prior to the expiration of the then-current term. In addition, the Ginkgo Collaboration Agreement provides that the parties will evaluate the performance of the Ginkgo Collaboration as of the

18

-month anniversary of the Ginkgo Collaboration Agreement, and if either party has been repeatedly unable to perform or meet its commitments under the Ginkgo Collaboration Agreement, the other party will have the right to terminate the Ginkgo Collaboration Agreement on

30

days written notice.

The Company recognized

zero

of collaboration revenue under the Initial Ginkgo Agreement and the Ginkgo Collaboration Agreement for the

three

months ended

March

31,

2017.

As of

March

31,

2017,

$3.0

million is payable by the Company to Ginkgo under the Ginkgo Collaboration Agreement for its share of collaboration payments and license .fees

(December

31,

2016,

$1.6

million).

Intellectual Property License and Strain Access Agreement with Blue California

In

December

2016,

the Company entered into an Intellectual Property License and Strain Access Agreement with Phyto Tech Corp. (d/b/a Blue California), a food ingredients and nutraceuticals company. Pursuant to the agreement, the Company granted Blue California a royalty-free, non-exclusive, worldwide, license to access and use certain Company intellectual property for the purpose of research and development, scale-up, manufacturing and commercialization activities. In exchange for such license, Blue California agreed to pay the Company a fee of

$10

million in cash. On

March

31,

2017,

the Company entered into a subsequent agreement with Blue California whereby, among other things, Blue California’s affiliates will provide the Company with access to their fermentation manufacturing capacity in China and the Company will transfer additional intellectual property to Blue California for use in collaboration activities between the parties. See Note

18

“Subsequent Events” for further details.

Financing Agreements

At Market Issuance Sales Agreement

On

March

8,

2016,

the Company entered into an At Market Issuance Sales Agreement (ATM Sales Agreement) with FBR Capital Markets & Co. and MLV & Co. LLC (Agents) under which the Company

may

issue and sell shares of its common stock having an aggregate offering price of up to

$50.0

million (ATM Shares) from time to time through the Agents, acting as its sales agents, under the Company’s Registration Statement on Form S-

3

(File No.

333

-

203216),

effective

April

15,

2015.

Sales of the ATM Shares through the Agents, if any, will be made by any method that is deemed an “at the market offering” as defined in Rule

415

under the Securities Act, including by means of ordinary brokers’ transactions at market prices, in block transactions, or as otherwise agreed by the Company and the Agents. Each time that the Company wishes to issue and sell ATM Shares under the ATM Sales Agreement, the Company will notify

one

of the Agents of the number of ATM Shares to be issued, the dates on which such sales are anticipated to be made, any minimum price below which sales

may

not be made and other sales parameters as the Company deems appropriate. The Company will pay the designated Agent a commission rate of up to

3.0%

of the gross proceeds from the sale of any ATM Shares sold through such Agent as agent under the ATM Sales Agreement. The ATM Sales Agreement contains customary terms, provisions, representations and warranties. The ATM Sales Agreement includes no commitment by other parties to purchase shares the Company offers for sale.

During the

three

months ended

March

31,

2017,

the Company did not sell any shares of common stock under the ATM Sales Agreement. As of the date hereof,

$50.0

million remained available for future sales under the ATM Sales Agreement.

LSA Amendment

See Note

5,

“Debt and Mezzanine Equity” for details regarding the Fifth LSA Amendment.

Fidelity Notes Exchange

See Note

5,

“Debt and Mezzanine Equity” for details regarding the Fidelity Exchange.

Amendment to

March

2016

R&D Note

See Note

5,

“Debt and Mezzanine Equity” for details regarding the

March

2016

R&D Note Amendment.

XML

Note 9 - Goodwill and Intangible Assets

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Goodwill and Intangible Assets Disclosure [Text Block]

9.

Goodwill and Intangible Assets

The following table presents the components of the Company's intangible assets (in thousands):

		March 31, 2017							December 31, 2016
	Useful Life in Years	Gross Carrying Amount		Accumulated Amortization/ Impairment			Net Carrying Value		Gross Carrying Amount		Accumulated Amortization/ Impairment			Net Carrying Value
In-process research and development	Indefinite	$	8,560	$	(8,560	)	$	—	$	8,560	$	(8,560	)	$	—
Acquired licenses and permits	2		772		(772	)		—		772		(772	)		—
Goodwill	Indefinite		560		—			560		560		—			560
		$	9,892	$	(9,332	)	$	560	$	9,892	$	(9,332	)	$	560

The in-process research and development (IPR&D) of

$8.6

million was acquired through the acquisition of Draths in

October

2011

and was treated as indefinite lived intangible assets pending completion or abandonment of the projects to which the IPR&D related. The IPR&D was fully impaired in

2015.

The Company has a single reportable segment (see Note

15,

“Reporting Segments” for further details). Consequently, all of the Company's goodwill is attributable to that single reportable segment.

XML

Note 10 - Stockholders' Deficit

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Stockholders' Equity Note Disclosure [Text Block]

10.

Stockholders’ Deficit

Unexercised Common Stock Warrants

As of

March

 

31,

2017

and

2016,

the Company had

14,663,411

and

7,328,069,

respectively, of unexercised common stock warrants with exercise prices ranging from

$0.01

to

$10.67

per warrant and a weighted average remaining maturity of

5.1

years.

XML

Note 11 - Stock-based Compensation

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Disclosure of Compensation Related Costs, Share-based Payments [Text Block]

11.

Stock-Based Compensation

The Company’s stock option activity and related information for the

three

months ended

March

 

31,

2017

was as follows:

	Number Outstanding			Weighted- Average Exercise Price		Weighted- Average Remaining Contractual Life (Years)		Aggregate Intrinsic Value
								(in thousands)
Outstanding - December 31, 2016		13,487,685		$	3.63		6.70	$	443
Options granted		726,000		$	0.58		—		—
Options exercised		(500	)	$	0.28		—		—
Options cancelled		(695,912	)	$	1.82		—		—
Outstanding - March 31, 2017		13,517,273		$	3.55		6.83	$	44
Vested and expected to vest after March 31, 2017		12,347,493		$	3.79		6.63	$	38
Exercisable at March 31, 2017		7,478,686		$	5.42		5.28	$	1

The aggregate intrinsic value of options exercised under all option plans was

zero

for each of the

three

months ended

March

 

31,

2017

and

2016,

determined as of the date of option exercise.

The Company’s restricted stock units (or "RSUs") and restricted stock activity and related information for the

three

months ended

March

 

31,

2017

was as follows:

	RSUs			Weighted- Average Grant- Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2016		6,997,084		$	1.18		1.44
Awarded		825,980		$	0.59		—
Vested		(348,699	)	$	1.28		—
Forfeited		(250,329	)	$	1.03		—
Outstanding - March 31, 2017		7,224,036		$	1.11		1.39
Expected to vest after March 31, 2017		5,735,089		$	1.15		1.17

The following table summarizes information about stock options outstanding as of

March

 

31,

2017:

			Options Outstanding						Options Exercisable
Exercise Price			Number of Options		Weighted- Average Remaining Contractual Life (Years)		Weighted-Average Exercise Price		Number of Options		Weighted-Average Exercise Price
$0.28	—	$0.58		795,734		9.48	$	0.49		2,234	$	0.28
$0.59	—	$0.59		2,224,375		9.13	$	0.59		—	$	—
$0.69	—	$1.63		1,491,082		8.67	$	1.30		361,067	$	1.60
$1.64	—	$1.96		2,192,975		7.51	$	1.84		1,026,492	$	1.83
$1.98	—	$2.87		1,780,408		6.07	$	2.69		1,579,154	$	2.73
$2.96	—	$3.44		688,795		6.40	$	3.15		597,154	$	3.13
$3.51	—	$3.51		1,447,979		6.90	$	3.51		1,057,049	$	3.51
$3.55	—	$4.31		1,723,976		3.31	$	3.97		1,683,443	$	3.98
$4.35	—	$26.84		1,111,949		3.52	$	17.71		1,111,949	$	17.71
$30.17	—	$30.17		60,000		3.96	$	30.17		60,000	$	30.17
$0.28	—	$30.17		13,517,273		6.83	$	3.55		7,478,686	$	5.42

Stock-Based Compensation Expense

Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands):

	Three Months Ended March 31,
	2017		2016
Research and development	$	484	$	491
Sales, general and administrative		1,162		1,560
Total stock-based compensation expense	$	1,646	$	2,051

As of

March

 

31,

2017,

there was unrecognized compensation expense of

$3.7

million and

$4.7

million related to stock options and RSUs, respectively, the Company expects to recognize this expense over a weighted average period of

2.71

years and

2.58

years, respectively.

Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on their fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions:

	Three Months Ended March 31,
	2017			2016
Expected dividend yield		—	%		—	%
Risk-free interest rate		2.1	%		1.4	%
Expected term (in years)		6.15			6.23
Expected volatility		80	%		73	%

Expected Dividend Yield

—The Company has never paid dividends and does not expect to pay dividends.

Risk-Free Interest Rate

—The risk-free interest rate was based on the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.

Expected Term

—Expected term represents the period that the Company’s stock-based awards are expected to be outstanding. The Company’s assumptions about the expected term have been based on that of companies that have similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.

Expected Volatility

—The expected volatility is based on a combination of historical volatility for the Company's stock and the historical stock volatilities of several of the Company’s publicly listed comparable companies over a period equal to the expected terms of the options, as the Company does not have a long trading history.

Forfeiture Rate

—The Company estimates its forfeiture rate based on an analysis of its actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior, and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual number of future forfeitures differs from that estimated by the Company, the Company

may

be required to record adjustments to stock-based compensation expense in future periods.

Each of the inputs discussed above is subjective and generally requires significant management and director judgment.

XML

Note 12 - Employee Benefit Plan

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Pension and Other Postretirement Benefits Disclosure [Text Block]

12.

Employee Benefit Plan

The Company established a

401(k)

Plan to provide tax deferred salary deductions for all eligible employees. Participants

may

make voluntary contributions to the

401(k)

Plan up to

90%

of their eligible compensation, limited by certain Internal Revenue Service (or the "IRS") restrictions. Effective

January

2014,

the Company implemented a discretionary employer match plan whereby the Company will match employee contributions up to the IRS limit or

90%

of compensation, with a minimum

one

year of service required for vesting. The total matching amount for each of the

three

months ended

March

 

31,

2017

and

2016

was

$0.1

million.

XML

Note 13 - Related Party Transactions

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Related Party Transactions Disclosure [Text Block]

13.

Related Party Transactions

Related Party Financings

See Note

5,

“Debt and Mezzanine Equity” for a description of the

February

2016

Private Placement transaction with Foris Ventures, LLC (or Foris), Naxyris S.A. and Biolding Investment SA, each a related party of the Company, the

March

2016

R&D Note transaction with Total and the

June

2016

and

October

2016

Private Placement transactions with Foris. In addition, see Note

18,

“Subsequent Events” for related party financings and related transactions subsequent to

March

31,

2017.

As of

March

 

31,

2017

and

December

 

31,

2016,

convertible notes and loan with related parties were outstanding in an aggregate amount of

$73.9

million and

$72.4

million, respectively, net of debt and issuance costs of

$6.0

million and

$6.7

million, respectively.

The fair value of the derivative liability related to the related party convertible notes as of

March

 

31,

2017

and

December

 

31,

2016

was

$1.4

million and

$0.8

million, respectively. The Company recognized a gain from change in fair value of the derivative instruments of

$1.1

million and

$4.5

million for the

three

months ended

March

 

31,

2017

and

2016,

respectively, (see Note

3,

"Fair Value of Financial Instruments" for further details).

Related Party Revenues

The Company recognized no related party revenues from product sales to Total for each of the

three

months ended

March

31,

2017

and

2016.

Related party accounts receivable from Total as of

March

31,

2017

and

December

31,

2016,

were

$0.3

million and

$0.8

million, respectively. In addition, in

October

2016

the Company entered into an assistance agreement with the United States Department of Energy, in which Total and Renmatix participate as subcontractors. There was no amount accrued by or due to Total or Renmatix for the

three

months ended

March

31,

2017

and for the year ended

December

31,

2016.

Loans to Related Parties

See Note

7,

"Joint Ventures and Noncontrolling Interest" for details of the Company's transactions with its affiliate, Novvi LLC.

Joint Venture with Total

In

November

2013,

the Company and Total formed TAB as discussed above under Note

7,

"Joint Ventures and Noncontrolling Interest."

Pilot Plant Agreements

In

May

2014,

the Company received the final consents necessary for the Pilot Plant Services Agreement (Pilot Plant Services Agreement) and a Sublease Agreement (Sublease Agreement), each dated as of

April

4,

2014

(collectively the Pilot Plant Agreements), between the Company and Total. The Pilot Plant Agreements generally have a term of

five

years. Under the terms of the Pilot Plant Services Agreement, the Company agreed to provide certain fermentation and downstream separations scale-up services and training to Total and receives an aggregate annual fee payable by Total for all services in the amount of up to approximately

$0.9

million per annum. In

July

2015,

Total and the Company entered into Amendment

#1

(Pilot Plant Agreement Amendment) to the Pilot Plant Services Agreement whereby the Company agreed to waive a portion of these fees, up to approximately

$2.0

million, over the term of the Pilot Plant Services Agreement in connection with the restructuring of TAB discussed above. Prior to

February

28,

2017,

Total charged its

secondees

to the Company for research and development services pursuant to an Amended and Restated Secondment Agreement, dated

August

1,

2012,

between the Company and Total. On

February

28,

2017,

the Company and Total entered into an amendment to the Amended and Restated Secondment Agreement, which provided that Total would not charge Amyris for the cost of Total’s

secondees

on or after

May

1,

2016,

other than overhead charges. Total charges its

secondees

to the Company for research and development services. The payable to Total under these arrangements was

$1.7

million and

$2.2

million as of

March

31,

2017

and

December

31,

2016,

respectively.

As of

March

31,

2017,

the Company had received

$1.7

million in cash under the Pilot Plant Agreements from Total. In connection with these arrangements, sublease payments and service fees of

$0.0

million and

$0.2

million was offset against cost and operating expenses for the

three

months ended

March

31,

2017

and

2016,

respectively.

XML

Note 14 - Income Taxes

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Income Tax Disclosure [Text Block]

14.

Income Taxes

The Company recorded a benefit from income taxes of

$0.04

million for the

three

months ended

March

31,

2017

and a provision for income taxes of

$0.1

million for the

three

months ended

March

31,

2016.

The provision for income taxes for the

three

months ended

March

31,

2017

and

2016

consisted of an accrual of Brazilian withholding tax on intercompany interest on intercompany loans. Other than the above mentioned income tax amounts, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations.

On

December

15,

2011,

the IRS completed its audit of the Company for tax year

2008

which concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year

2008,

the US federal tax carryforwards (net operating losses and tax credits)

may

be adjusted by the IRS in the year in which the carryforward is utilized.

XML

Note 15 - Reporting Segments

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Segment Reporting Disclosure [Text Block]

15.

Reportable Segments

The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has

one

business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure.

Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands):

Revenues

	Three Months Ended March 31,
	2017		2016
Europe	$	5,376	$	4,372
United States		3,096		3,462
Asia		4,433		590
Brazil		19		375
Other		56		12
Total	$	12,980	$	8,811

Long-Lived Assets (Property, Plant and Equipment)

	March 31, 2017		December 31, 2016
Brazil	$	39,137	$	44,153
United States		13,683		9,342
Europe		225		240
Total	$	53,045	$	53,735

XML

Note 16 - Comprehensive Loss

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Comprehensive Income (Loss) Note [Text Block]

16.

Comprehensive Loss

Comprehensive loss represents all changes in stockholders’ deficit except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive loss excluded from the Company’s net loss and have been disclosed in the condensed consolidated statements of comprehensive loss for the periods presented.

The components of accumulated other comprehensive loss are as follows (in thousands):

	March 31, 2017			December 31, 2016
Foreign currency translation adjustment, net of tax	$	(40,581	)	$	(40,904	)
Total accumulated other comprehensive loss	$	(40,581	)	$	(40,904	)

XML

Note 17 - Net Loss Attributable to Common Stockholders and Net Loss Per Share

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Earnings Per Share [Text Block]

17.

Net Loss Attributable to Common Stockholders and Net Loss per Share

The Company computes net loss per share in accordance with ASC

260,

“Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants and convertible promissory notes using the treasury stock method or the as converted method, as applicable. For the

three

months ended

March

31,

2017,

basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss was the same for that period.

The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts):

	Three Months Ended March 31,
	2017			2016
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(37,371	)	$	(15,308	)
Interest on convertible debt		—			1,817
Accretion of debt discount		—			1,633
Gain from change in fair value of derivative instruments		—			(18,415	)
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$	(37,371	)	$	(30,273	)
Denominator:
Weighted average shares of common stock outstanding for basic EPS		290,039,216			207,199,563
Basic and diluted loss per share	$	(0.13	)	$	(0.07	)
Weighted average shares of common stock outstanding		290,039,216			207,199,563
Effect of dilutive securities:
Convertible promissory notes		—			53,732,522
Weighted common stock equivalents		—			53,732,522
Diluted weighted-average common shares		290,039,216			260,932,085
Diluted loss per share	$	(0.13	)	$	(0.12	)

The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock because including them would have been anti-dilutive:

	Three Months Ended March 31,
	2017		2016
Period-end stock options to purchase common stock		13,517,273		12,159,154
Convertible promissory notes (1)		72,826,108		99,648,739
Period-end common stock warrants		5,021,087		5,885,762
Period-end restricted stock units		7,224,036		5,175,430
Total		98,588,504		122,869,085

______________

(1) The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

XML

Note 18 - Subsequent Events

3 Months Ended

Mar. 31, 2017

Notes to Financial Statements

Subsequent Events [Text Block]

18.

Subsequent Events

Ginkgo Collaboration Note

On

April

13,

2017,

the Company issued a secured promissory note to Ginkgo, in the principal amount of

$3

million dollars (or the Ginkgo Collaboration Note), in satisfaction of certain payments owed by the Company to Ginkgo under the Ginkgo Collaboration Agreement (see Note

8,

“Significant Agreements” above for details regarding the Ginkgo Collaboration Agreement). The Ginkgo Collaboration Note is collateralized by a

second

priority lien on the assets securing the Company’s obligations under the Senior Secured Loan Facility, and is subordinate to the Company’s obligations under the Senior Secured Loan Facility pursuant to a Subordination Agreement, dated as of

October

27,

2016

and ratified on

April

13,

2017,

by and among the Company, Ginkgo and Stegodon. Interest will accrue on the Ginkgo Collaboration Note from and including

April

13,

2017

at a rate of

13.50%

per annum and is payable in full on

May

15,

2017,

the maturity date of the Ginkgo Collaboration Note, unless the Ginkgo Collaboration Note is prepaid in accordance with their terms prior to such date. The Ginkgo Collaboration Note contains customary terms, provisions, representations and warranties, including certain events of default after which the Ginkgo Collaboration Note

may

be due and payable immediately, as set forth in the Ginkgo Collaboration Note.

April

2017

Convertible Note Offering

On

April

13,

2017,

the Company entered into a securities purchase agreement (or the

April

2017

Purchase Agreement) between the Company and a private investor (or the Purchaser) relating to the sale of up to

$15.0

million aggregate principal amount of convertible notes (or the

April

2017

Convertible Notes) that are convertible into shares of the Company’s common stock at an initial conversion price of

$1.90

per share. The

April

2017

Purchase Agreement includes customary representations, warranties and covenants by the Company. The

April

2017

Purchase Agreement also provides the Purchaser with a right of

first

refusal with respect to any variable rate transaction, subject to certain exceptions, on the same terms and conditions as are offered to a

third

-party purchaser for as long as the Purchaser holds any

April

2017

Convertible Notes or shares of common stock underlying the

April

2017

Convertible Notes.

The

April

2017

Convertible Notes will be issued and sold in

two

separate closings. The initial closing occurred on

April

17,

2017.

At the initial closing, the Company issued and sold an

April

2017

Convertible Note in a principal amount of

$7.0

million to the Purchaser. If the Purchaser so elects at its option and in its sole discretion, the

second

closing will occur on or prior to

December

31,

2017,

subject to the satisfaction of certain closing conditions, including certain equity conditions. At the

second

closing, the Company will issue and sell an

April

2017

Convertible Note in a principal amount of

$8.0

million to the Purchaser. 

The

April

2017

Convertible Notes are general unsecured obligations of the Company. Unless earlier converted or redeemed, the

April

2017

Convertible Notes will mature on or about the

18

-month anniversary of their respective issuance, subject to the rights of the holders to extend the maturity date in certain circumstances.

The

April

2017

Convertible Notes are payable in monthly installments, in either cash at

118%

of such installment amount or, at the Company’s option, subject to the satisfaction of certain equity conditions, shares of common stock at a discount to the then-current market price, subject to a price floor. In addition, in the event that the Company elects to pay all or any portion of a monthly installment in common stock, the holders of the

April

2017

Convertible Notes shall have the right to require that the Company repay in common stock an additional amount of the

April

2017

Convertible Notes not to exceed

50%

of the cumulative sum of the aggregate amounts by which the dollar-weighted trading volume of the common stock for all trading days during the applicable installment period exceeds

$200,000.

The

April

2017

Convertible Notes contain customary terms and covenants, including certain events of default after which the holders

may

require the Company to redeem all or any portion of their

April

2017

Convertible Notes in cash at a price equal to the greater of (i) 

118%

of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

In the event of a Fundamental Transaction (as defined in the

April

2017

Convertible Notes), holders of the

April

2017

Convertible Notes

may

require the Company to redeem all or any portion of their

April

2017

Convertible Notes at a price equal to the greater of (i) 

118%

of the amount being redeemed and (ii) the intrinsic value of the shares of common stock issuable upon an installment payment of the amount being redeemed in shares.

The Company has the right to redeem the

April

2017

Convertible Notes for cash, in whole, at any time, or in part, from time to time, at a redemption price equal to

118%

of the principal amount of the

April

2017

Convertible Notes to be redeemed.

The

April

2017

Convertible Notes will be convertible from time to time, at the election of the holders, into shares of common stock at an initial conversion price of 

$1.90

 per share. The conversion price will be subject to adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

Notwithstanding the foregoing, the holders will not have the right to convert any portion of an

April

2017

Convertible Note, and the Company will not have the option to pay any amount in shares of common stock, if (a) the holder, together with its affiliates, would beneficially own in excess of

4.99%

(or such other percentage as determined by the holder and notified to the Company in writing, not to exceed

9.99%,

provided that any increase of such percentage will not be effective until

61

days after notice thereof) of the number of shares of common stock outstanding immediately after giving effect to such conversion or payment, as applicable, or (b) the aggregate number of shares issued with respect to the

April

2017

Convertible Notes (and any other transaction aggregated for such purpose) after giving effect to such conversion or payment, as applicable, would exceed

54,676,770

shares of common stock (or the Exchange Cap). In the event that the Company is prohibited from issuing any shares of common stock under the

April

2017

Convertible Notes as a result of the Exchange Cap, the Company will pay cash in lieu of any shares that would otherwise be deliverable in excess of the Exchange Cap. In addition, pursuant to the

April

2017

Purchase Agreement, in the event that the aggregate number of shares of common stock issuable with respect to the

April

2017

Convertible Notes (and any other transaction aggregated for such purpose) would equal or exceed

49,233,710

of shares of common stock, the Company will be required to take all actions necessary for, and use its reasonable best efforts to solicit and obtain, stockholder approval for the issuance of shares of common stock in excess of the Exchange Cap.

For as long as they hold

April

2017

Convertible Notes or shares of common stock issued under the

April

2017

Convertible Notes, the holders

may

not sell any shares of common stock at a price less than

$1.05

per share; provided, that with respect to any shares of Common Stock issued under the

April

2017

Convertible Notes at a price less than

$1.00,

the holders

may

sell such shares at a price not less than the price floor applicable to the installment period with respect to which such shares were issued.

Amendment to Convertible Notes

On

May

2,

2017,

in connection with the Purchaser agreeing to extend the time period for certain obligations of the Company under the

April

2017

Purchase Agreement, the Company and the Purchaser entered into an Amendment Agreement (or the Amendment Agreement) with respect to the

December

2016

Purchase Agreement, the

April

2017

Purchase Agreement, the

December

2016

Convertible Note and the

April

2017

Convertible Notes (or the Amended Notes). Pursuant to the Amendment Agreement, the Company and the Purchaser agreed, among other things, to amend the

December

2016

Convertible Note and the

April

2017

Convertible Notes to (i) reduce the price at which the Company

may

pay monthly installments under the Amended Notes in shares of common stock from a

10%

discount to a market-based price to a

20%

discount to a market-based price and (ii) reduce the price floor related to any such payment from

80%

of, in the case of the

December

2016

Convertible Note, the volume-weighted average price per share (VWAP) of the Company’s common stock on the trading day immediately preceding the applicable installment date and, in the case of the

April

2017

Convertible Notes, the arithmetic average of the VWAP of the Company’s common stock for the

five

trading days immediately preceding the applicable installment date, to

70%

of such amount. The closing of the Amendment Agreement and the issuance of the Amended Notes is subject to customary closing conditions.

Blue California

In

April

2017,

the Company announced that it had amended the terms of its

December

2016

Intellectual Property License and Strain Access Agreement with Blue California to take a minority equity stake in SweeGen, Inc. (or SweeGen),

one

of Blue California’s affiliates focused on the sweetener market, in lieu of a

$10

million cash payment for intellectual property transferred to Blue California in

December

2016.

On

April

21,

2017,

Amyris received

850,115

shares of SweeGen common stock in satisfaction of Blue California’s payment obligation under the Intellectual Property License and Strain Access Agreement.

May

2017

Financing Transactions

On

May

8,

2017,

the Company entered into a Securities Purchase Agreement (or the

May

2017

Purchase Agreement) with certain investors for the issuance and sale of

22,140

shares of the Company’s Series A

17.38%

Convertible Preferred Stock, par value

$0.0001

per share (or the Series A Preferred Stock),

65,203.8756

shares of the Company’s Series B

17.38%

Convertible Preferred Stock, par value

$0.0001

per share (or the Series A Preferred Stock and, together with the Series A Preferred Stock, the Preferred Stock), which Preferred Stock is convertible into the Company’s common stock, par value

$0.0001

per share as described below, and Cash Warrants (as defined below) to purchase an aggregate of

207,954,414

shares of Common Stock and Dilution Warrants (as defined below) (or, collectively, the

May

2017

Warrants, and the shares of common stock issuable upon exercise of the Warrants, the

May

2017

Warrant Shares) (or the

May

2017

Offering).

On

May

11,

2017,

the Company and the investors closed the issuance and sale of the Series A Preferred Stock, Series B Preferred Stock and

May

2017

Warrants (or the

May

2017

Offering Closing). The net proceeds to the Company from the

May

2017

Offering were approximately

$44.5

million after payment of the estimated offering expenses and placement agent fees. The Series A Preferred Stock and

May

2017

Warrants relating thereto were sold to the purchasers thereof in exchange for aggregate cash consideration of

$22,140,000,

and the Series B Preferred Stock and

May

2017

Warrants relating thereto were sold to the purchasers thereof in exchange for (i) aggregate cash consideration of

$25,000,000

and (ii) the cancellation of approximately

$40.2

million of outstanding indebtedness (including accrued interest thereon) owed by the Company to such purchasers, as further described below.

The

May

2017

Purchase Agreement includes customary representations, warranties and covenants of the parties. In addition, pursuant to the

May

2017

Purchase Agreement, the Company, subject to certain exceptions, including the issuance of the Second Tranche Securities (as defined below), (i)

may

not issue, enter into any agreement to issue or announce the issuance or proposed issuance of any shares of Common Stock or securities convertible into or exercisable or exchangeable for Common Stock until

July

31,

2017

and (ii)

may

not enter into an agreement to effect any issuance by the Company involving a variable rate transaction until

one

year from the

May

2017

Offering Closing (as defined below).

Series A Preferred Stock

Each share of Series A Preferred Stock has a stated value of

$1,000

and is convertible at any time, at the option of the holder, into Common Stock at an initial conversion price of

$1.15

per share (or the Preferred Stock Conversion Rate). The Preferred Stock Conversion Rate is subject to adjustment in the event of any dividends or distributions of common stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction. If not previously converted at the option of the holder, each share of Series A Preferred Stock will be automatically converted, without any further action by the holder, on the

90th

day following the date that the Stockholder Approval (as defined below) has been obtained and effected.

Dividends, at a rate per year equal to

17.38%

of the stated value of the Series A Preferred Stock, will be payable semi-annually from the issuance of the Series A Preferred Stock until the

tenth

anniversary of the date of issuance, on each

October

15

and

April

15,

beginning

October

15,

2017,

on a cumulative basis, at the Company’s option, in cash, out of any funds legally available for the payment of dividends, or, subject to the satisfaction of certain conditions, in Common Stock at the Preferred Stock Conversion Rate, or a combination thereof. In addition, upon the conversion of the Series A Preferred Stock prior to the

tenth

anniversary of the date of issuance, the holders of the Series Preferred A Stock shall be entitled to a payment equal to

$1,738

per

$1,000

of stated value of the Series A Preferred Stock, less the amount of all prior semi-annual dividends paid on such converted Series A Preferred Stock prior to the relevant conversion date (the Preferred Stock Make-Whole Payment), at the Company’s option, in cash, out of any funds legally available for the payment of dividends, or, subject to the satisfaction of certain conditions, in Common Stock at the Preferred Stock Conversion Rate, or a combination thereof. If the Company elects to pay any dividend in the form of cash, it shall provide each holder with notice of such election not later than the

first

day of the month of prior to the applicable dividend payment date.

Unless and until converted into common stock in accordance with its terms, the Series A Preferred Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the Series A Preferred Stock.

In the event of a fundamental transaction, the holders of the Series A Preferred Stock will have the right to receive the consideration receivable as a result of such fundamental transaction by a holder of the number of shares of Common Stock for which the Series A Preferred Stock is convertible immediately prior to such fundamental transaction (without regard to whether such Series A Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of Common Stock.

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series A Preferred Stock shall be entitled to receive out of the assets of the Company the same amount that a holder of Common Stock would receive if the Series A Preferred Stock were fully converted to Common Stock immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series A Preferred Stock is convertible at such time) , which amount shall be paid pari passu with all holders of Common Stock.

Notwithstanding the foregoing, the holders (other than the Designated Holder (as defined below)) will not have the right to convert any Series A Preferred Stock, and the Company shall not effect any conversion of the Series A Preferred Stock, if the holder, together with its affiliates, would beneficially own in excess of

4.99%

(or such other percentage as determined by the holder and notified to the Company in writing, not to exceed

9.99%,

provided that any increase of such percentage will not be effective until

61

days after notice thereof) of the number of shares of common stock outstanding immediately after giving effect to the issuance of shares of common stock issuable upon conversion of such Series A Preferred Stock.

On

May

8,

2017,

the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series A

17.38%

Convertible Preferred Stock with the Secretary of State of Delaware.

Series B Preferred Stock

The Series B Preferred Stock will have substantially identical terms to the Series A Preferred Stock (as described above), except that the issuance of the shares of common stock issuable upon conversion of the Series B Preferred Stock or as payment of dividends or the Make-Whole Payment on the Series B Preferred Stock (or the Series B Conversion Shares) will be subject to the Stockholder Approval (as defined below).

The investors that purchased shares of the Series B Preferred Stock included existing stockholders of the Company affiliated with certain members of our Board of Directors (or the Affiliated Investors): Foris Ventures, LLC (Foris, an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder), which purchased

30,728.589

shares of Series B Preferred Stock and

May

2017

Warrants to purchase

73,160,764

shares of Common Stock; and Naxyris S.A. (or Naxyris, an investment vehicle owned by Naxos Capital Partners SCA Sicar; director Carole Piwnica is Director of NAXOS UK, which is affiliated with Naxos Capital Partners SCA Sicar), which purchased

2,333.216

shares of Series B Preferred Stock and

May

2017

Warrants to purchase

5,556,038

shares of common stock. The Affiliated Investors purchased their respective shares of Series B Preferred Stock and Warrants in exchange for the cancellation of existing indebtedness of the Company held by such Affiliated Investors: Foris agreed to exchange an aggregate principal amount of

$27.0

million of indebtedness, plus accrued interest thereon, issued to Foris by the Company on

February

12,

2016,

June

24,

2016

and

October

21,

2016,

as described above in Note

5,

“Debt and Mezzanine Equity”; and Naxyris exchanged an aggregate principal amount of

$2.0

million of indebtedness, plus accrued interest thereon, issued to Naxyris by the Company on

February

12,

2016,

as described above in Note

5,

“Debt and Mezzanine Equity”.

In addition, the investors that purchased shares of the Series B Preferred Stock included holders of certain of the Company’s existing indebtedness, including the

2014

144A

Notes and the

2015

144A

Notes (see Note

5,

“Debt and Mezzanine Equity” for details regarding the terms of the

2014

144A

Notes and the

2015

144A

Notes), which investors exchanged all or a portion of their holding of such indebtedness, including accrued interest thereon, representing an aggregate of

$3.4

million of

2014

144A

Notes and approximately

$3.7

million of

2015

144A

Notes, for Series B Preferred Stock and

May

2017

Warrants in the

May

2017

Offering. Upon the

May

2017

Offering Closing, such indebtedness was cancelled and the agreements relating thereto, including any note purchase agreements or unsecured or secured promissory notes (including any security interest relating thereto), were terminated, except to the extent such investors or other investors retain a portion of such indebtedness.

The Series B Preferred Stock was issued in a private placement pursuant to the exemption from registration under Section

4(a)(2)

of the Securities Act and Regulation D promulgated under the Securities Act.

On

May

8,

2017,

the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series B

17.38%

Convertible Preferred Stock with the Secretary of State of Delaware.

May

2017

Warrants

Pursuant to the

May

2017

Purchase Agreement, at the

May

2017

Offering Closing the Company issued to each investor (i) a warrant, with an exercise price of

$0.52

per share, to purchase a number of shares of Common Stock equal to

50%

of the shares of common stock into which such investor’s shares of Preferred Stock were initially convertible (including shares of Common Stock issuable as payment of the Make-Whole Payment, assuming that the Make-Whole Payment is made in Common Stock), representing warrants to purchase

103,977,207

shares of common stock in the aggregate for all investors and (ii) a warrant, with an exercise price of

$0.62

per share, to purchase a number of shares of Common Stock equal to

50%

of the shares of common stock into which such investor’s shares of Preferred Stock were initially convertible (including shares of Common Stock issuable as payment of the Make-Whole Payment, assuming that the Make-Whole Payment is made in Common Stock), representing warrants to purchase

103,977,207

shares of common stock in the aggregate for all investors (or, collectively, the Cash Warrants). The exercise price of the Cash Warrants is subject to standard adjustments as well as full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the

three

-year period following the

May

2017

Offering Closing at a per share price (including any conversion or exercise price, if applicable) less than the then-current exercise price of the Cash Warrants, subject to certain exceptions.

In addition, at the

May

2017

Offering Closing, the Company issued to each investor a warrant, with an exercise price of

$0.0001

per share (or, collectively, the Dilution Warrants), to purchase a number of shares of common stock sufficient to provide the investor with full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the

three

-year period following the

May

2017

Offering Closing at a per share price (including any conversion or exercise price, if applicable) less than

$0.42

per share, the effective per share price paid by the investors for the shares of common stock issuable upon conversion of the Preferred Stock purchased by the investors in the

May

2017

Offering (including shares of common stock issuable as payment of dividends or the Make-Whole Payment, assuming that all such dividends and the Make-Whole Payment are made in common stock), subject to certain exceptions.

The exercise of the

May

2017

Warrants will be subject to the Stockholder Approval (as defined below). The

May

2017

Warrants each have a term of

five

years from the date the Warrants are initially exercisable following the Stockholder Approval.

The

May

2017

Warrants were issued in a private placement pursuant to the exemption from registration under Section

4

(a)(2)

of the Securities Act and Regulation D promulgated under the Securities Act.

Stockholder Approval

Pursuant to the

May

2017

Purchase Agreement, the Company has agreed to solicit from the Company’s stockholders (i) any approval for the transactions contemplated by the

May

2017

Purchase Agreement required by the rules and regulations of the NASDAQ Stock Market, including without limitation the issuance of shares of common stock upon conversion of the Series B Preferred Stock and upon exercise of the

May

2017

Warrants (or the NASDAQ Approval) and (ii) approval to effect a reverse stock split of the common stock (together with the NASDAQ Approval, collectively, the Stockholder Approval) at an annual or special meeting of stockholders to be held on or prior to

July

10,

2017,

and to use commercially reasonable efforts to secure the Stockholder Approval. As described in more detail below, the parties subject to the Voting Agreements (as defined below) have agreed to vote in favor of the Stockholder Approval. The Company has presented a

15

-for-

1

reverse stock split to its stockholders for approval at its

2017

Annual Meeting of Stockholders to be held on

May

23,

2017

(or the Annual Meeting), and intends to solicit the NASDAQ Approval at a special meeting of stockholders to occur on or prior to

July

10,

2017

(or the Special Meeting and, together with the Annual Meeting, the Stockholder Meetings) Pursuant to the

May

2017

Purchase Agreement, if the Company does not obtain Stockholder Approval at the Stockholder Meetings, the Company will call a stockholder meeting every

four

months thereafter to seek the Stockholder Approval until the earlier of the date Stockholder Approval is obtained or the Preferred Stock and

May

2017

Warrants are no longer outstanding.

Registration Rights

Pursuant to the

May

2017

Purchase Agreement, within

30

calendar days of the date of the Stockholder Approval, the Company has agreed to file a registration statement on Form S-

3

(or other appropriate form if the Company is not then S-

3

eligible) providing for the resale by the Investors of the Series B Conversion Shares and

May

2017

Warrant Shares. The Company shall use commercially reasonable efforts to cause such registration statement to become effective within

181

days following the Closing and commercially reasonable efforts to keep such registration statement effective at all times until (i) no Investor owns any Series B Conversion Shares or

May

2017

Warrant Shares or (ii) the Series B Conversion Shares and

May

2017

Warrant Shares are eligible for resale under Rule

144

without regard to volume limitations.

Stockholder Agreement

In connection with, and as a condition to, the

May

2017

Offering Closing, on

May

11,

2017,

the Company and

one

of the investors, DSM International B.V. (or the Designated Holder), a subsidiary of Koninklijke DSM N.V., entered into a Stockholder Agreement (or the Stockholder Agreement) setting forth certain rights and obligations of the Designated Holder and the Company. The Designated Holder purchased

25,000

shares of Series B Preferred Stock, Cash Warrants for the purchase of

59,521,740

shares of Common Stock and Dilution Warrants in the

May

2017

Offering in exchange for aggregate cash consideration of

$25,000,000.

Pursuant to the Stockholder Agreement, the Designated Holder will have the right to designate

one

director selected by the Designated Holder (a Designated Holder Director), subject to certain restrictions, to the Company’s Board of Directors (or the Board). The Company will agree to appoint the Designated Holder Director and to use reasonable efforts, consistent with the Board’s fiduciary duties, to cause the Designated Holder Director to be re-nominated in the future; provided, that the Designated Holder will no longer have the right to designate any Designated Holder Director at such time as the Designated Holder holds less than

4.5%

of the Company’s outstanding common stock. In addition, for as long as there is a Designated Holder Director serving on the Board, the Company will agree not to engage in certain commercial or financial transactions or arrangements without the consent of any then-serving Designated Holder Director. The Company will also agree to provide the Designated Holder with certain exclusive negotiating rights in connection with certain future commercial projects and arrangements, whereby the Designated Holder will have a

60

-day negotiation period with respect to any such projects, as well as a right to use a portion of the Company’s manufacturing capacity for toll manufacturing of the Designated Holder’s products, subject to certain conditions, including, with respect to the toll manufacturing option, that the Designated Holder provide the Company with a minimum annual level of cash funding in connection with commercial activity between the Company and the Designated Holder, beginning in

2018.

The Designated Holder will also have the right to purchase additional shares of capital stock of the Company in connection with a sale of equity or equity-linked securities by the Company in a capital raising transaction for cash, subject to certain exceptions, to maintain its proportionate ownership percentage in the Company. At the

May

2017

Offering Closing, the Company and the Designated Holder entered into licenses granted by the Company to the Designated Holder with respect to certain Company intellectual property useful in the Designated Holder’s business, which licenses will become effective upon the occurrence of certain events specified therein.

Pursuant to the Stockholder Agreement, the Designated Holder agreed not to sell or transfer any of the shares of Series B Preferred Stock or

May

2017

Warrants purchased by the Designated Holder in the Offering, any Second Tranche Securities (as defined below), or any shares of Common Stock issuable upon conversion or exercise thereof (or the Transfer Restricted Shares), other than to its affiliates, without the consent of the Company during the

one

-year period following the

May

2017

Closing. Thereafter, the Designated Holder will have the right to sell or transfer the Transfer Restricted Shares to any

third

party, other than a competitor of the Company or any controlled affiliate of a competitor of the Company; provided, that the Company will have a customary right of

first

offer with respect to any such sale or transfer other than to affiliates of the Designated Holder. In addition, the Designated Holder will agree that, other than in connection with the purchase, conversion or exercise of (i) the Series B Preferred Stock or

May

2017

Warrants purchased by the Designated Holder pursuant to the

May

2017

Purchase Agreement or (ii) the Second Tranche Securities (as defined below) in accordance with their terms or the exercise of its pre-emptive rights, until

three

months after there is no Designated Holder Director on the Board, the Designated Holder will not, without the prior consent of the Board, among other things, purchase any Common Stock, any options or other rights to acquire Common Stock or any indebtedness of the Company, or make any public offer to acquire common stock, options or other rights to acquire common stock or indebtedness of the Company, that would result in the Designated Holder and its affiliates beneficially owning more than

33%

of the Company’s outstanding voting securities at the time of acquisition (assuming the exercise or conversion, whether then exercisable or convertible, of any shares of Series B Preferred Stock,

May

2017

Warrants or Second Tranche Securities beneficially owned by the Designated Holder and/or its affiliates), join in any solicitation of proxies for any matter not previously approved by the Board, or join any “group” (as such term is defined in Section

13(d)(3)

of the Securities Exchange Act of

1934)

with respect to any of the foregoing.

In addition, the Company has agreed to register, via

one

or more registration statements filed with the SEC under the Securities Act, the shares of common stock issuable upon conversion or exercise, as applicable, of the Series B Preferred Stock,

May

2017

Warrants and Second Tranche Securities held by the Designated Holder. Under the terms of the Stockholder Agreement, the Company is required to file such registration statement within

180

days following the

May

2017

Closing, and to use its commercially reasonable efforts to cause the Registration Statement to be declared effective by the SEC as soon as practicable and no later than the

225th

day following the

May

2017

Closing. In addition, the Designated Holder

may

request that up to

three

of such registrations provide for an underwritten offering of such shares. In addition, if the Company registers any of its securities for public sale under the Securities Act, the Designated Holder will have the right to include their shares in the registration statement, subject to certain exceptions. The managing underwriter of any underwritten offering will have the right to limit, due to marketing reasons, the number of shares registered by the Designated Holder to

25%

of the total shares covered by the registration statement. The Company will agree to pay all expenses incurred in connection with the exercise of such demand and piggyback registration rights, except for legal costs of the Designated Holder, stock transfer taxes and underwriting discounts and commissions.

Pursuant to the Stockholder Agreement, the Company and the Designated Holder have agreed to negotiate in good faith during the

90

-day period following the

May

2017

Closing to mutually agree on certain terms and conditions upon which the Designated Holder shall purchase additional shares of Series B Preferred Stock and warrants (or the Second Tranche Securities), in an amount to be agreed by the Company and the Designated Holder, provided such amount is no less than

$25

million and no more than

$30

million (such amount, the Second Tranche Funding Amount) prior to the end of such

90

-day period (or the Second Tranche Funding). The Second Tranche Funding is subject to approval of the Designated Holder’s managing board. In connection with the Second Tranche Funding, the Company and the Designated Holder shall enter into an amendment to the Stockholder Agreement providing for a

second

Designated Holder Director on terms to be agreed by the parties, and certain of the License Agreements will become effective. If the Second Tranche Funding occurs, the parties will thereafter negotiate in good faith regarding an agreement concerning the development of certain products in the health and nutrition field. In the event that the parties do not reach such agreement prior to the earlier of

90

days after the Second Tranche Funding or

December

31,

2017,

(a) the exclusive negotiating right granted to the Designated Holder in connection with certain future commercial projects and arrangements of the Company will expire, (b) on the

first

anniversary of the closing of the Second Tranche Funding and each subsequent anniversary thereof, the Company will make a

$5

million cash payment to the Designated Holder, provided that the aggregate amount of such payments shall not exceed the Second Tranche Funding Amount, and (c) an intellectual property escrow agreement relating to the License Agreements, entered into by the Company and the Designated Holder at the Closing, will become effective.

Exchange

In connection with the transactions contemplated by the

May

2017

Purchase Agreement, on

May

8,

2017,

the Company entered into a Security Holder Agreement with Foris and Naxyris. Pursuant to the Security Holder Agreement, Foris and Naxyris agreed to exchange (or the

May

2017

Exchange) their outstanding shares of common stock, representing a total of

20,920,578

shares, for

20,920.578

shares of the Company’s Series C Convertible Preferred Stock, par value

$0.0001

per share (or the Series C Preferred Stock). In addition, pursuant to the Security Holder Agreement, Foris and Naxyris agreed to not convert any of their outstanding convertible promissory notes, warrants and any other equity-linked securities of the Company until the Stockholder Approval, to not sell or otherwise transfer or assign any voting securities of the Company prior to the Stockholder Approval, and to vote any shares of Common Stock and Series C Preferred Stock beneficially owned by them in favor of the Stockholder Approval. The Exchange was consummated concurrently with the closing of the

May

2017

Offering.

Series C Preferred Stock

Each share of Series C Preferred Stock has a stated value of

$1,000

and will automatically convert into common stock upon the approval by the Company’s stockholders and implementation of the reverse stock split, on a

1

:1

basis (i.e., each

$1

of stated value of the Series C Preferred Stock will convert into

1

share of Common Stock) (or the Series C Conversion Rate). The Series C Conversion Rate is subject to adjustment in the event of any dividends or distributions of the common stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction.

The Series C Preferred Stock will be entitled to participate with the common stock on an as-converted basis with respect to any dividends or other distributions to holders of common stock.

The Series C Preferred Stock shall vote together as

one

class with the Common Stock on an as-converted basis, and shall also vote with respect to matters specifically affecting the Series C Preferred Stock.

In the event of a fundamental transaction, the holders of the Series C Preferred Stock will have the right to receive the consideration receivable as a result of such fundamental transaction by a holder of the number of shares of common stock for which the Series C Preferred Stock is convertible immediately prior to such fundamental transaction (without regard to whether such Series C Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of common stock.

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series C Preferred stock shall be entitled to receive out of the assets of the Company an amount equal to the greater of (i) the par value of each share of Series C Preferred Stock, plus any accrued and unpaid dividends or other amounts due on such Series C Preferred Stock, prior to any distribution or payment to the holders of common stock or (ii) the amount that a holder would receive if the Series C Preferred Stock were fully converted to common stock immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series C Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of Common Stock.

On

May

8,

2017,

the Company filed the Certificate of Designation of Preferences, Rights and Limitations of Series C Convertible Preferred Stock with the Secretary of State of Delaware.

The Series C Preferred Stock will be issued in a private exchange pursuant to the exemption from registration under Section

3(a)(9)

of the Securities Act.

Voting Agreements

In connection with the transactions contemplated by the

May

2017

Purchase Agreement, the Company and certain stockholders of the Company, including Total, Temasek and Biolding Investment SA, entered into Voting Agreements, pursuant to which such existing stockholders agreed to vote their shares of common stock in favor of the Stockholder Approval. The stockholders who are party to the Voting Agreements held approximately

51.2%

of the Company’s outstanding common stock as of

April

30,

2017.

Nenter Termination Agreement

In connection with the transactions contemplated by the

May

2017

Purchase Agreement and the Stockholder Agreement, on

May

8,

2017,

the Company and Nenter & Co., Inc. (or Nenter) entered into a letter agreement to terminate the Cooperation Agreement, dated as of

October

26,

2016,

between the Company and Nenter, pursuant to which the parties had agreed to collaborate to create and develop certain compounds and, in the event the parties achieved certain specified development targets, to establish and implement a worldwide manufacturing and commercialization plan relating thereto. In connection with the termination of the Cooperation Agreement, the Company agreed to pay Nenter a fee of

$2.5

million on or before

June

22,

2017.

Temasek Letter Agreement

On

May

5,

2017,

the Company entered into a letter agreement with Temasek, pursuant to which the Company and Temasek agreed that Temasek’s Remaining Notes under the Maturity Treatment Agreement

($10.0

million s of

March

31,

2017)

would no longer be subject to mandatory conversion by Temasek at or prior to the maturity of such Remaining Notes. Accordingly, the Company will be required to pay any portion of such Remaining Notes that remain outstanding at maturity in cash in accordance with the terms of such Remaining Notes. See Note

5,

“Debt and Mezzanine Equity” for details regarding the Maturity Treatment Agreement and the Remaining Notes.

XML

Significant Accounting Policies (Policies)

3 Months Ended

Mar. 31, 2017

Accounting Policies [Abstract]

Basis of Accounting, Policy [Policy Text Block]

Basis of Presentation

The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (or “GAAP”) and with the instructions for Form

10

-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form

10

-K for the fiscal year ended

December

31,

2016

as filed with the Securities and Exchange Commission (or the “SEC”) on

April

17,

2017.

The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

The Company uses the equity method to account for investments in companies, if its investments provide it with the ability to exercise significant influence over operating and financial policies of the investee. Consolidated net income or loss includes the Company’s proportionate share of the net income or loss of these companies. Judgments made by the Company regarding the level of influence over each equity method investment include considering key factors such as the Company’s ownership interest, representation on the board of directors, participation in policy-making decisions and material intercompany transactions.

Consolidation, Policy [Policy Text Block]

Principles of Consolidation

The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and

two

consolidated variable interest entities (or “VIEs”), with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 

7,

"Joint Ventures and Noncontrolling Interest."

Consolidation, Variable Interest Entity, Policy [Policy Text Block]

Variable Interest Entities

The Company has interests in joint venture entities that are VIEs. Determining whether to consolidate a VIE requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.

Use of Estimates, Policy [Policy Text Block]

Use of Estimates

In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements, except for the impact of adoption of certain accounting standards as described below, and in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented. In the quarter ended

March

31,

2017

the Company adopted Accounting Standards Update (“ASU”) No.

2015

-

11,

Simplifying the Measurement of Inventory

, ASU No.

2016

-

06,

Contingent Put and Call Options in Debt Instruments

, ASU No.

2016

-

09,

Compensation - Stock Compensation (Topic

718):

Improvements to Employee Share-Based Payment Accounting

. None of the ASU’s adopted had a material impact on the Company’s condensed consolidated financial statements.

The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.

New Accounting Pronouncements, Policy [Policy Text Block]

Recent Accounting Pronouncements

In

November

2016,

the Financial Accounting Standards Board (FASB) issued ASU

2016

-

18

Statement of Cash Flows - Restricted Cash.

The amendments in this update require that a statement of cash flows explain the change during the period in the total of cash, cash equivalents, and amounts generally described as restricted cash or restricted cash equivalents. Therefore, amounts generally described as restricted cash and restricted cash equivalents should be included with cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. The amendments in this update are effective for public business entities for fiscal years beginning after

December

15,

2017,

and interim periods within those fiscal years. Early adoption is permitted, including adoption in an interim period. The amendments in this update should be applied using a retrospective transition method to each period presented. The Company has not adopted the update. Upon adoption this would result in a change in the presentation of restricted cash in the statement of cash flows.

In

October

2016,

FASB issued ASU

2016

-

16,

Intra-Entity Transfers of Assets Other Than Inventory

on simplifying the accounting for income taxes related to intra-entity asset transfers. The new guidance allows an entity to recognize the tax expense from the sale of an asset in the seller’s tax jurisdiction when the transfers occur, even though the pre-tax effects of that transaction are eliminated in consolidation. This guidance will be effective for fiscal years, and interim periods within those fiscal years, beginning after

December

15,

2017.

Early adoption is permitted only in the

first

quarter of

2017.

The Company does not expect a material impact on its financial statements upon adoption of this standard.

In

August

2016,

FASB issued ASU

2016

-

15

Classification of Certain Cash Receipts and Cash Payments

on the statement of cash flows. The new guidance clarifies classification of certain cash receipts and cash payments in the statement of cash flows. This guidance will be effective for fiscal years, and interim periods within those fiscal years, beginning after

December

15,

2017

and interim periods within those fiscal years. Early adoption is permitted. The Company is evaluating the impact of adopting this accounting standard update on the financial statements and related disclosures.

In

June

2016,

FASB issued ASU No.

2016

-

13,

Allowance for Loan and Lease Losses (Financial Instruments - Credit Losses Topic

326)

. New impairment guidance for certain financial instruments (including trade receivables) will replace the current “incurred loss” model for estimating credit losses with a forward looking “expected loss” model. The ASU is effective for the Company for fiscal years beginning after

December

15,

2019,

including interim periods within those fiscal years. Early application is permitted as of the fiscal years beginning after

December

15,

2018,

including interim periods within those fiscal years. The Company is evaluating the impact of this standard on its financial statements.

In

February

2016,

FASB issued Accounting Standards

Update2016

-

02

-

Leases

with fundamental changes to how entities account for leases. Lessees will need to recognize a right-of-use asset and a lease liability for virtually all of their leases (other than leases that meet the definition of a short-term lease). The liability will be equal to the present value of lease payments. The asset will be based on the liability, subject to adjustment, such as for initial direct costs. Additional disclosures for leases will also be required. The standard is effective for fiscal years, and interim periods within those fiscal years, beginning after

December

15,

2018.

Early adoption is permitted. The new standard must be adopted using a modified retrospective transition, and provides for certain practical expedients. The new standard

may

materially impact the Company’s financial statements.

In

January

2016,

FASB issued Accounting Standards Update

2016

-

01

Financial Instruments-Overall

, which address certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. The amendments in this update are effective for fiscal years beginning after

December

15,

2017,

including interim periods within those fiscal years. Earlier application is permitted under specific circumstances. The Company expects the new standard to impact the extent of its disclosures of financial instruments, particularly in relation to fair value disclosures, but otherwise does not expect a significant impact from the new standard.

In

May

2014,

FASB issued new guidance related to revenue recognition. In

March,

April,

May

and

December

2016,

the FASB issued additional amendments to the new revenue guidance relating to reporting revenue on a gross versus net basis, identifying performance obligations, licensing arrangements, collectability, noncash consideration, presentation of sales tax, and transition. This new standard will replace all current GAAP guidance on this topic and eliminate all industry-specific guidance. The new revenue recognition update guidance provides a unified model to determine how revenue is recognized. The core principle of the guidance is that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The FASB has issued several updates to the standard which i) clarify the application of the principal versus agent guidance (ASU

2016

-

08);

ii) clarify the guidance on inconsequential and perfunctory promises and licensing (ASU

2016

-

10)

and iii) narrow-scope improvements and practical expedients (ASU

2016

-

12).

On

July

9,

2015,

the FASB voted to defer the effective date by

one

year to

December

15,

2017

for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of

December

15,

2016.

Entities have the option of using either a full retrospective or a modified retrospective approach to adopt the new standard. Therefore, the new standard will be effective commencing with our quarter ending

March

31,

2018.

The Company is currently assessing the potential impact of this new standard on its financial statements and has not selected the transition method. While the Company continues to assess the impact of the new guidance on its revenue recognition policies, it is expected that a key area will be the assessment of contract modifications and collaboration contracts to determine if identification of performance obligations is impacted, which

may

impact the timing of revenue recognition. In addition, the Company expects additional disclosures related to revenue.

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Note 3 - Fair Value of Financial Instruments (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis [Table Text Block]

	Level 1		Level 2		Level 3		Balance as of March 31, 2017
Financial Assets
Money market funds	$	297	$	—	$	—	$	297
Certificates of deposit		1,188		—		—		1,188
Total financial assets	$	1,485	$	—	$	—	$	1,485
Financial Liabilities
Loans payable (1)	$	—	$	51,378	$	—	$	51,378
Credit facilities  (1)		—		50,891		—		50,891
Convertible notes (1)		—		—		115,268		115,268
Compound embedded derivative liabilities		—		—		2,728		2,728
Currency interest rate swap derivative liability		—		2,961		—		2,961
Total financial liabilities	$	—	$	105,230	$	117,996	$	223,226

	Level 1		Level 2		Level 3		Balance as of December 31, 2016
Financial Assets
Money market funds	$	1,549	$	—	$	—	$	1,549
Certificates of deposit		1,373		—		—		1,373
Total financial assets	$	2,922	$	—	$	—	$	2,922
Financial Liabilities
Loans payable (1)	$	—	$	53,579	$	—	$	53,579
Credit facilities  (1)		—		51,261		—		51,261
Convertible notes (1)		—		—		117,767		117,767
Compound embedded derivative liabilities		—		—		4,135		4,135
Currency interest rate swap derivative liability		—		3,343		—		3,343
Total financial liabilities	$	—	$	108,183	$	121,902	$	230,085

Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Table Text Block]

	2017
Balance at January 1	$	117,767
New instruments		15,049
Conversion/extinguishment of convertible notes		(21,077	)
Change in fair value of convertible notes		3,529
Balance at March 31	$	115,268

Fair Value, Net Derivative Asset (Liability) Measured on Recurring Basis, Unobservable Input Reconciliation [Table Text Block]

	2017
Balance at January 1	$	4,135
Gain from change in fair value of derivative liabilities		(1,984	)
Additions		577
Balance at March 31	$	2,728

Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Table Text Block]

	March 31, 2017			March 31, 2016
Risk-free interest rate	0.74%	-	1.30%	0.80%	-	0.89%
Risk-adjusted yields	12.50%	-	22.63%	35.00%	-	45.13%
Stock-price volatility		45%			45%
Probability of change in control		5%			5%
Stock price		$0.53			$1.11
Credit spread	11.28%	-	21.35%	34.16%	-	44.25%
Estimated conversion dates	2017	-	2019	2016	-	2019

Derivative Instruments, Gain (Loss) [Table Text Block]

Type of Derivative Contract	Income Statement Classification	Three Months Ended March 31,
		2017		2016
Currency interest rate swap	Gain from change in fair value of derivative instruments	$	355	$	845

Schedule of Derivative Liabilities at Fair Value [Table Text Block]

	March 31, 2017		December 31, 2016
Fair market value of compound embedded derivative liabilities	$	2,150	$	4,135
Non-current fair value of  swap obligations		2,979		3,343
Total derivative liabilities	$	5,129	$	7,478

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Note 4 - Balance Sheet Components (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Inventory, Current [Table Text Block]

	March 31,  2017		December 31,  2016
Raw materials	$	3,038	$	3,159
Work-in-process		1,343		1,848
Finished goods		2,696		1,206
Inventories, net	$	7,077	$	6,213

Property, Plant and Equipment [Table Text Block]

	March 31, 2017			December 31, 2016
Machinery and equipment	$	84,853		$	82,688
Leasehold improvements		38,828			38,785
Computers and software		9,658			9,585
Buildings		4,834			4,699
Furniture and office equipment		2,350			2,333
Vehicles		136			164
Land		460			460
Construction in progress		2,465			2,216
		143,584			140,930
Less: accumulated depreciation and amortization		(90,539	)		(87,195	)
Property, plant and equipment, net	$	53,045		$	53,735

Schedule of Other Assets, Noncurrent [Table Text Block]

	March 31, 2017		December 31, 2016
Recoverable taxes from Brazilian government entities	$	14,894	$	13,723
Deposits on property and equipment, including taxes		499		291
Other		1,401		1,450
Total other assets	$	16,794	$	15,464

Schedule of Accrued and Other Current Liabilities [Table Text Block]

	March 31, 2017		December 31, 2016
Withholding tax related to conversion of related party notes	$	1,370	$	1,370
Professional services		5,358		6,876
SMA relocation accrual		3,746		3,641
Accrued interest		8,259		4,847
Tax-related liabilities		2,480		2,610
Accrued vacation		2,228		2,034
Payroll and related expenses		2,761		4,310
Deferred rent, current portion		1,111		1,111
Contractual obligations to contract manufacturers		381		—
Other		1,960		2,389
Total accrued and other current liabilities	$	29,654	$	29,188

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Note 5 - Debt and Mezzanine Equity (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Debt [Table Text Block]

	March 31, 2017			December 31, 2016
Senior secured loan facility	$	27,844		$	27,658
BNDES credit facility		904			1,172
FINEP credit facility		637			696
Guanfu credit facility		19,858			19,564
Total credit facilities		49,243			49,090
Convertible notes		75,218			78,981
Related party convertible notes		43,335			42,754
Related party loan payable		30,554			29,691
Loans payable		22,588			26,527
Total debt		220,938			227,043
Less: current portion		(49,455	)		(59,155	)
Long-term debt	$	171,483		$	167,888
Mezzanine equity	$	5,000		$	5,000

Schedule of Long-term Debt Instruments [Table Text Block]

Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Related Party Loans payable			Credit Facility			Total
2017 (remaining nine months)	$	4,537		$	12,677		$	11,899		$	31,511		$	5,271		$	65,895
2018		16,290			21,803			2,878			—			33,710			74,681
2019		34,913			93,287			2,766			—			2,580			133,546
2020		—			—			2,656			—			2,500			5,156
2021		—			—			2,543			—			27,396			29,939
Thereafter		—			—			1,442			—			—			1,442
Total future minimum payments (1)		55,740			127,767			24,184			31,511			71,457			310,659
Less: amount representing interest (2)		(12,405	)		(52,549	)		(1,596	)		(957	)		(22,214	)		(89,721	)
Present value of minimum debt payments		43,335			75,218			22,588			30,554			49,243			220,938
Less: current portion		(3,611	)		(2,288	)		(11,780	)		(30,554	)		(1,222	)		(49,455	)
Noncurrent portion of debt	$	39,724		$	72,930		$	10,808		$	—		$	48,021		$	171,483

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Note 6 - Commitments and Contingencies (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule Of Future Minimum Payments For Lease Obligations [Table Text Block]

Years ending December 31:	Capital Leases			Operating Leases		Total Lease Obligations
2017 (remaining nine months)	$	734		$	5,194	$	5,928
2018		106			6,909		7,015
2019		9			6,782		6,791
2020		—			7,012		7,012
2021		—			7,248		7,248
Thereafter		—			10,993		10,993
Total future minimum lease payments		849		$	44,138	$	44,987
Less: amount representing interest		(39	)
Present value of minimum lease payments		810
Less: current portion		(405	)
Long-term portion	$	405

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Note 7 - Joint Ventures and Noncontrolling Interest (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Variable Interest Entities [Table Text Block]

(In thousands)	March 31, 2017		December 31, 2016
Assets	$	2,306	$	2,277
Liabilities	$	158	$	135

Noncontrolling Interest [Table Text Block]

	2017		2016
Balance at January 1	$	937	$	391
Acquisition of noncontrolling interest		—		(277	)
Balance at March 31	$	937	$	114

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Note 9 - Goodwill and Intangible Assets (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Intangible Assets and Goodwill [Table Text Block]

		March 31, 2017							December 31, 2016
	Useful Life in Years	Gross Carrying Amount		Accumulated Amortization/ Impairment			Net Carrying Value		Gross Carrying Amount		Accumulated Amortization/ Impairment			Net Carrying Value
In-process research and development	Indefinite	$	8,560	$	(8,560	)	$	—	$	8,560	$	(8,560	)	$	—
Acquired licenses and permits	2		772		(772	)		—		772		(772	)		—
Goodwill	Indefinite		560		—			560		560		—			560
		$	9,892	$	(9,332	)	$	560	$	9,892	$	(9,332	)	$	560

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Note 11 - Stock-based Compensation (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity [Table Text Block]

	Number Outstanding			Weighted- Average Exercise Price		Weighted- Average Remaining Contractual Life (Years)		Aggregate Intrinsic Value
								(in thousands)
Outstanding - December 31, 2016		13,487,685		$	3.63		6.70	$	443
Options granted		726,000		$	0.58		—		—
Options exercised		(500	)	$	0.28		—		—
Options cancelled		(695,912	)	$	1.82		—		—
Outstanding - March 31, 2017		13,517,273		$	3.55		6.83	$	44
Vested and expected to vest after March 31, 2017		12,347,493		$	3.79		6.63	$	38
Exercisable at March 31, 2017		7,478,686		$	5.42		5.28	$	1

Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity [Table Text Block]

	RSUs			Weighted- Average Grant- Date Fair Value		Weighted Average Remaining Contractual Life (Years)
Outstanding - December 31, 2016		6,997,084		$	1.18		1.44
Awarded		825,980		$	0.59		—
Vested		(348,699	)	$	1.28		—
Forfeited		(250,329	)	$	1.03		—
Outstanding - March 31, 2017		7,224,036		$	1.11		1.39
Expected to vest after March 31, 2017		5,735,089		$	1.15		1.17

Schedule of Share-based Compensation, Shares Authorized under Stock Option Plans, by Exercise Price Range [Table Text Block]

			Options Outstanding						Options Exercisable
Exercise Price			Number of Options		Weighted- Average Remaining Contractual Life (Years)		Weighted-Average Exercise Price		Number of Options		Weighted-Average Exercise Price
$0.28	—	$0.58		795,734		9.48	$	0.49		2,234	$	0.28
$0.59	—	$0.59		2,224,375		9.13	$	0.59		—	$	—
$0.69	—	$1.63		1,491,082		8.67	$	1.30		361,067	$	1.60
$1.64	—	$1.96		2,192,975		7.51	$	1.84		1,026,492	$	1.83
$1.98	—	$2.87		1,780,408		6.07	$	2.69		1,579,154	$	2.73
$2.96	—	$3.44		688,795		6.40	$	3.15		597,154	$	3.13
$3.51	—	$3.51		1,447,979		6.90	$	3.51		1,057,049	$	3.51
$3.55	—	$4.31		1,723,976		3.31	$	3.97		1,683,443	$	3.98
$4.35	—	$26.84		1,111,949		3.52	$	17.71		1,111,949	$	17.71
$30.17	—	$30.17		60,000		3.96	$	30.17		60,000	$	30.17
$0.28	—	$30.17		13,517,273		6.83	$	3.55		7,478,686	$	5.42

Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Table Text Block]

	Three Months Ended March 31,
	2017		2016
Research and development	$	484	$	491
Sales, general and administrative		1,162		1,560
Total stock-based compensation expense	$	1,646	$	2,051

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]

	Three Months Ended March 31,
	2017			2016
Expected dividend yield		—	%		—	%
Risk-free interest rate		2.1	%		1.4	%
Expected term (in years)		6.15			6.23
Expected volatility		80	%		73	%

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Note 15 - Reporting Segments (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Revenue from External Customers Attributed to Foreign Countries by Geographic Area [Table Text Block]

	Three Months Ended March 31,
	2017		2016
Europe	$	5,376	$	4,372
United States		3,096		3,462
Asia		4,433		590
Brazil		19		375
Other		56		12
Total	$	12,980	$	8,811

Schedule of Disclosure on Geographic Areas, Long-Lived Assets in Individual Foreign Countries by Country [Table Text Block]

	March 31, 2017		December 31, 2016
Brazil	$	39,137	$	44,153
United States		13,683		9,342
Europe		225		240
Total	$	53,045	$	53,735

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Note 16 - Comprehensive Loss (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Accumulated Other Comprehensive Income (Loss) [Table Text Block]

	March 31, 2017			December 31, 2016
Foreign currency translation adjustment, net of tax	$	(40,581	)	$	(40,904	)
Total accumulated other comprehensive loss	$	(40,581	)	$	(40,904	)

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Note 17 - Net Loss Attributable to Common Stockholders and Net Loss Per Share (Tables)

3 Months Ended

Mar. 31, 2017

Notes Tables

Schedule of Earnings Per Share, Basic and Diluted [Table Text Block]

	Three Months Ended March 31,
	2017			2016
Numerator:
Net loss attributable to Amyris, Inc. common stockholders	$	(37,371	)	$	(15,308	)
Interest on convertible debt		—			1,817
Accretion of debt discount		—			1,633
Gain from change in fair value of derivative instruments		—			(18,415	)
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$	(37,371	)	$	(30,273	)
Denominator:
Weighted average shares of common stock outstanding for basic EPS		290,039,216			207,199,563
Basic and diluted loss per share	$	(0.13	)	$	(0.07	)
Weighted average shares of common stock outstanding		290,039,216			207,199,563
Effect of dilutive securities:
Convertible promissory notes		—			53,732,522
Weighted common stock equivalents		—			53,732,522
Diluted weighted-average common shares		290,039,216			260,932,085
Diluted loss per share	$	(0.13	)	$	(0.12	)

Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share [Table Text Block]

	Three Months Ended March 31,
	2017		2016
Period-end stock options to purchase common stock		13,517,273		12,159,154
Convertible promissory notes (1)		72,826,108		99,648,739
Period-end common stock warrants		5,021,087		5,885,762
Period-end restricted stock units		7,224,036		5,175,430
Total		98,588,504		122,869,085

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Note 1 - The Company (Details Textual) $ in Thousands	3 Months Ended
	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)
Number of Operating Segments	1
Working Capital	$ (77,600)
Retained Earnings (Accumulated Deficit)	(1,171,809)	$ (1,134,438)
Cash, Cash Equivalents, and Short-term Investments	2,500
Debt Instrument, Unamortized Discount	42,000
Long-term Debt	220,938	227,043
Long-term Debt, Current Maturities, Including Due to Related Parties	49,455	$ 59,155
Interest Payable	$ 20,800

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Note 2 - Summary of Significant Accounting Policies (Details Textual)	3 Months Ended
	Mar. 31, 2017
Variable Interest Entity, Number of Entities	2

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Note 3 - Fair Value of Financial Instruments (Details Textual) $ in Thousands, BRL in Millions	Mar. 31, 2017 USD ($)	Mar. 31, 2017 BRL	Dec. 31, 2016 USD ($)
Banco Pine July 2012 Loan Agreement [Member] | Interest Rate Swap [Member]
Derivative, Notional Amount	$ 6,900	BRL 22
Derivative, Fixed Interest Rate	3.94%	3.94%
Fair Value, Inputs, Level 3 [Member] | Derivative Liability, Compound Embedded Derivatives [Member]
Fair Value, Measurement with Unobservable Inputs Reconciliations, Recurring Basis, Liability Value	$ 2,728		$ 4,135
Derivative Liabilities [Member] | Fair Value, Inputs, Level 3 [Member] | Derivative Liability, Compound Embedded Derivatives [Member]
Fair Value, Measurement with Unobservable Inputs Reconciliations, Recurring Basis, Liability Value	$ 2,700		$ 4,100

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Note 3 - Fair Value of Financial Instruments - Fair Value, Assets, and Liabilities Measured on Recurring Basis (Details) - Fair Value, Measurements, Recurring [Member] - USD ($) $ in Thousands	Mar. 31, 2017		Dec. 31, 2016
Money market funds	$ 297		$ 1,549
Certificates of deposit	1,188		1,373
Total financial assets	1,485		2,922
Loans payable	51,378	[1]	53,579	[2]
Credit facilities	50,891	[1]	51,261	[2]
Convertible notes	115,268	[1]	117,767	[2]
Compound embedded derivative liabilities	2,728		4,135
Currency interest rate swap derivative liability	2,961		3,343
Total financial liabilities	223,226		230,085
Fair Value, Inputs, Level 1 [Member]
Money market funds	297		1,549
Certificates of deposit	1,188		1,373
Total financial assets	1,485		2,922
Loans payable		[1]		[2]
Credit facilities		[1]		[2]
Convertible notes		[1]		[2]
Compound embedded derivative liabilities
Currency interest rate swap derivative liability
Total financial liabilities
Fair Value, Inputs, Level 2 [Member]
Money market funds
Certificates of deposit
Total financial assets
Loans payable	51,378	[1]	53,579	[2]
Credit facilities	50,891	[1]	51,261	[2]
Convertible notes		[1]		[2]
Compound embedded derivative liabilities
Currency interest rate swap derivative liability	2,961		3,343
Total financial liabilities	105,230		108,183
Fair Value, Inputs, Level 3 [Member]
Money market funds
Certificates of deposit
Total financial assets
Loans payable		[1]		[2]
Credit facilities		[1]		[2]
Convertible notes	115,268	[1]	117,767	[2]
Compound embedded derivative liabilities	2,728		4,135
Currency interest rate swap derivative liability
Total financial liabilities	$ 117,996		$ 121,902

[1] These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.

[2] These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis (noting that the Remaining Notes subject to the Maturity Treatment Agreement were revalued to fair value on July 29, 2015, see Note 5 "Debt and Mezzanine Equity" and Note 18, "Subsequent Events" for details).

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Note 3 - Fair Value of Financial Instruments - Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation (Details) - Fair Value, Inputs, Level 3 [Member] - Convertible Debt [Member] $ in Thousands	3 Months Ended
	Mar. 31, 2017 USD ($)
Balance, convertible notes	$ 117,767
New instruments	15,049
Conversion/extinguishment of convertible notes	(21,077)
Change in fair value of convertible notes	3,529
Balance, convertible notes	$ 115,268

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Note 3 - Fair Value of Financial Instruments - Reconciliation for Compound Embedded Derivative Liability (Details) - Fair Value, Inputs, Level 3 [Member] - Derivative Liability, Compound Embedded Derivatives [Member] $ in Thousands	3 Months Ended
	Mar. 31, 2017 USD ($)
Balance, convertible notes	$ 4,135
Gain from change in fair value of derivative liabilities	(1,984)
Additions	577
Balance, convertible notes	$ 2,728

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Note 3 - Fair Value of Financial Instruments - Market-based Assumption and Estimates for Compound Embedded Derivative Liabilities Valuation (Details) - $ / shares	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Risk-free interest rate
Risk-adjusted yields
Expected volatility	45.00%	45.00%
Probability of change in control	5.00%	5.00%
Stock price (in dollars per share)	$ 0.53	$ 1.11
Credit spread
Estimated conversion dates
Minimum [Member]
Risk-free interest rate	0.74%	0.80%
Risk-adjusted yields	12.50%	35.00%
Credit spread	11.28%	34.16%
Estimated conversion dates	2017	2016
Maximum [Member]
Risk-free interest rate	1.30%	0.89%
Risk-adjusted yields	22.63%	45.13%
Credit spread	21.35%	44.25%
Estimated conversion dates	2019	2019

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Note 3 - Fair Value of Financial Instruments - Derivative Instruments Classification (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Currency Interest Rate Swap [Member] | Not Designated as Hedging Instrument [Member] | Gain (Loss) From Change in Fair Value of Derivative Instruments [Member]
Currency interest rate swap	$ 355	$ 845

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Note 3 - Fair Value of Financial Instruments - Derivative Liabilities (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Fair market value of compound embedded derivative liabilities	$ 2,150	$ 4,135
Non-current fair value of swap obligations	2,979	3,343
Total derivative liabilities	$ 5,129	$ 7,478

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Note 4 - Balance Sheet Components (Details Textual) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016	Dec. 31, 2016
Property, Plant and Equipment, Gross	$ 143,584		$ 140,930
Accumulated Depreciation, Depletion and Amortization, Property, Plant, and Equipment	90,539		87,195
Depreciation, Depletion and Amortization	2,715	$ 2,869
Property, Plant and Equipment, Including Capital Leases [Member]
Depreciation, Depletion and Amortization	2,700	$ 2,900
Capital Lease Obligations [Member]
Accumulated Depreciation, Depletion and Amortization, Property, Plant, and Equipment	100		600
Capital Lease Obligations [Member] | Machinery and Equipment, Furniture and Office Equipment Under Capital Lease [Member]
Property, Plant and Equipment, Gross	$ 3,100		$ 3,100

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Note 4 - Balance Sheet Components - Inventory, Current (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Raw materials	$ 3,038	$ 3,159
Work-in-process	1,343	1,848
Finished goods	2,696	1,206
Inventories, net	$ 7,077	$ 6,213

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Note 4 - Balance Sheet Components - Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Property, plant and equipment	$ 143,584	$ 140,930
Less: accumulated depreciation and amortization	(90,539)	(87,195)
Property, plant and equipment, net	53,045	53,735
Machinery and Equipment [Member]
Property, plant and equipment	84,853	82,688
Leasehold Improvements [Member]
Property, plant and equipment	38,828	38,785
Computer Equipment and Software [Member]
Property, plant and equipment	9,658	9,585
Building [Member]
Property, plant and equipment	4,834	4,699
Furniture and Fixtures [Member]
Property, plant and equipment	2,350	2,333
Vehicles [Member]
Property, plant and equipment	136	164
Land [Member]
Property, plant and equipment	460	460
Construction in Progress [Member]
Property, plant and equipment	$ 2,465	$ 2,216

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Note 4 - Balance Sheet Components - Other Assets, Noncurrent (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Recoverable taxes from Brazilian government entities	$ 14,894	$ 13,723
Deposits on property and equipment, including taxes	499	291
Other	1,401	1,450
Total other assets	$ 16,794	$ 15,464

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Note 4 - Balance Sheet Components - Accrued and Other Current Liabilities (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Withholding tax related to conversion of related party notes	$ 1,370	$ 1,370
Professional services	5,358	6,876
SMA relocation accrual	3,746	3,641
Accrued interest	8,259	4,847
Tax-related liabilities	2,480	2,610
Accrued vacation	2,228	2,034
Payroll and related expenses	2,761	4,310
Deferred rent, current portion	1,111	1,111
Contractual obligations to contract manufacturers	381
Other	1,960	2,389
Total accrued and other current liabilities	$ 31,806	$ 29,188

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Note 5 - Debt and Mezzanine Equity (Details Textual) $ / shares in Units, BRL in Millions																						1 Months Ended																		3 Months Ended			6 Months Ended	8 Months Ended	12 Months Ended
	May 15, 2017 USD ($)	May 11, 2017 USD ($)	May 08, 2017 USD ($)	Jan. 11, 2017 USD ($)	Dec. 28, 2016 USD ($)	Dec. 02, 2016 USD ($)	Oct. 27, 2016 USD ($)	Oct. 26, 2016 USD ($)	Oct. 21, 2016 USD ($)	Jun. 24, 2016 USD ($)	May 10, 2016 USD ($)	Feb. 15, 2016 USD ($) $ / shares shares	Feb. 12, 2016 USD ($) $ / shares shares	Feb. 12, 2016 EUR (€)	Dec. 02, 2015 USD ($)	Nov. 30, 2015 USD ($)	Oct. 20, 2015 USD ($)	Oct. 14, 2015 USD ($) $ / shares shares	Jul. 29, 2015 USD ($) $ / shares shares	Apr. 02, 2015	Aug. 01, 2013	Feb. 28, 2017 USD ($)	Jan. 31, 2017 USD ($)	Dec. 31, 2016 USD ($) $ / shares	Mar. 31, 2016 USD ($) $ / shares shares	Mar. 31, 2016 EUR (€)	Feb. 29, 2016 USD ($) $ / shares shares	Nov. 30, 2015 USD ($)	Jul. 31, 2015 USD ($) $ / shares shares	Jun. 30, 2014 USD ($)	May 31, 2014 USD ($) $ / shares	Mar. 31, 2014 USD ($)	Jan. 31, 2014 USD ($) $ / shares	Dec. 31, 2013 USD ($)	Oct. 31, 2013 USD ($) $ / shares	Aug. 31, 2013 USD ($) $ / shares shares	Jul. 31, 2012 USD ($)	Dec. 31, 2011 BRL	Nov. 30, 2010	Mar. 31, 2017 USD ($) $ / shares shares	Mar. 31, 2017 BRL	Mar. 31, 2016 USD ($) $ / shares shares	Dec. 31, 2016 USD ($) $ / shares	Dec. 31, 2016 USD ($) $ / shares shares	Dec. 31, 2016 USD ($) $ / shares	Dec. 31, 2015 USD ($)	May 02, 2017 $ / shares	Mar. 31, 2017 BRL shares	Dec. 31, 2016 BRL	Dec. 19, 2016 USD ($)	Dec. 01, 2016 USD ($) $ / shares	Sep. 30, 2016 USD ($)	Sep. 30, 2016 BRL	Sep. 02, 2016 USD ($)	May 31, 2016 shares	May 30, 2016 USD ($) $ / shares	Feb. 28, 2016 shares	Feb. 24, 2016	Feb. 16, 2016 $ / shares	Oct. 31, 2015 USD ($)	Jun. 30, 2015	Mar. 31, 2015 USD ($)	Jan. 31, 2015 USD ($) $ / shares	Jul. 31, 2014 USD ($) $ / shares	Apr. 30, 2014 USD ($) $ / shares	Oct. 04, 2013	Sep. 30, 2013 USD ($) shares	Jul. 31, 2013 USD ($) $ / shares	Jun. 30, 2013 USD ($) $ / shares	Mar. 31, 2013 $ / shares	Sep. 14, 2012 USD ($) $ / shares	Jul. 31, 2012 BRL	Jul. 30, 2012 USD ($)	Jun. 30, 2012 USD ($)	Feb. 28, 2012 USD ($) $ / shares
Repayments of Long-term Debt																																								$ 4,273,000		$ 729,000
Proceeds from Issuance of Debt																																								1,500,000
Gain (Loss) on Extinguishment of Debt																									$ 4,200,000															$ 96,000		$ (216,000)
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares																									$ 10.67															$ 0.01		$ 10.67
Debt Instrument, Unamortized Discount																																								$ 42,000,000
Class of Warrant or Right, Term																																								5 years 36 days	5 years 36 days
Class of Warrant or Right, Outstanding | shares																									7,328,069															14,663,411		7,328,069						14,663,411
Long-term Debt																								$ 227,043,000																$ 220,938,000			$ 227,043,000	$ 227,043,000	$ 227,043,000
Letters of Credit Outstanding, Amount																																																																										$ 1,000,000
Restricted Cash and Cash Equivalents, Noncurrent																								957,000																958,000			957,000	957,000	957,000
Debt Future Minimum Payments Due in Two Years																																								$ 74,681,000
Exchange Warrants [Member]
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares																			$ 0.01
JVCO Joint Venture [Member]
Equity Method Investment, Ownership Percentage													25.00%												25.00%															25.00%		25.00%						25.00%
Subsequent Event [Member]
Extinguishment of Debt, Amount		$ 40,200,000
Total [Member]
Debt Conversion, Original Debt, Amount																													$ 70,000,000
Convertible Debt																													$ 5,000,000
Debt Conversion, Converted Instrument, Shares Issued | shares																													30,400,000
Total [Member] | JVCO Joint Venture [Member]
Equity Method Investment, Percentage Investment Sold																									50.00%	50.00%
Equity Method Investment, Ownership Percentage by Counterparty													75.00%												75.00%																	75.00%
Conversion of All Outstanding Fidelity Notes for Aggregate Principal Amount of 2015 144A Notes [Member]
Debt Conversion, Original Debt, Amount					$ 19,100,000
Debt Conversion, Converted Instrument, Exchange Ratio of Converted Debt to Original Debt					1.25
Proceeds from Issuance of Debt				$ 19,100,000
Gain (Loss) on Extinguishment of Debt																																								$ 100,000
Related Party Convertible Notes [Member]
Gain (Loss) on Extinguishment of Debt																																	$ (9,400,000)
Convertible Debt																								42,800,000																43,300,000			42,800,000	42,800,000	42,800,000
Debt Instrument, Debt Discount, Related Party																								5,400,000																5,600,000			5,400,000	5,400,000	5,400,000
Long-term Debt																								42,754,000																43,335,000			42,754,000	42,754,000	42,754,000
Debt Future Minimum Payments Due in Two Years																																								16,290,000
Related Party Convertible Notes [Member] | The Second Tranche [Member]
Debt Instrument, Term																																	1 year
Debt Instrument, Convertible, Conversion Price | $ / shares																																	$ 2.87
Convertible Promissory Notes, Period After Which Notes Will Be Due																																	5 years
Convertible Note Discount, Number of Days for Trailing Weighted-average Closing Price																																	60 days
Debt Instrument, Convertible, Conversion Price, Interest Accrued, Rate Applicable to the First 180 Days																																	13.00%
Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter																																	16.00%
Debt Instrument, Convertible, Conversion Price, Interest Accrued for Defaults																																	12.00%
Convertible Notes, Recurring Term of Option to Prepay After Initial Payment Period																																	180 days
Convertible Notes Exchanged and Cancelled																																	$ 6,000,000
Debt Instrument, Convertible, Conversion Price, Interest Accrued																																	10.00%
Debt Instrument, Convertible, Conversion Price, Interest Period																																	3 years
Rule 144A Related Party Convertible Notes [Member]
Convertible Debt																								17,300,000																17,600,000			17,300,000	17,300,000	17,300,000
Debt Instrument, Debt Discount, Related Party																								7,400,000																7,100,000			7,400,000	7,400,000	7,400,000
Senior Secured Loan Facility [Member]
Long-term Line of Credit																																								27,800,000
Debt Issuance Costs, Line of Credit Arrangements, Net																																								700,000
BNDES Credit Facility [Member]
Long-term Line of Credit																								1,200,000																900,000			1,200,000	1,200,000	1,200,000			BRL 2.9	BRL 3.8
Line of Credit Facility, Maximum Borrowing Capacity																																						BRL 22.4		7,100,000
Debt Instrument, Interest Rate, Stated Percentage																																						7.00%
Debt Instrument, Number of Monthly Installments																																						60
Line of Credit Facility, Unused Capacity, Commitment Fee Percentage																																						0.10%
Collateral Provided by Company Certain Equipment and Other Tangible Assets, Amount																																						BRL 24.9		7,900,000
Line of Credit Facility Bank Guarantee Percentage																																						10.00%
Guarantor Obligations, Liquidation Proceeds, Percentage																																						130.00%
BNDES Credit Facility [Member] | First Tranche [Member]
Line of Credit Facility, Maximum Borrowing Capacity | BRL																																						BRL 19.1
BNDES Credit Facility [Member] | The Second Tranche [Member]
Line of Credit Facility, Maximum Borrowing Capacity | BRL																																						BRL 3.3
Line of Credit Facility Bank Guarantee Percentage																																						90.00%
Line of Credit Facility, Borrowings Above Which is New Tranche | BRL																																						BRL 19.1
FINEP Credit Facility [Member]
Long-term Line of Credit																								700,000																$ 700,000			700,000	700,000	700,000			BRL 2.0	BRL 2.3
Line of Credit Facility, Maximum Borrowing Capacity																																																				$ 2,000,000	BRL 6.4
Debt Instrument, Interest Rate, Stated Percentage																																							5.00%
Debt Instrument, Number of Monthly Installments																																							81
DebtDefualtPenaltyAndFineOnObligationInDefaultPercentage																																							10.00%
Debt Instrument Interest On Late Balance Percentage Per Month																																							1.00%
FINEP Credit Facility [Member] | Threshold Met [Member]
Debt Instrument, Interest Rate, Stated Percentage																																							11.00%
Total [Member]
Extinguishment of Debt, Amount | €																										€ 50,000
Letter of Credit [Member]
Restricted Cash and Cash Equivalents, Noncurrent																																																																										$ 1,000,000
Private Placement February 2016 [Member]
Line of Credit Facility, Maximum Borrowing Capacity																											$ 1,000,000
Debt Instrument, Interest Rate, Stated Percentage												13.50%
Debt Instrument, Face Amount																											20,000,000
Proceeds from Issuance of Private Placement												$ 2,000,000	$ 18,000,000														$ 20,000,000
Private Placement February 2016 [Member] | Unsecured Promissory Notes, 2016 [Member]
Debt Instrument, Face Amount												$ 2,000,000	$ 18,000,000
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares												285,714	2,571,428
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares												$ 0.01	$ 0.01
Private Placement February 2016 [Member] | Stegodon [Member]
Debt Instrument, Fee Amount, Current																								425,000																			425,000	425,000	425,000
Debt Instrument, Fee Amount, Noncurrent																								450,000																			450,000	450,000	450,000
Private Placement February 2016 [Member] | Stegodon [Member] | Ginkgo Collaboration Agreement [Member] | Senior Secured Loan Facility [Member]
Debt Instrument, Additional Monies Agreed to Apply Toward Repayment of Outstanding Loans, Maximum																								3,000,000																			3,000,000	3,000,000	3,000,000
Private Placement February 2016 [Member] | Foris Ventures, LLC [Member]
Proceeds from Issuance of Private Placement												$ 16,000,000
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares												2,285,714
Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Related Party Convertible Notes [Member]
Debt Instrument, Face Amount																																																																				$ 20,000,000
Guanfu Credit Agreement [Member] | Guanfu Holding Co., Ltd [Member] | Unsecured Debt [Member]
Long-term Line of Credit																								$ 25,000,000																			$ 25,000,000	$ 25,000,000	$ 25,000,000
Line of Credit Facility, Maximum Borrowing Capacity								$ 25,000,000
Debt Instrument, Interest Rate, Stated Percentage								10.00%
Debt Instrument, Term								5 years
Debt Instrument, Redemption Price, Percentage								100.00%
Common Stock, Volume Weighted Average Closing Sale Price, Percentage								90.00%
Common Stock, Volume Weighted Average Closing Sale Price, Number of Trading Days								90 days
Trading Days, Number of Days Proceeding Default								2 days
Fidelity Convertible Notes [Member]
Debt Instrument, Face Amount																																																												$ 57,600,000
Debt Instrument, Convertible, Conversion Price | $ / shares																																																																											$ 7.0682
Debt Instrument, Repurchase Amount																																																												8,800,000
Debt Instrument, Repurchased Face Amount																																																												$ 9,700,000
Debt Instrument, Convertible, Number of Equity Instruments																																								2,165,898	2,165,898
Convertible Promissory Note, Acquisition Right Amount Redeemable, Percentage																																																																											101.00%
Convertible Promissory Note, Maximum Allowable Debt																																																																											$ 200,000,000
Convertible Promissory Notes, Debt Percentage of Total Assets																																																																											50.00%
Convertible Promissory Note, Maximum Amount of Secured Debt																																																																											$ 125,000,000
Convertible Promissory Note, Secured Debt as a Percentage of Consolidated Total Assets																																																																											30.00%
Convertible Promissory Note, Bridge Loan Amount, Convertible Promissory Note Covenants Waived																																			$ 35,000,000
Additional Consideration for Covenant Waiving, Convertible Promissory Notes																																			7,600,000
Fidelity Convertible Notes [Member] | Convertible Subordinated Debt [Member]
Convertible Notes Payable																																																																											$ 25,000,000
Debt Instrument, Interest Rate, Effective Percentage																																																																											3.00%
Rule 144A Convertible Note Offering [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																															$ 3.74
Convertible Note Offering																															$ 75,000,000
Additional Convertible Note Offering																															15,000,000
Proceeds from Convertible Debt																															72,000,000
Proceeds from Convertible Debt Used to Repay Previously Issued Convertible Debt																															$ 9,700,000
Debt Instrument, Convertible, Threshold Trading Days																															20
Debt Instrument, Convertible, Threshold Consecutive Trading Days																															30
Debt Instrument, Convertible, Threshold Days for Conversion Notification																															5 days
Convertible Note Substantial Change, Discount Rate Used in Calculate Value of Remaining Interest Payments																															0.75%
Convertible Note Substantial Change, Percentage of Principal Repurchase Price																															100.00%
Rule 144A Convertible Note Offering [Member] | Affiliated Entity [Member]
Debt Instrument, Interest Rate, Stated Percentage																															6.50%
Debt Instrument, Face Amount																															$ 57,600,000
Debt Instrument, Repurchase Amount																															18,300,000
Debt Instrument, Repurchased Face Amount																															22,900,000
Amount of Convertible Debt Purchased by Affiliated Entities																															$ 24,700,000
Rule 144A Convertible Note Offering [Member] | Convertible Debt Securities [Member]
Debt Instrument, Interest Rate, Effective Percentage																															6.50%
Rule 144A Convertible Note Offering [Member] | Numerator [Member]
Debt Instrument, Convertible, Conversion Ratio																															267.037
Rule 144A Convertible Note Offering [Member] | Denominator [Member]
Debt Instrument, Convertible, Conversion Rate, Principle Amount | $ / shares																															$ 1,000
Convertible Senior Notes, 9.5% [Member]
Debt Instrument, Interest Rate, Stated Percentage																		9.50%
Debt Instrument, Face Amount																		$ 57,600,000
Debt Instrument, Convertible, Conversion Price | $ / shares																		$ 2.25						$ 1.41																			$ 1.41	$ 1.41	$ 1.41
Debt Instrument, Repurchase Amount													$ 3,700,000												$ 3,700,000																	$ 3,700,000
Debt Instrument, Convertible, Number of Equity Instruments																		38,415,626
Convertible Promissory Note, Maximum Allowable Debt																		$ 200,000,000
Convertible Promissory Note, Maximum Amount of Secured Debt																		$ 65,000,000
Convertible Promissory Note, Secured Debt as a Percentage of Consolidated Total Assets																		30.00%
Proceeds from Convertible Debt																	$ 54,400,000
Debt Instrument, Convertible, Conversion Rate, Principle Amount | $ / shares																		$ 1,000									$ 1,000																	$ 1,000
Convertible Note Substantial Change, Discount Rate Used in Calculate Value of Remaining Interest Payments																		0.75%
Convertible Note Substantial Change, Percentage of Principal Repurchase Price																		100.00%
Debt Instrument, Convertible, Conversion Rate, Shares | shares																		443.6557									446.8707																	711.1209
Debt Instrument, Convertible Percentage of Average Price Per Share the Stock will be Valued upon Early Conversion																		92.50%
Number of Trading Days Notes Become Convertible																		10 days
Debt Restrictions, Maximum Outstanding Debt																		$ 25,000,000
Class of Warrant or Right, Term													5 years	5 years
Long-term Debt																								$ 19,600,000																			$ 19,600,000	$ 19,600,000	$ 19,600,000
Convertible Senior Notes, 9.5% [Member] | Subsequent Event [Member]
Convertible Promissory Note, Additional Principal Amount Issued During Period																							$ 19,100,000
Debt Instrument, Decrease, Forgiveness																							$ 15,300,000
Convertible Senior Notes, 6.5% [Member]
Debt Instrument, Repurchase Amount																	18,300,000
Debt Instrument, Repurchased Face Amount																	22,900,000
Convertible Senior Notes, 3% [Member]
Debt Instrument, Repurchase Amount																	8,800,000
Debt Instrument, Repurchased Face Amount																	$ 9,700,000
The May 2016 Convertible Notes [Member] | Convertible Subordinated Debt [Member]
Debt Instrument, Face Amount																																																								$ 15,000,000
Debt Instrument, Redemption Price, Percentage																																													118.00%
Debt Instrument, Convertible, Conversion Price | $ / shares																																																								$ 1.90
Proceeds from Convertible Debt											$ 9,900,000																																$ 5,000,000
Convertible Debt, Aggregate Number of Shares Issued With Respect to the Initial Closing, Maximum Percentage																								19.99%																			19.99%	19.99%	19.99%				19.99%							19.99%
Convertible Debt											$ 10,000,000																																											$ 2
Debt Instrument, Face Amount, Contingent Second Closing																								$ 5,000,000																			$ 5,000,000	$ 5,000,000	$ 5,000,000
Debt Instrument, Additional Common Stock Payment, Maximum Percent of Aggregate Amount																								50.00%																			50.00%	50.00%	50.00%				50.00%
Debt Instrument, Threshold Amount of Dollar-weighted Volume of Common Stock																								$ 200,000																			$ 200,000	$ 200,000	$ 200,000
Convertible Debt, Length of Time from Date of Issuance, Threshold																																													120 days
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage Except Under Specified Conditions																								4.99%																			4.99%	4.99%	4.99%				4.99%
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage Under Specified Conditions																								9.99%																			9.99%	9.99%	9.99%				9.99%
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage, Conditions, Number of Days After Written Notice																																													61 days
Convertible Debt, Holder Limitations, Maximum Sale Price Per Share of Common Stock | $ / shares																								$ 1.05																			$ 1.05	$ 1.05	$ 1.05
Convertible Debt, Holders May Not Sell Shares, Price Floor, Threshold | $ / shares																								$ 1																			$ 1	$ 1	$ 1
The May 2016 Convertible Notes [Member] | Convertible Subordinated Debt [Member] | Threshold 2 [Member]
Debt Instrument, Redemption Price, Percentage upon Triggering Event																																													112.00%
The December 2016 Convertible Note [Member] | Convertible Subordinated Debt [Member]
Debt Instrument, Face Amount																																																			$ 10,000,000
Debt Instrument, Convertible, Conversion Price | $ / shares																																																			$ 1.90
Proceeds from Convertible Debt						$ 9,900,000
Convertible Debt, Aggregate Number of Shares Issued With Respect to the Initial Closing, Maximum Percentage																								19.99%																			19.99%	19.99%	19.99%				19.99%
Debt Instrument, Additional Common Stock Payment, Maximum Percent of Aggregate Amount																								50.00%																			50.00%	50.00%	50.00%				50.00%
Debt Instrument, Threshold Amount of Dollar-weighted Volume of Common Stock																								$ 200,000																			$ 200,000	$ 200,000	$ 200,000
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage Except Under Specified Conditions																								4.99%																			4.99%	4.99%	4.99%				4.99%
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage Under Specified Conditions																								9.99%																			9.99%	9.99%	9.99%				9.99%
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage, Conditions, Number of Days After Written Notice																																													61 days
Convertible Debt, Holder Limitations, Maximum Sale Price Per Share of Common Stock | $ / shares																								$ 1.05																			$ 1.05	$ 1.05	$ 1.05
Convertible Debt, Holders May Not Sell Shares, Price Floor, Threshold | $ / shares																								$ 1																			$ 1	$ 1	$ 1
Total Purchase Agreement [Member] | Total [Member]
Debt Instrument, Face Amount																																					$ 105,000,000
Unsecured Senior Convertible Promissory Notes [Member] | Total [Member]
Debt Instrument, Face Amount																																		$ 69,000,000
Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Related Party Convertible Notes [Member]
Debt Instrument, Face Amount																																																																				$ 30,000,000	$ 10,000,000
Unsecured Senior Convertible Promissory Notes [Member] | Initial Closing [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																																																							$ 7.0682
Unsecured Senior Convertible Promissory Notes [Member] | Initial Closing [Member] | Total [Member]
Debt Instrument, Interest Rate, Stated Percentage																																					1.50%																																			1.50%
Debt Instrument, Face Amount																																																																							$ 15,000,000		$ 38,300,000
Number of Installments																																					2
Unsecured Senior Convertible Promissory Notes [Member] | Initial Closing [Member] | Total [Member] | New Funding [Member]
Debt Instrument, Face Amount																																																																									15,000,000
Unsecured Senior Convertible Promissory Notes [Member] | Initial Closing [Member] | Total [Member] | Diesel Research and Development Funding [Member]
Debt Instrument, Face Amount																																																																									$ 23,300,000
Unsecured Senior Convertible Promissory Notes [Member] | Second Closing [Member] | Related Party Convertible Notes [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																																																				$ 3.08
Unsecured Senior Convertible Promissory Notes [Member] | Second Closing [Member] | Total [Member] | Related Party Convertible Notes [Member]
Debt Instrument, Face Amount																																																																				$ 20,000,000	$ 10,000,000
Number of Installments																																					2
Unsecured Senior Convertible Promissory Notes [Member] | Two Installments in Second Closing [Member] | Total [Member] | Related Party Convertible Notes [Member]
Debt Instrument, Face Amount																																																																				$ 30,000,000
Unsecured Senior Convertible Promissory Notes [Member] | Third Closing [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																																															$ 4.11
Unsecured Senior Convertible Promissory Notes [Member] | Third Closing [Member] | Total [Member]
Debt Instrument, Face Amount																																																															$ 10,850,000	$ 10,850,000
Number of Installments																																					2
Unsecured Senior Convertible Promissory Notes [Member] | Two Installments In Third Closing [Member] | Total [Member]
Debt Instrument, Face Amount																																																															$ 21,700,000	$ 21,700,000
Debt Instrument, Convertible, Conversion Price | $ / shares																																																																$ 4.11
March 2013 Letter Agreement [Member] | Total [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																																																					$ 3.08	$ 7.0682
Debt Instrument Closing Price Plus Incremental Rate | $ / shares																																																																						0.01
Senior Secured Convertible Note [Member] | Total [Member]
Debt Instrument, Interest Rate, Stated Percentage																																		1.50%
July 2012 Agreements [Member] | Total [Member]
Debt Instrument, Face Amount																																																																$ 10,850,000
Debt Instrument, Convertible, Conversion Price | $ / shares																																																																	$ 7.0682
March 2014 Letter Agreement [Member] | Subsequent Event [Member]
Debt Conversion, Original Debt, Amount			$ 3,400,000
March 2014 Letter Agreement [Member] | Total [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																																																	$ 4.11
Convertible Debt																																																																	$ 75,000,000
March 2014 Letter Agreement [Member] | Two Installments In Third Closing [Member] | Total [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																																															$ 4.11
Unsecured Promissory Notes, 2016 [Member] | Total [Member]
Extinguishment of Debt, Amount																									1,300,000
March 2016 R&D Note [Member]
Extinguishment of Debt, Amount																									5,000,000
Replacement Notes [Member]
Long-term Line of Credit																								$ 3,700,000																$ 3,700,000			$ 3,700,000	$ 3,700,000	$ 3,700,000
Debt Instrument, Interest Rate, Effective Percentage																								1.50%																			1.50%	1.50%	1.50%				1.50%
Convertible Promissory Note, Maximum Allowable Debt																								$ 200,000,000																			$ 200,000,000	$ 200,000,000	$ 200,000,000
Convertible Promissory Notes, Debt Percentage of Total Assets																								50.00%																			50.00%	50.00%	50.00%				50.00%
Convertible Promissory Note, Maximum Amount of Secured Debt																								$ 125,000,000																			$ 125,000,000	$ 125,000,000	$ 125,000,000
Convertible Promissory Note, Secured Debt as a Percentage of Consolidated Total Assets																								30.00%																			30.00%	30.00%	30.00%				30.00%
Debt Instrument Default Rate																								2.50%																			2.50%	2.50%	2.50%				2.50%
Percentage of Principal Amount of Notes, Required to Be Repaid in Change of Control																																													101.00%
Long-term Debt																									$ 3,700,000																	$ 3,700,000
August 2013 Convertible Notes [Member] | Total [Member]
Cancellation of Convertible Debt																																				$ 13,000,000
August 2013 Convertible Notes [Member] | Total [Member] | Common Stock [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																																				1,000,000
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares																																				$ 0.01
August 2013 Convertible Notes [Member] | Total [Member] | First Tranche [Member]
Cancellation of Convertible Debt																																				$ 7,600,000
August 2013 Convertible Notes [Member] | Total [Member] | Second Tranche [Member]
Cancellation of Convertible Debt																																				5,400,000
August 2013 Convertible Notes [Member] | Total and Temasek [Member]
Debt Instrument, Face Amount																																				$ 73,000,000
Private Placement Convertible Notes, Period																																				2 years
Debt Instrument, Number of Tranches																					2
August 2013 Convertible Notes [Member] | Total and Temasek [Member] | First Tranche [Member]
Debt Instrument, Face Amount																																				$ 42,600,000
August 2013 Convertible Notes [Member] | Total and Temasek [Member] | Second Tranche [Member]
Debt Instrument, Face Amount																																				30,400,000
August 2013 Convertible Notes [Member] | Temasek [Member]
Extinguishment of Debt, Amount																																				35,000,000
Bridge Loan																																			$ 35,000,000
August 2013 Convertible Notes [Member] | Temasek [Member] | Second Tranche [Member]
Proceeds from Convertible Debt																																				$ 25,000,000
August 2013 Convertible Notes [Member] | Private Placement [Member]
Debt Instrument, Face Amount																																																																			$ 110,000,000
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																																																																			1,000,000
Temasek Bridge Loan [Member] | Temasek [Member]
Debt Instrument, Interest Rate, Stated Percentage																																																																		5.50%
First Tranche [Member] | Related Party Convertible Notes [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																			$ 2.44
Gain (Loss) on Extinguishment of Debt																																			$ (19,900,000)
Proceeds from Convertible Debt																																			7,600,000
Cancellation of Convertible Debt																																			$ 44,200,000
Convertible Promissory Notes, Period After Which Notes Will Be Due																																			5 years
Convertible Notes, Discount Percentage to Determine Conversion Price																																			15.00%
Convertible Note Discount, Number of Days for Trailing Weighted-average Closing Price																																			60 days
Convertible Notes, Period After Which Convertible at the Option of Holder																																			1 year 180 days
Plant Manufacturing Production, Product Sales, Percentage																																			5.00%
Debt Instrument, Convertible, Conversion Price, Interest Accrued, Rate Applicable to the First 180 Days																																			6.50%
Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter																																			8.00%
Debt Instrument, Convertible, Conversion Price, Interest Accrued for Defaults																																			6.50%
Convertible Notes, Period Over Which Interest is Payable in Kind																																			2 years 180 days
Convertible Notes, Recurring Term of Option to Prepay After Initial Payment Period																																			180 days
Convertible Notes, Initial Prepayment Term																																			2 years 180 days
First Tranche [Member] | Related Party Convertible Notes [Member] | Total [Member]
Debt Instrument, Face Amount																																			$ 51,800,000
Extinguishment of Debt, Amount																																			9,200,000
First Tranche [Member] | Related Party Convertible Notes [Member] | Temasek [Member]
Extinguishment of Debt, Amount																																			35,000,000
Second Tranche [Member] | Related Party Convertible Notes [Member]
Future Cancellation of Debt, Amount																																			$ 9,200,000
Second Tranche [Member] | Related Party Convertible Notes [Member] | Wolverine [Member]
Debt Instrument, Face Amount																																		$ 3,000,000
Cancellation of Convertible Debt																																		$ 25,000,000
The Second Tranche [Member] | Related Party Convertible Notes [Member]
Debt Instrument, Face Amount																																	$ 34,000,000
The Second Tranche [Member] | Related Party Convertible Notes [Member] | Temasek [Member]
Convertible Notes Purchased																																	25,000,000
The Second Tranche [Member] | Related Party Convertible Notes [Member] | Wolverine [Member]
Convertible Notes Purchased																																	3,000,000
The Second Tranche [Member] | Related Party Convertible Notes [Member] | Total [Member]
Convertible Notes Purchased																																	$ 6,000,000
Tranche I and Tranche II Notes [Member] | Related Party Convertible Notes [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																													$ 1.42																											$ 1.14			$ 1.40
Debt Conversion, Original Debt, Amount																													$ 71,000,000
Convertible Debt																								$ 21,800,000																$ 22,100,000			$ 21,800,000	$ 21,800,000	$ 21,800,000
Debt Conversion, Converted Instrument, Shares Issued | shares																													30,860,000
Percentage of Principal Amount of Notes, Required to Be Repaid in Change of Control																																	101.00%
Debt Instrument, Unamortized Discount																								$ 0																			$ 0	$ 0	$ 0	$ 0
Tranche I and Tranche II Notes [Member] | Related Party Convertible Notes [Member] | Subsequent Event [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																															$ 0.50
Tranche I Notes [Member] | Temasek Funding Warrant [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																																																							2,335,342		127,194
Tranche I Notes [Member] | Subsequent Event [Member] | Temasek Funding Warrant [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																																								16,886,320								16,886,320
Convertible Notes 2016 [Member] | Subsequent Event [Member]
Debt Conversion, Original Debt, Amount	$ 18,000,000
June 2016 Private Placement [Member]
Debt Instrument, Interest Rate, Stated Percentage																																																										13.50%
Debt Instrument, Face Amount										$ 5,000,000
Proceeds from Issuance of Private Placement										$ 5,000,000
October 2016 Private Placement [Member] | Foris Ventures, LLC [Member] | Convertible Subordinated Debt [Member]
Proceeds from Issuance of Long-term Debt									$ 6,000,000
Debt Instrument, Interest Rate, Stated Percentage									13.50%
Debt Instrument, Face Amount									$ 6,000,000
October 2016 Private Placement [Member] | Ginkgo Bioworks, Inc. [Member] | Convertible Subordinated Debt [Member]
Proceeds from Issuance of Long-term Debt							$ 8,500,000
Debt Instrument, Face Amount							$ 8,500,000
Salisbury Note [Member] | Salisbury Partners, LLC [Member]
Debt Instrument, Interest Rate, Stated Percentage																								5.00%																			5.00%	5.00%	5.00%				5.00%
Debt Instrument, Face Amount																								$ 3,500,000																			$ 3,500,000	$ 3,500,000	$ 3,500,000
Debt Instrument, Term																								13 years
Debt Instrument, Delinquency Penalty																								5.00%																			5.00%	5.00%	5.00%				5.00%
Debt Instrument, Delinquency Penalty, Threshold																								5 days
Nikko Note [Member] | Nikko [Member]
Debt Instrument, Interest Rate, Stated Percentage																								5.00%																			5.00%	5.00%	5.00%				5.00%
Debt Instrument, Face Amount																								$ 3,900,000																			$ 3,900,000	$ 3,900,000	$ 3,900,000					$ 3,900,000
Debt Instrument, Term																								13 years
Debt Instrument, Delinquency Penalty																								5.00%																			5.00%	5.00%	5.00%				5.00%
Debt Instrument, Delinquency Penalty, Threshold																								5 days
Debt Instrument, Percentage of Joint Venture Interests Owned By the Company Securing the Debt Instrument																								10.00%																			10.00%	10.00%	10.00%				10.00%
Debt Instrument, Additional Payments Required in Four Monthly Installments																								$ 400,000																			$ 400,000	$ 400,000	$ 400,000
Debt Instrument, Additional Equal Monthly Installments, Amount																								100,000
Aprinnova Notes [Member] | Aprinnova JV [Member] | Nikko [Member]
Debt Instrument, Interest Rate, Stated Percentage																						2.75%
Debt Instrument, Face Amount																						$ 1,500,000
Debt Instrument, Periodic Payment																						$ 375,000
Nomis Bay Convertible Note [Member]
Debt, Future Minimum Payments Due, Next Twelve Months																								3,900,000																			3,900,000	3,900,000	3,900,000
Maturity Treatment Agreement [Member]
Debt Future Minimum Payments Due in Two Years																								46,800,000																			46,800,000	46,800,000	46,800,000
Related Party and Non-Related Party Convertible Debt [Member]
Debt Instrument, Unamortized Discount																								$ 42,000,000																			$ 42,000,000	$ 42,000,000	$ 42,000,000
TJLP Adjustment Factor [Member]
DebtInstruementInterestRateOfTheCentralBankOfBrazilUsedAsAThreshold																																							6.00%
TJLP Adjustment Factor [Member] | FINEP Credit Facility [Member] | Threshold Met [Member]
Debt Instrument, Basis Spread on Variable Rate																																							5.00%
Minimum [Member] | The May 2016 Convertible Notes [Member] | Convertible Subordinated Debt [Member]
Debt Instrument, Convertible Stock Price Trigger for Deferred Installments | $ / shares																								$ 0.50																			$ 0.50	$ 0.50	$ 0.50
Debt Instrument, Convertible Threshold Consecutive Trading Days, Deferred Installments																																													5 days
Minimum [Member] | March 2013 Letter Agreement [Member] | Total [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																																																																						$ 3.08
Maximum [Member] | The May 2016 Convertible Notes [Member] | Convertible Subordinated Debt [Member]
Debt Instrument, Convertible Stock Price Trigger for Deferred Installments | $ / shares																								$ 1																			$ 1	$ 1	$ 1
Debt Instrument, Convertible Threshold Consecutive Trading Days, Deferred Installments																																													30 days
Hercules Technology Growth Capital, Inc. (Hercules) [Member]
Loans Payable																																$ 25,000,000
Debt Instrument, Prepayment Penalty, Percentage																																1.00%
Debt Instrument, Facility Charge, Percentage																																1.00%																													5.00%
Debt Instrument, End of Term Fee, Percentage																																10.00%
Long-term Line of Credit																																$ 25,000,000
Debt Instrument, Forbearance Fee, Forgiven																														$ 10,000,000
Debt Instrument, Required Equity Financing, Amount																														$ 50,000,000
Debt Instrument, Unencumbered, Unrestricted, Cash Required, Percentage																														50.00%
Line of Credit Facility, Maximum Borrowing Capacity																																																														$ 15,000,000
Line of Credit Facility, Amount to be Raised Through Equity Triggering Withdrawal of the Credit Facility																																																														$ 20,000,000
Line of Credit Facility, Commitment Fee Percentage																				3.00%
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Hercules Credit Additional Amount [Member]
Debt Instrument, Additional Amount Required																														$ 5,000,000
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Third Hercules Amendment [Member]
Loans Payable															$ 31,700,000
Proceeds from Issuance of Long-term Debt																												$ 10,960,000
Repayments of Long-term Debt															$ 9,100,000
Debt Instrument, Interest Rate, Stated Percentage																9.50%												9.50%
Debt Instrument, Periodic Payment Terms, Balloon Payment to be Paid																$ 767,200												$ 767,200
Payments of Debt Issuance Costs																1,000,000
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Third Hercules Amendment [Member] | Portion of Debt Costs Owed in Connection with Expired Facility [Member]
Payments of Debt Issuance Costs																750,000
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Third Hercules Amendment [Member] | Portion of Debt Costs Related to the Third Hercules Amendment [Member]
Payments of Debt Issuance Costs																$ 250,000
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Prime Rate [Member] | Third Hercules Amendment [Member]
Debt Instrument, Basis Spread on Variable Rate																												6.25%
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Minimum [Member] | Prime Rate [Member]
Debt Instrument, Basis Spread on Variable Rate																																6.25%
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Minimum [Member] | Prime Rate [Member] | Hercules Credit Additional Amount [Member]
Debt Instrument, Basis Spread on Variable Rate																														5.25%
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Maximum [Member] | Prime Rate [Member]
Debt Instrument, Basis Spread on Variable Rate																																9.50%
Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Maximum [Member] | Prime Rate [Member] | Hercules Credit Additional Amount [Member]
Debt Instrument, Basis Spread on Variable Rate																														8.50%
Nossa Caixa and Banco Pine Agreements [Member]
Long-term Line of Credit																								$ 11,100,000																$ 10,900,000			$ 11,100,000	$ 11,100,000	$ 11,100,000
Debt Instrument, Interest Rate, Stated Percentage																																					5.50%																																			5.50%
Debt Instrument, Face Amount																																								16,400,000								BRL 52.0
Collateral Provided by Company Certain Equipment and Other Tangible Assets, Amount																																								$ 21,500,000	BRL 68.0
Certain Farnesene Production Assets Pledged as Collateral for Loans | BRL																																																																								BRL 52.0
Debt Instrument, Period of Interest Only QuarterlyPayments																																					2 years
Banco Pine [Member]
Debt Instrument, Face Amount | BRL																																																																								22.0
Nossa Caixa [Member]
Debt Instrument, Face Amount | BRL																																																																								BRL 30.0
Temasek [Member]
Debt Conversion, Original Debt, Amount																			$ 71,000,000
Debt Conversion, Converted Instrument, Shares Issued | shares																			30,860,633
Temasek [Member] | Temasek Warrant 1 [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																			14,677,861
Temasek [Member] | Temasek Warrant 2 [Member]
Class of Warrant or Right, Numerator One																			30.60%
Class of Warrant or Right, Denominator One																			69.40%
Class of Warrant or Right, Numerator Two																			13.30%
Class of Warrant or Right, Denominator Two																			86.70%
Temasek [Member] | Temasek Warrant Three [Member]
Class of Warrant or Right, Term																			10 years
Class of Warrant or Right, Common Stock Shares Used In Calculation | shares																			880,339
Class of Warrant or Right, Threshold Number of Securities | shares																			2,000,000
Temasek [Member] | The 2013 Warrant [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																			1,000,000																					12,700,244								12,700,244
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares																			$ 0.01
Class of Warrant or Right, Outstanding | shares																																								2,462,536								2,462,536
Temasek [Member] | If Total R&D Warrant is Exercised in Full [Member]
Class of Warrant or Right, Threshold Number of Securities | shares																																								2,000,000								2,000,000
Temasek [Member] | If Total R&D Warrant is Exercised in Full [Member] | Temasek Warrant Three [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																			880,339
Class of Warrant or Right, Common Stock Shares Used In Calculation | shares																																								880,339								880,339
Temasek [Member] | Rule 144A Convertible Notes [Member]
Convertible Notes Payable																			$ 10,000,000
Total [Member]
Convertible Notes Payable																			25,000,000
Debt Conversion, Original Debt, Amount																			$ 70,000,000
Debt Conversion, Converted Instrument, Shares Issued | shares																			30,434,782
Extinguishment of Debt, Amount | €														€ 50,000
Total [Member] | Total Funding Warrant [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																			18,924,191
Class of Warrant or Right, Term																			5 years
Total [Member] | Total R&D Warrant [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																			2,000,000
Total [Member] | Temasek Warrant 2 [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																			2,000,000
Total [Member] | Unsecured Senior Convertible Promissory Notes [Member]
Extinguishment of Debt, Amount													$ 1,300,000
Total [Member] | Tranche I and Tranche II Notes [Member]
Convertible Notes Payable																			$ 15,300,000
Total [Member] | Rule 144A Convertible Notes [Member]
Convertible Notes Payable																			$ 9,700,000
Total and Temasek [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares																			$ 2.30
Interest Expense, Debt																																														$ 39,200,000

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Note 5 - Debt and Mezzanine Equity - Debt Components (Details) - USD ($) $ in Thousands		Mar. 31, 2017	Dec. 31, 2016
Debt		$ 220,938	$ 227,043
Less: current portion		(49,455)	(59,155)
Noncurrent portion of debt		171,483	167,888
Mezzanine equity	[1]	5,000	5,000
Senior Secured Loan Facility [Member]
Debt		27,844	27,658
BNDES Credit Facility [Member]
Debt		904	1,172
FINEP Credit Facility [Member]
Debt		637	696
Guanfu Credit Facility [Member]
Debt		19,858	19,564
Credit Facility [Member]
Debt		49,243	49,090
Noncurrent portion of debt		48,021
Convertible Debt [Member]
Debt		75,218	78,981
Noncurrent portion of debt		72,930
Related Party Convertible Notes [Member]
Debt		43,335	42,754
Noncurrent portion of debt		39,724
Related Party Loan Payable [Member]
Debt		30,554	29,691
Noncurrent portion of debt
Loans Payable [Member]
Debt		22,588	$ 26,527
Noncurrent portion of debt		$ 10,808

[1] See Note 8, "Significant Agreements" for details regarding the Bill & Melinda Gates Foundation Investment, classified as mezzanine equity.

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Note 5 - Debt and Mezzanine Equity - Long-term Debt Instruments (Details) - USD ($) $ in Thousands		Mar. 31, 2017	Dec. 31, 2016
2017 (remaining nine months)		$ 65,895
Debt Future Minimum Payments Due in Two Years		74,681
2019		133,546
2020		5,156
2021		29,939
Thereafter		1,442
Total future minimum payments(1)	[1]	310,659
Less: amount representing interest(2)	[2]	(89,721)
Present value of minimum debt payments		220,938
Less: current portion		(49,455)
Noncurrent portion of debt		171,483	$ 167,888
Related Party Convertible Notes [Member]
2017 (remaining nine months)		4,537
Debt Future Minimum Payments Due in Two Years		16,290
2019		34,913
2020
2021
Thereafter
Total future minimum payments(1)	[1]	55,740
Less: amount representing interest(2)	[2]	(12,405)
Present value of minimum debt payments		43,335
Less: current portion		(3,611)
Noncurrent portion of debt		39,724
Convertible Debt [Member]
2017 (remaining nine months)		12,677
Debt Future Minimum Payments Due in Two Years		21,803
2019		93,287
2020
2021
Thereafter
Total future minimum payments(1)	[1]	127,767
Less: amount representing interest(2)	[2]	(52,549)
Present value of minimum debt payments		75,218
Less: current portion		(2,288)
Noncurrent portion of debt		72,930
Loans Payable [Member]
2017 (remaining nine months)		11,899
Debt Future Minimum Payments Due in Two Years		2,878
2019		2,766
2020		2,656
2021		2,543
Thereafter		1,442
Total future minimum payments(1)	[1]	24,184
Less: amount representing interest(2)	[2]	(1,596)
Present value of minimum debt payments		22,588
Less: current portion		(11,780)
Noncurrent portion of debt		10,808
Related Party Loan Payable [Member]
2017 (remaining nine months)		31,511
Debt Future Minimum Payments Due in Two Years
2019
2020
2021
Thereafter
Total future minimum payments(1)	[1]	31,511
Less: amount representing interest(2)	[2]	(957)
Present value of minimum debt payments		30,554
Less: current portion		(30,554)
Noncurrent portion of debt
Credit Facility [Member]
2017 (remaining nine months)		5,271
Debt Future Minimum Payments Due in Two Years		33,710
2019		2,580
2020		2,500
2021		27,396
Thereafter
Total future minimum payments(1)	[1]	71,457
Less: amount representing interest(2)	[2]	(22,214)
Present value of minimum debt payments		49,243
Less: current portion		(1,222)
Noncurrent portion of debt		$ 48,021

[1] Including $11.8 million in 2017 related to Nomis Bay convertible note which , at the Company's election, may be settled in shares or cash, be settled in shares and $46.8 million in 2018 and 2019 subject to Maturity Treatment Agreement, which will be converted to common stock at maturity, subject to there being no default under the terms of the debt.

[2] Including debt discount and issuance cost of $42.5 million associated with the related party and non-related party debt which will be accreted to interest expense under the effective interest method over the term of the debt.

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Note 6 - Commitments and Contingencies (Details Textual) BRL in Millions	1 Months Ended	3 Months Ended
	Dec. 31, 2011 BRL	Mar. 31, 2017 USD ($)	Mar. 31, 2017 BRL	Mar. 31, 2016 USD ($)	Dec. 31, 2016 USD ($)	Dec. 31, 2013 USD ($)	Nov. 30, 2010
Operating Leases, Rent Expense		$ 1,300,000		$ 1,300,000
Long-term Debt		220,938,000			$ 227,043,000
Purchase Obligation		3,700,000			800,000
Contractual Obligation		0			600,000
Liabilities for Guarantees on Long-Duration Contracts, Guaranteed Benefit Liability, Net		0			$ 0
Nossa Caixa and Banco Pine Agreements [Member]
Collateral Provided by Company Certain Equipment and Other Tangible Assets, Amount		21,500,000	BRL 68.0
Related Party Convertible Notes [Member] | Unsecured Debt [Member]
Debt Instrument, Face Amount						$ 69,000,000
Debt Instrument, Interest Rate, Stated Percentage						1.50%
Related Party Convertible Notes [Member] | Secured Debt [Member]
Debt Instrument, Face Amount						$ 10,850,000
Purchase Obligation, Due in Second Year						$ 10,850,000
Replacement Notes [Member]
Long-term Debt				$ 3,700,000
Manufacturing Agreement, Aprinnova JV [Member]
Contractual Obligation		10,000,000
FINEP Credit Facility [Member]
Debt Instrument, Interest Rate, Stated Percentage							5.00%
FINEP Credit Facility [Member] | Chattel Mortgage [Member]
Research and Development Asset Acquired Other than Through Business Combination, Fair Value Acquired		1,900,000	6.0
BNDES Credit Facility [Member]
Collateral Provided by Company Certain Equipment and Other Tangible Assets, Amount	BRL 24.9	7,900,000
Debt Instrument, Interest Rate, Stated Percentage	7.00%
BNDES Credit Facility [Member] | BNDES [Member]
Collateral Provided by Company Certain Equipment and Other Tangible Assets, Amount		$ 7,900,000	BRL 24.9

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Note 6 - Commitments and Contingencies - Future Minimum Payments for Lease Obligations (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Capital leases 2017 (remaining nine months)	$ 734
Operating leases 2017 (remaining nine months)	5,194
Total lease obligations 2017 (remaining nine months)	5,928
Capital leases 2018	106
Operating leases 2018	6,909
Total lease obligations 2018	7,015
Capital leases 2019	9
Operating leases 2019	6,782
Total lease obligations 2019	6,791
Capital leases 2020	0
Operating leases 2020	7,012
Total lease obligations 2020	7,012
Capital leases 2021	0
Operating leases 2021	7,248
Total lease obligations 2021	7,248
Capital leases thereafter	0
Operating leases thereafter	10,993
Total lease obligations thereafter	10,993
Total future minimum capital lease payments	849
Total future minimum operating lease payments	44,138
Total future minimum lease payments	44,987
Less: amount representing interest	(39)
Present value of minimum lease payments	810
Less: current portion	(405)	$ (922)
Capital lease obligation, net of current portion	$ 405	$ 334

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Note 7 - Joint Ventures and Noncontrolling Interest (Details Textual)					1 Months Ended									3 Months Ended			12 Months Ended
	Dec. 19, 2016 USD ($)	Dec. 05, 2016 USD ($)	Feb. 12, 2016 USD ($)	Feb. 12, 2016 EUR (€)	Dec. 31, 2016 USD ($) shares	Dec. 31, 2016 BRL shares	Nov. 30, 2016 USD ($) shares	Feb. 29, 2016 USD ($)	Nov. 30, 2014 USD ($)	Oct. 31, 2014 USD ($)	Sep. 30, 2014 USD ($)	Apr. 30, 2014 USD ($)	Feb. 28, 2014	Mar. 31, 2017 USD ($)	Mar. 31, 2016 USD ($)	Mar. 31, 2013 USD ($)	Dec. 31, 2016 USD ($)	Mar. 31, 2017 EUR (€)	Dec. 31, 2016 BRL	Jul. 19, 2016 USD ($)	Dec. 31, 2015 USD ($)	Oct. 14, 2015 USD ($)	May 31, 2015 USD ($)	Dec. 31, 2013 USD ($)
Operating Leases, Rent Expense														$ 1,300,000	$ 1,300,000
Total [Member]
Extinguishment of Debt, Amount | €				€ 50,000
Unsecured Senior Convertible Promissory Notes [Member] | Total [Member]
Debt Instrument, Face Amount																								$ 69,000,000
Unsecured Senior Convertible Promissory Notes [Member] | Total [Member]
Extinguishment of Debt, Amount			$ 1,300,000
Convertible Senior Notes, 9.5% [Member]
Debt Instrument, Repurchase Amount			$ 3,700,000												$ 3,700,000
Debt Instrument, Face Amount																						$ 57,600,000
Nikko Note [Member] | Nikko [Member]
Debt Instrument, Face Amount	$ 3,900,000				$ 3,900,000												$ 3,900,000
Novvi LLC [Member]
Equity Method Investment, Ownership Percentage								50.00%								50.00%
Initial Term of Joint Venture																20 years
IP License, Value																$ 10,000,000
Equity Method Investments					$ 0											$ 0	$ 0				$ 0
Joint Venture, Additional Membership Units Purchased, Aggregate Purchase Price								$ 600,000
Investments in and Advance to Affiliates, Subsidiaries, Associates, and Joint Ventures												$ 2,100,000
Loan Granted to Joint Venture									$ 1,900,000		$ 3,700,000										$ 1,600,000		$ 1,100,000
Loan Granted to Joint Venture, Stated Annual Interest Rate											0.36%
Loan to Joint Venture, Percentage Provided by Each the Company and the Partner									50.00%		50.00%
Loan Granted to Joint Venture, Amount Disbursed by Company									$ 1,000,000		$ 1,800,000
Loan Granted to Joint Venture, Amount of First Installment Paid by Company											$ 1,200,000
Loan Granted to Joint Venture, Amount of Second Installment Paid by Company										$ 600,000
Novvi S.A. [Member]
Joint Venture, Additional Membership Units Purchased, Aggregate Purchase Price												$ 200,000
JVCO Joint Venture [Member]
Equity Method Investment, Ownership Percentage			25.00%											25.00%	25.00%			25.00%
Capitalization, Long-term Debt and Equity														$ 100,000				€ 100,000
JVCO Joint Venture [Member] | Total [Member]
Equity Method Investment, Ownership Percentage Exchanged for Cancellation of Debt			25.00%
Equity Method Investment, Ownership Percentage by Counterparty			75.00%												75.00%
SMA Industria Quimica S.A. [Member]
Equity Method Investment, Ownership Percentage					100.00%								50.00%				100.00%		100.00%
Initial Term of Joint Venture														20 years
Operation Commencement Timeline Requirement, Extension													1 year 180 days
Share Purchase and Sale Agreement Purchase Price of Shares					$ 15,780	BRL 50,000
Share Purchase and Sale Agreement, Number of Shares Purchased | shares					50,000	50,000
Operating Leases, Rent Expense						BRL 9,853											$ 3,110
SMA Industria Quimica S.A. [Member] | SMSA [Member]
Due from Joint Ventures					$ 19,500,000												$ 19,500,000		BRL 61,800,000
Glycotech and Salisbury [Member]
Joint Venture, Additional Membership Units Purchased, Aggregate Purchase Price		$ 4,350,000
Joint Venture, Aggregate Purchase Price, Promissory Note Consideration		$ 3,500,000
Neossance JV [Member]
Loan Granted to Joint Venture	$ 500,000
Cosan [Member] | Novvi LLC [Member]
Equity Method Investment, Ownership Percentage																50.00%
Obligation to Fund Agreement, Cash Portion																$ 10,000,000
Joint Venture, Additional Membership Units Purchased, Aggregate Purchase Price								$ 600,000
Loan to Joint Venture, Percentage Provided by Each the Company and the Partner					50.00%												50.00%		50.00%				50.00%
American Refining Group [Member] | Novvi LLC [Member]
Obligation to Fund Agreement, Cash Portion					$ 10,000,000												$ 10,000,000			$ 10,000,000
Chevron U.S.A. [Member] | Novvi LLC [Member]
Obligation to Fund Agreement, Cash Portion							$ 1,000,000
Joint Venture, Membership Units | shares							20,000
Joint Venture, Ownership Stake							3.00%
Joint Venture, Additional Ownership Stake							25.00%
Nikko [Member] | Neossance JV [Member]
Equity Method Investment, Ownership Percentage	50.00%
Loan Granted to Joint Venture	$ 1,500,000
Cash Investment Joint Venture	10,000,000
Joint Venture, Maximum Distributions	$ 10,000,000

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Note 7 - Joint Ventures and Noncontrolling Interest - Variable Interest Entities (Details) - Variable Interest Entity, Primary Beneficiary [Member] - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Assets	$ 2,306	$ 2,277
Liabilities	$ 158	$ 135

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Note 7 - Joint Ventures and Noncontrolling Interest - Noncontrolling Interest (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Balance, noncontrolling interest	$ 937
Balance, noncontrolling interest	937
Noncontrolling Interest [Member]
Balance, noncontrolling interest	937	$ 391
Acquisition of noncontrolling interest	0	(277)
Balance, noncontrolling interest	$ 937	$ 114

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Note 8 - Significant Agreements (Details Textual) $ / shares in Units, shares in Millions										1 Months Ended								3 Months Ended		6 Months Ended	9 Months Ended	12 Months Ended
	Jan. 15, 2018 USD ($)	Jan. 15, 2017 USD ($)	Dec. 29, 2016 USD ($)	Nov. 30, 2016 USD ($)	Sep. 30, 2016	Jul. 25, 2016 USD ($)	Jun. 30, 2016 USD ($) $ / shares shares	Mar. 08, 2016 USD ($)	Apr. 30, 2014 USD ($)	Dec. 31, 2016 USD ($)	Jun. 30, 2016 USD ($) $ / shares shares	Apr. 30, 2016	Sep. 30, 2015 USD ($)	Mar. 31, 2015 USD ($)	Mar. 31, 2014 USD ($)	Mar. 31, 2013 USD ($)	Feb. 28, 2011	Mar. 31, 2017 USD ($) $ / shares	Mar. 31, 2016 USD ($) $ / shares	Mar. 31, 2017 USD ($) $ / shares	Mar. 31, 2017 USD ($) $ / shares	Dec. 31, 2016 USD ($)	Aug. 06, 2016 $ / shares shares
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares																		$ 0.01	$ 10.67	$ 0.01	$ 0.01
At the Market Offering [Member]
Common Stock, Value, Subscriptions								$ 50,000,000										$ 50,000,000		$ 50,000,000	$ 50,000,000
Commission Rate								3.00%
Stock Issued During Period, Value, New Issues																		0
Technology Investment Agreement with DARPA [Member]
Collaboration Agreement Period													4 years
Revenue from Related Parties																		1,000,000	$ 400,000
Maximum DARPA Funding to be Received if all Milestones are Achieved													$ 35,000,000
Collective Obligation Due													$ 15,500,000
Firmenich [Member]
Additional Grants and Collaboration Funding																		5,000,000
Firmenich [Member] | Collaborative Arrangement [Member]
Revenue from Related Parties																		1,100,000	3,000,000
Firmenich [Member] | Flavors and Fragrances Compounds [Member]
Collaboration Agreement Period																10 years
Collaboration Agreement, Automatic Renewal Period																3 years
Collaborative Agreement, Notice Requirement before Terminating Current Term, Minimum																12 years
Collaboration Agreement Annual Funding Year One																$ 10,000,000
Collaboration Agreement Annual Funding Year Three														$ 10,000,000
Collaboration Agreement Annual Funding Year Two															$ 10,000,000
Firmenich [Member] | Flavors and Fragrances Compounds [Member] | Master Collaboration Agreement [Member]
Revenue from Related Parties																		1,200,000	2,000,000
Sales Margin Company Percentage Split																30.00%
Return Required for Collaboration Partner Before Adjusting Split on Sales Margin																$ 15,000,000
Sales Margin Company Percentage Split Following Return Requirements																50.00%
Success Bonus																$ 2,500,000
Sales Margin Collaborator Percentage Split																70.00%
Sales Margin Collaborator Percentage Split Following Return Requirements																30.00%
Firmenich [Member] | Flavors and Fragrances Compounds [Member] | Amended Collaboration Agreement [Member]
Royalty Rate, Percent of Net Revenue										10.00%
Kuraray [Member] | Collaborative Arrangement [Member]
Collaboration Agreement Period															2 years
Revenue from Related Parties																		100,000	400,000
Proceeds from Collaborators		$ 500,000							$ 2,000,000					$ 2,000,000	$ 4,000,000
Collaborative Agreement Number Of Installments				2											2
Deferred Revenue				$ 1,000,000
Kuraray [Member] | Collaborative Arrangement [Member] | Scenario, Forecast [Member]
Proceeds from Collaborators	$ 500,000
Kuraray [Member] | Product Sales [Member]
Revenue from Related Parties																		1,600,000	0
Nenter & Co., Inc. [Member] | Supply Agreements [Member]
Revenue from Related Parties																		2,300,000
Supply Agreement, Renewable Terms												5 years
Givaudan International, SA [Member] | Collaborative Arrangement [Member]
Collaboration Agreement Period																	5 years
Collaboration Agreement, Automatic Renewal Period																	2 years
Revenue from Related Parties																		1,500,000
Collaboration Agreement, Maxium Number of Extension Renewals																	3
Semi Annual Installments, Amount											$ 3,000,000
Givaudan International, SA [Member] | Collaborative Arrangement [Member] | Deferred Revenue [Member]
Proceeds from Collaborators			$ 3,000,000				$ 3,000,000
Givaudan International, SA [Member] | Collaborative Arrangement [Member] | Scenario, Forecast [Member]
Proceeds from Collaborators											12,000,000
Givaudan International, SA [Member] | Supply Agreements [Member]
Revenue from Related Parties																		600,000	$ 0
Ginkgo Bioworks [Member]
Collaboration Agreement Period					3 years
Collaboration Agreement, Automatic Renewal Period					1 year
Collaborative Agreement, Notice Requirement before Terminating Current Term, Minimum					90 days
Proceeds from Collaborators						$ 15,000,000					$ 20,000,000
Royalty Percentage							10.00%				10.00%
Collaboration Agreement, Common Stock Options Agreed to Issue | shares							5				5
Collaboration Agreement, Common Stock Options Agreed to Issue, Exercise Price Per Share | $ / shares							$ 0.50				$ 0.50
Collaboration Agreement, Common Stock Options Agreed to Issue, Term Exercisable from Date of Issuance											1 year
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares																							5
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares																							$ 0.50
Collaborative Agreement, Notice Requirement before Terminating Current Term Due to Lack of Commitment					30 days
Ginkgo Bioworks [Member] | Scenario, Forecast [Member]
Proceeds from Collaborators																		5,000,000		5,000,000
Collaborative Agreement Number Of Installments																					2
Ginkgo Bioworks [Member] | Ginkgo Collaboration Agreement [Member]
Revenue from Related Parties																						$ 0
Due to Related Parties										$ 1,600,000								$ 3,000,000		$ 3,000,000	$ 3,000,000	$ 1,600,000
Blue California [Member] | Intellectual Property License and Strain Access Agreement [Member]
Revenue from Related Parties										$ 10,000,000

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Note 9 - Goodwill and Intangible Assets (Details Textual) $ in Millions	1 Months Ended
	Oct. 31, 2011 USD ($)
Draths Corporation [Member] | In Process Research and Development, Indefinite [Member]
Indefinite-lived Intangible Assets Acquired	$ 8.6

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Note 9 - Goodwill and Intangible Assets - Intangible Assets and Goodwill (Details) - USD ($) $ in Thousands	3 Months Ended	12 Months Ended
	Mar. 31, 2017	Dec. 31, 2016
Goodwill, carrying amount	$ 560	$ 560
Goodwill, net carrying value	560	560
Goodwill and intangible assets, gross	9,892	9,892
Intangible assets impairment and accumulated amortization	(9,332)	(9,332)
Goodwill and intangible assets, net	560	560
Acquired Licenses and Permits [Member]
Intangible assets, gross	$ 772	772
Acquired licenses and permits, useful life (Year)	2 years
Accumulated amortization of intangible assets	$ (772)	(772)
In Process Research and Development, Indefinite [Member]
Intangible assets, gross	8,560	8,560
Impairment of intangible assets	(8,560)	(8,560)
Intangible assets, net

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Note 10 - Stockholders' Deficit (Details Textual) - $ / shares	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Class of Warrant or Right, Outstanding	14,663,411	7,328,069
Class of Warrant or Right, Exercise Price of Warrants or Rights	$ 0.01	$ 10.67
Class of Warrant or Right, Term	5 years 36 days

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Note 11 - Stock-based Compensation (Details Textual) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period, Intrinsic Value	$ 0	$ 0
Employee Stock Option [Member]
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized	$ 3,700
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized, Period for Recognition	2 years 259 days
Restricted Stock Units (RSUs) [Member]
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized	$ 4,700
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized, Period for Recognition	2 years 211 days

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Note 11 - Stock-based Compensation - Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended	12 Months Ended
	Mar. 31, 2017	Dec. 31, 2016	Mar. 31, 2017
Outstanding (in shares)	13,487,685
Outstanding, weighted average exercise price (in dollars per share)	$ 3.63
Outstanding, weighted average remaining contractual life (Year)	6 years 302 days	6 years 255 days
Outstanding, aggregate intrinsic value	$ 443
Options granted (in shares)	726,000
Options granted, weighted average exercise price (in dollars per share)	$ 0.58
Options exercised (in shares)	(500)
Options exercised, weighted average exercise price (in dollars per share)	$ 0.28
Options cancelled (in shares)	(695,912)
Options cancelled, weighted average exercise price (in dollars per share)	$ 1.82
Outstanding (in shares)	13,517,273	13,487,685
Outstanding, weighted average exercise price (in dollars per share)	$ 3.55	$ 3.63
Outstanding, aggregate intrinsic value	$ 443	$ 443	$ 44
Vested and expected to vest after March 31, 2017 (in shares)			12,347,493
Vested and expected to vest after December 31, 2016, weighted average exercise price (in dollars per share)			$ 3.79
Vested and expected to vest after December 31, 2016, weighted average remaining contractual life (Year)	6 years 229 days
Vested and expected to vest after December 31, 2016, aggregate intrinsic value			$ 38
Exercisable at March 31, 2017 (in shares)			7,478,686
Options Exercisable Weighted-Average Exercise Price (in dollars per share)			$ 5.42
Exercisable at December 31, 2016, weighted average remaining contractual life (Year)	5 years 102 days
Exercisable at December 31, 2016, aggregate intrinsic value			$ 1

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Note 11 - Stock-based Compensation - Temporal Display of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity (Details) - Restricted Stock Units (RSUs) [Member] - $ / shares	3 Months Ended	12 Months Ended
	Mar. 31, 2017	Dec. 31, 2016
Outstanding, RSUs (in shares)	6,997,084
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 1.18
Outstanding, weighted average remaining contractual life (Year)	1 year 142 days	1 year 160 days
Awarded (in shares)	825,980
Awarded (in dollars per share)	$ 0.59
Vested (in shares)	(348,699)
Vested (in dollars per share)	$ 1.28
Forfeited (in shares)	(250,329)
Forfeited (in dollars per share)	$ 1.03
Outstanding, RSUs (in shares)	7,224,036	6,997,084
Outstanding, weighted average grant-date fair value (in dollars per share)	$ 1.11	$ 1.18
Expected to vest after March 31, 2017 (in shares)	5,735,089
Expected to vest after December 31, 2016, weighted average grant-date fair value (in dollars per share)	$ 1.15
Expected to vest after December 31, 2016, weighted average remaining contractual life (Year)	1 year 62 days

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Note 11 - Share-based Compensation - Shares Authorized Under Stock Option Plans, by Exercise Price Range (Details)	3 Months Ended
	Mar. 31, 2017 $ / shares shares
Exercise Price, Lower (in dollars per share)	$ 0.28
Exercise Price, Upper (in dollars per share)	$ 30.17
Options Outstanding Number (in shares) | shares	13,517,273
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	6 years 302 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 3.55
Options Exercisable Number Options (in shares) | shares	7,478,686
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 5.42
Exercise Price Range 1 [Member]
Exercise Price, Lower (in dollars per share)	0.28
Exercise Price, Upper (in dollars per share)	$ 0.58
Options Outstanding Number (in shares) | shares	795,734
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	9 years 175 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 0.49
Options Exercisable Number Options (in shares) | shares	2,234
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 0.28
Exercise Price Range 2 [Member]
Exercise Price, Lower (in dollars per share)	0.59
Exercise Price, Upper (in dollars per share)	$ 0.59
Options Outstanding Number (in shares) | shares	2,224,375
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	9 years 47 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 0.59
Options Exercisable Number Options (in shares) | shares
Options Exercisable Weighted-Average Exercise Price (in dollars per share)
Exercise Price Range 3 [Member]
Exercise Price, Lower (in dollars per share)	0.69
Exercise Price, Upper (in dollars per share)	$ 1.63
Options Outstanding Number (in shares) | shares	1,491,082
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	8 years 244 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 1.30
Options Exercisable Number Options (in shares) | shares	361,067
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 1.60
Exercise Price Range 4 [Member]
Exercise Price, Lower (in dollars per share)	1.64
Exercise Price, Upper (in dollars per share)	$ 1.96
Options Outstanding Number (in shares) | shares	2,192,975
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	7 years 186 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 1.84
Options Exercisable Number Options (in shares) | shares	1,026,492
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 1.83
Exercise Price Range 5 [Member]
Exercise Price, Lower (in dollars per share)	1.98
Exercise Price, Upper (in dollars per share)	$ 2.87
Options Outstanding Number (in shares) | shares	1,780,408
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	6 years 25 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 2.69
Options Exercisable Number Options (in shares) | shares	1,579,154
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 2.73
Exercise Price Range 6 [Member]
Exercise Price, Lower (in dollars per share)	2.96
Exercise Price, Upper (in dollars per share)	$ 3.44
Options Outstanding Number (in shares) | shares	688,795
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	6 years 146 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 3.15
Options Exercisable Number Options (in shares) | shares	597,154
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 3.13
Exercise Price Range 7 [Member]
Exercise Price, Lower (in dollars per share)	3.51
Exercise Price, Upper (in dollars per share)	$ 3.51
Options Outstanding Number (in shares) | shares	1,447,979
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	6 years 328 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 3.51
Options Exercisable Number Options (in shares) | shares	1,057,049
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 3.51
Exercise Price Range 8 [Member]
Exercise Price, Lower (in dollars per share)	3.55
Exercise Price, Upper (in dollars per share)	$ 4.31
Options Outstanding Number (in shares) | shares	1,723,976
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	3 years 113 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 3.97
Options Exercisable Number Options (in shares) | shares	1,683,443
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 3.98
Exercise Price Range 9 [Member]
Exercise Price, Lower (in dollars per share)	4.35
Exercise Price, Upper (in dollars per share)	$ 26.84
Options Outstanding Number (in shares) | shares	1,111,949
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	3 years 189 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 17.71
Options Exercisable Number Options (in shares) | shares	1,111,949
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 17.71
Exercise Price Range 10 [Member]
Exercise Price, Lower (in dollars per share)	30.17
Exercise Price, Upper (in dollars per share)	$ 30.17
Options Outstanding Number (in shares) | shares	60,000
Options Outstanding Weighted- Average Remaining Contractual Life (Year)	3 years 350 days
Options Outstanding Weighted-Average Exercise Price (in dollars per share)	$ 30.17
Options Exercisable Number Options (in shares) | shares	60,000
Options Exercisable Weighted-Average Exercise Price (in dollars per share)	$ 30.17

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Note 11 - Stock-based Compensation - Employee Service Share-based Compensation, Allocation of Recognized Period Costs (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Allocated share-based compensation expense	$ 1,646	$ 2,051
Research and Development Expense [Member]
Allocated share-based compensation expense	484	491
Selling, General and Administrative Expenses [Member]
Allocated share-based compensation expense	$ 1,162	$ 1,560

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Note 11 - Stock-based Compensation - Share-based Payment Award, Stock Options, Valuation Assumptions (Details) - Employee Stock Option [Member]	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Risk-free interest rate	2.10%	1.40%
Expected term (in years) (Year)	6 years 54 days	6 years 83 days
Expected volatility	80.00%	73.00%

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Note 12 - Employee Benefit Plan (Details Textual) - USD ($) $ in Millions	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Defined Contribution Plan, Maximum Annual Contributions Per Employee, Percent	90.00%
Defined Contribution Plan, Employer Matching Contribution, Percent of Employees' Gross Pay	90.00%
Defined Contribution Plan, Minimum Service, Vesting Period	1 year
Defined Contribution Plan, Employer Discretionary Contribution Amount	$ 0.1	$ 0.1

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Note 13 - Related Party Transactions (Details Textual) - USD ($)	1 Months Ended		3 Months Ended
	Jul. 31, 2015	May 31, 2014	Mar. 31, 2017	Mar. 31, 2016	Mar. 31, 2015	Dec. 31, 2016
Debt Instrument, Unamortized Discount			$ 42,000,000
Accounts Receivable, Related Parties			416,000			$ 872,000
Related Party Convertible Notes [Member]
Convertible Debt			73,900,000			72,400,000
Debt Instrument, Unamortized Discount			6,000,000			6,700,000
Derivative Liability			1,400,000			800,000
Derivative, Gain (Loss) on Derivative, Net			1,100,000	$ 4,500,000
Total [Member]
Convertible Debt	$ 5,000,000
Accounts Receivable, Related Parties			300,000			800,000
Revenue from Related Parties			0	0
Total [Member] | Pilot Plant Agreements [Member]
Related Party Agreement Term		5 years
Related Party Transaction, Amounts of Transaction	28,000,000
Related Party Transaction, Fees Waived	$ 2,000,000
Due to Related Parties			1,700,000			$ 2,200,000
Total [Member] | Pilot Plant Agreements [Member] | Sublease Agreement [Member]
Related Party Transaction, Amounts of Transaction				$ 0	$ 200,000
Proceeds from Fees Received			$ 1,700,000
Total [Member] | Pilot Plant Agreements [Member] | Scale-up Services and Training [Member]
Related Party Transaction, Amounts of Transaction		$ 900,000

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Note 14 - Income Taxes (Details Textual) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Income Tax Expense (Benefit)	$ (41)	$ 115

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Note 15 - Reporting Segments (Details Textual)	3 Months Ended
	Mar. 31, 2017
Segment Reporting, Number Of Business Activities	1
Number of Operating Segments	1
Number of Reporting Units	1

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Note 15 - Reporting Segments - Revenues by Geography (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Revenues	$ 12,980	$ 8,811
Europe [Member]
Revenues	5,376	4,372
UNITED STATES
Revenues	3,096	3,462
Asia [Member]
Revenues	4,433	590
BRAZIL
Revenues	19	375
Other Area [Member]
Revenues	$ 56	$ 12

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Note 15 - Reporting Segments - Long-lived Assets by Geography (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Long-Lived Assets	$ 53,045	$ 53,735
BRAZIL
Long-Lived Assets	39,137	44,153
UNITED STATES
Long-Lived Assets	13,683	9,342
Europe [Member]
Long-Lived Assets	$ 225	$ 240

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Note 16 - Comprehensive Loss - Accumulated Other Comprehensive Income (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Foreign currency translation adjustment, net of tax	$ (40,581)	$ (40,904)
Total accumulated other comprehensive loss	$ (40,581)	$ (40,904)

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Note 17 - Net Loss Attributable to Common Stockholders and Net Loss Per Share - Calculation of Basic and Diluted Net Loss Per Share of Common Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Net loss attributable to Amyris, Inc. common stockholders	$ (37,371)	$ (15,308)
Interest on convertible debt		1,817
Accretion of debt discount		1,633
Gain from change in fair value of derivative instruments		(18,415)
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$ (37,371)	$ (30,273)
Basic (in shares)	290,039,216	207,199,563
Basic and diluted loss per share (in dollars per share)	$ (0.13)	$ (0.07)
Convertible promissory notes (in shares)		53,732,522
Weighted common stock equivalents (in shares)		53,732,522
Diluted weighted-average common shares (in shares)	290,039,216	260,932.09
Diluted (in dollars per share)	$ (0.13)	$ (0.12)

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Note 17 - Net Loss Attributable to Common Stockholders and Net Loss Per Share - Antidilutive Securities Excluded From Computation of Earnings Per Share (Details) - shares		3 Months Ended
		Mar. 31, 2017	Mar. 31, 2016
Antidilutive securities (in shares)		98,588,504	122,869,085
Stock Options to Purchase Common Stock [Member]
Antidilutive securities (in shares)		13,517,273	12,159,154
Convertible Promissory Notes [Member]
Antidilutive securities (in shares)	[1]	72,826,108	99,648,739
Common Stock Subject to Repurchase [Member]
Antidilutive securities (in shares)		5,021,087	5,885,762
Restricted Stock Units (RSUs) [Member]
Antidilutive securities (in shares)		7,224,036	5,175,430

[1] The potentially dilutive effect of convertible promissory notes was computed based on conversion ratios in effect as of the respective period end dates. A portion of the convertible promissory notes issued carries a provision for a reduction in conversion price under certain circumstances, which could potentially increase the dilutive shares outstanding. Another portion of the convertible promissory notes issued carries a provision for an increase in the conversion rate under certain circumstances, which could also potentially increase the dilutive shares outstanding.

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Note 18 - Subsequent Events (Details Textual)							2 Months Ended
	May 23, 2017	May 11, 2017 USD ($) $ / shares shares	May 08, 2017 USD ($) $ / shares shares	Apr. 30, 2017	Apr. 21, 2017 shares	Apr. 13, 2017 USD ($) $ / shares shares	Jun. 22, 2017 USD ($)	Dec. 31, 2017 USD ($)	May 02, 2017	May 01, 2017	Apr. 17, 2017 USD ($)	Mar. 31, 2017 USD ($) $ / shares	Dec. 31, 2016 USD ($) $ / shares	Mar. 31, 2016 $ / shares
Preferred Stock, Par or Stated Value Per Share | $ / shares												$ 0.0001	$ 0.0001
Common Stock, Par or Stated Value Per Share | $ / shares												0.0001	$ 0.0001
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares												$ 0.01		$ 10.67
Long-term Debt												$ 220,938,000	$ 227,043,000
Blue California [Member] | Intellectual Property License and Strain Access Agreement [Member]
Accounts Receivable, Gross													10,000,000
Scenario, Forecast [Member] | Reverse Stock Split [Member]
Stockholders' Equity Note, Stock Split, Conversion Ratio	15
Scenario, Forecast [Member] | Nenter & Co., Inc. [Member]
Loss on Contract Termination							$ 2,500,000
Convertible Debt [Member]
Long-term Debt												75,218,000	$ 78,981,000
Convertible Debt [Member] | Temasek [Member]
Long-term Debt												$ 10,000,000
Subsequent Event [Member]
Extinguishment of Debt, Amount		$ 40,200,000
Voting Agreement Aggregate Ownership Percentage				51.20%
Subsequent Event [Member] | Foris Ventures, LLC [Member]
Debt Conversion, Original Debt, Amount			$ 27,000,000
Subsequent Event [Member] | Naxyris S.A. [Member]
Debt Conversion, Original Debt, Amount			$ 2,000,000
Subsequent Event [Member] | Foris and Naxyris [Member] | Conversion of Common Stock Into Series C Preferred Stock [Member]
Conversion of Stock, Shares Converted | shares		20,920,578
Subsequent Event [Member] | May 2017 Offering Closing [Member]
Proceeds from Issuance or Sale of Equity		$ 44,500,000
Subsequent Event [Member] | May 2017 Warrants [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares			207,954,414
Subsequent Event [Member] | May 2017 Warrants, Warrant 1 [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares		103,977,207
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares		$ 0.52
Class of Warrant or Right, Common Stock Available for Conversion, Percentage		50.00%
Subsequent Event [Member] | May 2017 Warrants, Warrant 2 [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares		103,977,207
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares		$ 0.62
Class of Warrant or Right, Common Stock Available for Conversion, Percentage		50.00%
Subsequent Event [Member] | Dilution Warrants [Member]
Class of Warrant or Right, Exercise Price of Warrants or Rights | $ / shares		$ 0.0001
Preferred Stock Effective Conversion Price | $ / shares		$ 0.42
Subsequent Event [Member] | Series A Preferred Stock [Member]
Preferred Stock, Capital Shares Reserved for Future Issuance | shares			22,140
Preferred Stock, Dividend Rate, Percentage			17.38%
Preferred Stock, Par or Stated Value Per Share | $ / shares			$ 0.0001
Preferred Stock, Stated Value | $ / shares			1,000
Preferred Stock, Conversion Price Per Share to Common Stock | $ / shares			1.15
Preferred Stock, Anniversary Payment | $ / shares			$ 1,738
Subsequent Event [Member] | Series B Preferred Stock [Member]
Preferred Stock, Capital Shares Reserved for Future Issuance | shares			65,203.8756
Preferred Stock, Dividend Rate, Percentage			17.38%
Common Stock, Par or Stated Value Per Share | $ / shares			$ 0.0001
Subsequent Event [Member] | Series B Preferred Stock [Member] | Foris Ventures, LLC [Member]
Debt Conversion, Converted Instrument, Shares Issued | shares			30,728.589
Debt Conversion, Converted Instrument, Warrants or Options Issued | shares			73,160,764
Subsequent Event [Member] | Series B Preferred Stock [Member] | Naxyris S.A. [Member]
Debt Conversion, Converted Instrument, Shares Issued | shares			2,333.216
Debt Conversion, Converted Instrument, Warrants or Options Issued | shares			5,556,038
Subsequent Event [Member] | Series A Preferred Stock and Warrants [Member] | May 2017 Offering Closing [Member]
Proceeds from Issuance or Sale of Equity		$ 22,140,000
Subsequent Event [Member] | Series B Preferred Stock and Warrants [Member] | May 2017 Offering Closing [Member]
Proceeds from Issuance or Sale of Equity		$ 25,000,000
Subsequent Event [Member] | Series C Preferred Stock [Member]
Preferred Stock, Stated Value | $ / shares		$ 1,000
Subsequent Event [Member] | Series C Preferred Stock [Member] | Reverse Stock Split [Member]
Stockholders' Equity Note, Stock Split, Conversion Ratio			1
Subsequent Event [Member] | Series C Preferred Stock [Member] | Foris and Naxyris [Member] | Conversion of Common Stock Into Series C Preferred Stock [Member]
Conversion of Stock, Shares Issued | shares		20,920.578
Subsequent Event [Member] | Blue California [Member] | Intellectual Property License and Strain Access Agreement [Member] | SweeGen Common Stock [Member]
Shares Received in Satisfaction of Payment Obligation | shares					850,115
Subsequent Event [Member] | DSM International B.V. [Member]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights | shares		59,521,740
Proceeds from Issuance of Private Placement		$ 25,000,000
Ownership Percentage, Designated Director Threshold		4.50%
Sale of Stock, Percentage of Shares Available for Issuance		25.00%
Second Tranche Closing, Anniversary Payment		$ 5,000,000
Subsequent Event [Member] | DSM International B.V. [Member] | Series B Preferred Stock [Member]
Stock Issued During Period, Shares, New Issues | shares		25,000
Subsequent Event [Member] | Foris and Naxyris [Member] | Series C Preferred Stock [Member]
Preferred Stock, Par or Stated Value Per Share | $ / shares		$ 0.0001
Subsequent Event [Member] | Maximum [Member] | Series A Preferred Stock [Member]
Beneficiary Ownership, Conversion Percentage, Maximum			9.99%
Subsequent Event [Member] | Maximum [Member] | DSM International B.V. [Member]
Designated Holder Maximum Common Stock Ownership		33.00%
Reserved Second Tranche Securities		$ 30,000,000
Subsequent Event [Member] | Minimum [Member] | Series A Preferred Stock [Member]
Beneficiary Ownership, Conversion Percentage, Maximum			4.99%
Subsequent Event [Member] | Minimum [Member] | DSM International B.V. [Member]
Reserved Second Tranche Securities		$ 25,000,000
Ginkgo Collaboration Note [Member] | Subsequent Event [Member]
Debt Instrument, Face Amount						$ 3,000,000
Debt Instrument, Interest Rate, Stated Percentage						13.50%
The April 2017 Convertible Notes [Member] | Subsequent Event [Member] | Convertible Debt [Member]
Debt Instrument, Convertible, Conversion Price | $ / shares						$ 1.90
Debt Instrument, Redemption Price, Percentage						118.00%
Debt Instrument, Additional Common Stock Payment, Maximum Percent of Aggregate Amount						50.00%
Debt Instrument, Threshold Amount of Dollar-weighted Volume of Common Stock						$ 200,000
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage Except Under Specified Conditions						4.99%
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage Under Specified Conditions						9.99%
Convertible Debt, Beneficial Common Stock Ownership, Maximum Percentage, Conditions, Number of Days After Written Notice						61 days
Convertible Debt, Aggregate Number of Shares Issued With Respect to the Initial Closing, Maximum | shares						54,676,770
Convertible Debt, Aggregate Number of Shares Issued With Respect to the Initial Closing, Minimum | shares						49,233,710
Convertible Debt, Holder Limitations, Maximum Sale Price Per Share of Common Stock | $ / shares						$ 1.05
Convertible Debt, Holders May Not Sell Shares, Price Floor, Threshold | $ / shares						$ 1
The April 2017 Convertible Notes [Member] | Subsequent Event [Member] | Convertible Debt [Member] | Maximum [Member]
Debt Instrument, Face Amount						$ 15,000,000
The April 2017 Convertible Notes, Initial Closing [Member] | Subsequent Event [Member] | Convertible Debt [Member]
Debt Instrument, Face Amount											$ 7,000,000
The April 2017 Convertible Notes, Second Closing [Member] | Convertible Debt [Member] | Scenario, Forecast [Member]
Debt Instrument, Face Amount								$ 8,000,000
The Amended Notes [Member] | Subsequent Event [Member]
Convertible Debt Securities, Monthly Installment Discount									20.00%	10.00%
Convertible Debt Securities, Price Floor Payment Discount Rate									70.00%	80.00%
March 2014 Letter Agreement [Member] | Subsequent Event [Member]
Debt Conversion, Original Debt, Amount			$ 3,400,000
Conversion of All Outstanding Fidelity Notes for Aggregate Principal Amount of 2015 144A Notes [Member] | Subsequent Event [Member]
Debt Conversion, Original Debt, Amount			$ 3,700,000