Document:

Amyris2014-Q210-QEx0401A-RLetterAgreementreTrancheInvestorRegRights20140508

	
			
	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.

May 8, 2014
Amended and Restated Letter Agreement

To the Purchasers Listed
On Schedule A hereto

Dear Purchasers:
In connection with that certain Securities Purchase Agreement, dated as of August 8, 2013, as amended by that Amendment No. 1 to Securities Purchase Agreement dated as of October 16, 2013 and as further amended by that Amendment No. 2 to Securities Purchase Agreement and Tranche I Note Amendment Agreement of even date herewith (as amended, the “Purchase Agreement”), by and among Amyris, Inc., a Delaware corporation (the “Company”), and the purchasers listed on Schedule I thereto (each, a “Purchaser”, and collectively, the “Purchasers”) and that certain Amended and Restated Investors’ Rights Agreement dated as of June 21, 2010, as amended by (i) Amendment No. 1 to Amended and Restated Investors’ Rights Agreement, dated as of February 23, 2012, (ii) Amendment No. 2 to Amended and Restated Investors’ Rights Agreement, dated as of December 24, 2012, (iii) Amendment No. 3 to Amended and Restated Investors’ Rights Agreement, dated as of March 27, 2013, (iv) Amendment No. 4 to Amended and Restated Investors’ Rights Agreement, dated as of October 16, 2013 and (v) Amendment No. 5 to Amended and Restated Investors’ Rights Agreement, dated as of December 24, 2013 (as amended, the “Rights Agreement”), by and among the Company and certain of its stockholders party thereto, and because the Company and the Purchasers wish to amend and restate that certain Letter Agreement dated as of December 24, 2013 by and among the Company and the Purchasers (the “Original Letter Agreement”), the Company and the Purchasers are hereby entering into this amended and restated Letter Agreement (this “A&R Letter Agreement”).  Capitalized terms used herein but not otherwise defined shall have the meaning given to such terms in the Rights Agreement.
The Company and the undersigned Purchasers agree to the following:  
1.Definitions.  As used in this A&R Letter Agreement, the following terms shall have the following meanings:
(a)    “Effectiveness Period” means the earlier of (i) such time as all of the Registrable Securities covered by the Registration Statement have been publicly sold by the Purchasers or (ii) the date that all Registrable Securities covered by the Registration Statement may be sold by non-affiliates without volume or manner-of-sale restrictions pursuant to Rule 144, without the requirement for the Company to be in compliance with the current public information requirement under Rule 144 as determined by counsel to the Company pursuant to a written opinion letter to such effect, addressed and reasonably acceptable to the Company’s transfer agent.

(b)    “Prospectus” means the prospectus included in the Registration Statement (including, without limitation, a prospectus that includes any information previously omitted from a prospectus filed as part of an effective registration statement in reliance upon Rule 430A promulgated under the Act), as amended or supplemented by any prospectus supplement, with respect to the terms of the offering of any portion of the Registrable Securities covered by the Registration Statement, and all other amendments and supplements to the Prospectus, including post‐effective amendments, and all material incorporated by reference or deemed to be incorporated by reference in such Prospectus.
(c)    “Rule 144” means Rule 144 promulgated by the SEC pursuant to the Act, as such Rule may be amended from time to time, or any similar rule or regulation hereafter adopted by the SEC having substantially the same effect as such Rule.
(d)    “SEC Guidance” means (i) any publicly-available written or oral guidance, comments, requirements or requests of the SEC staff and (ii) the Act. 
2.    Registration.  The Company, upon receipt of a written request from any Purchaser (a “Registration Request”), hereby agrees that it will (i) within five days of receipt thereof, give written notice of such request to all other Purchasers, and (ii) file a registration statement (the “Registration Statement”) with the SEC covering all of the shares of the Company’s Common Stock that may become issuable upon conversion of the Tranche I Notes (as defined in the Purchase Agreement) and the Tranche II Notes (as defined in the Purchase Agreement) issued pursuant to the Purchase Agreement (such shares of Common Stock, the “Registrable Securities”) by no later than thirty (30) calendar days following the date of receipt of the Registration Request (the “Filing Deadline”); provided, however, that if the Filing Deadline falls on a Saturday, Sunday or other day that the SEC is closed for business, the Filing Deadline shall be extended to the next business day.  The Company shall 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 ninetieth (90th) day following the date of the Registration Request (or, in the event the SEC reviews and has written comments to the Registration Statement, the one hundred twentieth (120th) calendar day following the date of the Registration Request) (the “Effectiveness Deadline”); provided, however, that if the Effectiveness Deadline falls on a Saturday, Sunday or other day that the SEC is closed for business, the Effectiveness Deadline shall be extended to the next business day.  
3.    Applicable Provisions.  The provisions of Sections 1.4, 1.5, 1.6, 1.9 and 1.10 of the Rights Agreement are hereby incorporated by reference, mutatis mutandis, and shall be deemed to be a part hereof as if restated herein in their entirety; provided, however, that for purposes of this A&R Letter Agreement the references in Section 1.4(a) of the Rights Agreement to “one hundred twenty (120) days” and “120-day period” shall be deemed to be “one hundred eighty (180) days” and “180-day period,” respectively.
4.    Representations.  The Company hereby represents and warrants to each of the Purchasers that this A&R Letter Agreement and the Rights Agreement are the only agreements pursuant to which registration rights exist in respect of the Registrable Securities.

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5.    Liquidated Damages.  If: (i) following the receipt by the Company of a Registration Request, the Registration Statement is not filed with the SEC on or prior to the Filing Deadline, (ii) following the receipt by the Company of a Registration Request, the Registration Statement is not declared effective by the SEC (or otherwise does not become effective) for any reason on or prior to the later of (x) the Effectiveness Deadline or (y) if SEC Guidance prohibits the Registration Statement from being declared effective until such time as the Company’s definitive proxy statement for the 2014 annual stockholder meeting has been filed, the date immediately following such filing and upon which SEC Guidance permits the Registration Statement to be declared effective, (iii) after the effective date of the Registration Statement (following the receipt by the Company of a Registration Request), (A) the Registration Statement ceases for any reason (including without limitation by reason of a stop order, or the Company’s failure to update the Registration Statement), to remain continuously effective as to all Registrable Securities included in such Registration Statement or (B) the Purchasers are not permitted to utilize the Prospectus therein to resell the Registrable Securities for any reason for more than an aggregate of twenty (20) consecutive calendar days or forty (40) calendar days (which need not be consecutive days) during any twelve (12) month period, or (iv) the Company fails to satisfy the current public information requirement pursuant to Rule 144(c)(1) as a result of which the Purchasers who are not affiliates are unable to sell the Registrable Securities without restriction under Rule 144 (or any successor thereto), (any such failure or breach in clauses (i) through (iv) above being referred to as an “Event,” and, for purposes of clauses (i), (ii) or (iv), the date on which such Event occurs, or for purposes of clause (iii), the date on which such twenty (20) or forty (40) calendar day period is exceeded, being referred to as an “Event Date”), then in addition to any other rights the Purchasers may have hereunder or under applicable law, on each such Event Date and on each 30-day anniversary (or pro rata portion thereof) of each such Event Date (if the applicable Event shall not have been cured by such date) until the earlier of (1) the applicable Event is cured or (2) the Registrable Securities are eligible for resale pursuant to Rule 144 without manner of sale or volume restrictions, the Company shall pay to each Purchaser an amount in cash, as partial liquidated damages and not as a penalty (“Liquidated Damages”), equal (x) on the Event Date and through the fifth 30-day anniversary thereafter, one-half percent (0.5%) of the aggregate purchase price paid by such Purchaser pursuant to the Purchase Agreement for the Securities (as defined in the Purchase Agreement) with respect to which any unregistered Registrable Securities are then held by such Purchaser or would be held by such Purchaser if the Securities held by such Purchaser were converted, and (y) from the sixth 30-day anniversary of the Event Date and thereafter, one percent (1.0%) of the aggregate purchase price paid by such Purchaser pursuant to the Purchase Agreement for the Securities with respect to which any unregistered Registrable Securities are then held by such Purchaser or would be held by such Purchaser if the Securities held by such Purchaser were converted.  The parties agree that (1) notwithstanding anything to the contrary herein or in the Purchase Agreement, no Liquidated Damages shall be payable with respect to any period after the expiration of the Effectiveness Period (except in respect of an Event described in clause (iv) above), (it being understood that this sentence shall not relieve the Company of any Liquidated Damages accruing prior to the Effectiveness Deadline) and in no event shall the aggregate amount of Liquidated Damages (excluding Liquidated Damages payable in respect of an Event described in clause (iv) above) payable to a Purchaser exceed, in the aggregate, ten percent (10%) of the aggregate purchase price paid by such Purchaser pursuant to the Purchase Agreement (or twelve percent (12%) if the only Event is clause (iv)) and (2) in no event shall the 

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Company be liable in any thirty (30) day period for Liquidated Damages under this Agreement in excess of, (x) with respect to the first five 30-day anniversaries after the Event Date, and including the Event Date, one-half percent (0.5%) of the aggregate purchase price paid by the Purchasers pursuant to the Purchase Agreement, and (y) with respect to the sixth 30-day anniversary and any date thereafter, one percent (1.0%) of the aggregate purchase price paid by the Purchasers pursuant to the Purchase Agreement.  If the Company fails to pay any Liquidated Damages pursuant to this Section 5 in full within five (5) business days after the date payable, the Company will pay interest thereon at a rate of one and one-half percent (1.5%) per month (or such lesser maximum amount that is permitted to be paid by applicable law) to the Purchaser, accruing daily from the date such Liquidated Damages are due until such amounts, plus all such interest thereon, are paid in full.  The Liquidated Damages pursuant to the terms hereof shall apply on a daily pro-rata basis for any portion of a month prior to the cure of an Event.  Notwithstanding the foregoing, nothing shall preclude any Purchaser from pursuing or obtaining any available remedies at law, specific performance or other equitable relief with respect to this Section 5 in accordance with applicable law.  In such case, the Liquidated Damages shall be calculated to only apply to the percentage of Registrable Securities which are permitted in accordance with SEC Guidance to be included in the Registration Statement. The Effectiveness Deadline for the Registration Statement shall be extended without default or Liquidated Damages hereunder in the event that the Company’s failure to obtain the effectiveness of the Registration Statement on a timely basis results from the failure of a Purchaser to timely provide the Company with information requested by the Company and necessary to complete the Registration Statement in accordance with the requirements of the Act (in which the Effectiveness Deadline would be extended with respect to Registrable Securities held by such Purchaser).
6.    Amendment and Waiver.      No amendment, modification, termination or cancellation of this A&R Letter Agreement shall be effective unless it is in writing signed by the Company and each of the Purchasers party hereto. No waiver of any of the provisions of this A&R Letter Agreement shall be deemed or shall constitute a waiver of any other provisions hereof (whether or not similar) nor shall such waiver constitute a continuing waiver. 
7.    Entire Agreement.    This A&R Letter Agreement, the Purchase Agreement, the Rights Agreement and the agreements contemplated thereby set forth the entire understanding between the parties hereto relating to the subject matter hereof and supersedes and merges all previous written and oral negotiations, commitments, understandings and agreements relating to the subject matter hereof between the Company and the Purchasers, including, without limitation, the terms set forth in the Original Letter Agreement and the subsequent waivers pertaining thereto. 
8.    Assignment.    This A&R Letter Agreement may not be transferred or assigned (whether by operation of law or otherwise) by either party without the prior written consent of the other party.  
9.    Notices.    All notices, requests, and other communications hereunder shall be in writing and will be deemed to have been duly given and received (a) when personally delivered, (b) when sent by facsimile or e-mail upon confirmation of receipt, (c) one business day after the day on which the same has been delivered prepaid to a nationally recognized courier service, or 

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(d) five business days after the deposit in the United States mail, registered or certified, return receipt requested, postage prepaid, in each case addressed, as to the Company, to Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, Attn: General Counsel, facsimile number: [*], with a copy to Fenwick & West LLP, 801 California Street, Mountain View, CA 94041, Attn: [*], facsimile number: [*], and as to the Purchaser at the address, facsimile number and e-mail address set forth below the Purchaser’s signature on the signature pages of this A&R Letter Agreement. Any party hereto from time to time may change its address, facsimile number, or other information for the purpose of notices to that party by giving notice specifying such change to the other parties hereto. Each Purchaser and the Company may each agree in writing to accept notices and other communications to it hereunder by electronic communications pursuant to procedures reasonably approved by it; provided that approval of such procedures may be limited to particular notices or communications. 
10.    Governing Law.    
(a)    This A&R Letter Agreement shall be governed by and construed in accordance with the laws of the State of Delaware applicable to contracts entered into therein, without reference to principles of choice of law or conflicts of laws that might lead to the application of laws other than the laws of the State of Delaware. 
(b)    Any and all disputes arising out of, or in connection with, the interpretation, performance, or nonperformance of this A&R Letter Agreement or any and all disputes arising out of, or in connection with, transactions in any way related to this A&R Letter Agreement and/or the relationship between the parties shall be resolved pursuant to Section 9.6 of the Purchase Agreement.
11.    Counterparts.  This A&R Letter Agreement may be executed in one or more counterparts, which shall together constitute one agreement. 
Please indicate your agreement to the terms of this A&R Letter Agreement by executing the acknowledgement and agreement below and returning a copy to the attention of Nicholas Khadder, our General Counsel.
[Remainder of Page Intentionally Left Blank]

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                            Very truly yours, 
AMYRIS, INC.

/s/ John G. Melo 
                        Name: John G. Melo 
                        Title: President and Chief Executive Officer

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

	
			
	 
	 
	Maxwell (Mauritius) Pte Ltd

	By:
	 
	/s/ Rohit Sipahimalani

	 
	 
	   (signature)

	
			
	 
	 
	 

	 
	 

	Name:
	 
	 Rohit Sipahimalani

	 
	 
	(printed name)

	 
	 

	Title:
	 
	Authorized Signatory

	
			
	 
	 
	 

	 
	 

	Address:
	 
	60B Orchard Road #06-18
Tower 2, The Atrium @ Orchard
Singapore 238891

	 
	 
	 

	 
	 
	 

	
			
	 
	 
	 

	Fax:
	 
	 

	 
	 
	 

	E-mail:
	 
	 

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

	
			
	 
	 
	Total Energies Nouvelles Activités USA (f.k.a. Total Gas & Power USA, SAS)

	By:
	 
	 /s/ Bernard Clement

	 
	 
	   (signature)

	
			
	 
	 
	 

	 
	 

	Name:
	 
	  Bernard Clement

	 
	 
	(printed name)

	 
	 

	Title:
	 
	President

	
			
	 
	 
	 

	 
	 

	Address:
	 
	 

	
			
	 
	 
	 

	 

	 

	Fax:
	 
	 

	
			
	 
	 
	 

	E-mail:
	 
	 

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

PYRAMIS LIFECYCLE LARGE CAP STOCK  COMMINGLED POOL 

By:  /s/ Dana Rancourt
Name: Dana Rancourt 
Title: DIRECTOR
State Street Bank & Trust
PO Box 5756
Boston, Massachusetts 02206
Attn: FLAPPER CO. FBO Pyramis Lifecycle Large
Cap Stock Commingled Pool

Fax:                    
Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

VARIABLE INSURANCE PRODUCTS FUND III:  GROWTH & INCOME PORTFOLIO 

By:  /s/ Adrien Deberghes
Name: Adrien Deberghes 
Title: Deputy Treasurer
M.Gardiner & Co
C/O JPMorgan Chase Bank, N.A
P.O. Box 35308
Newark, NJ 07101-8006 

Fax:                    
Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

FIDELITY SECURITIES FUND:  FIDELITY GROWTH & INCOME PORTFOLIO 

By:  /s/ Adrien Deberghes
Name: Adrien Deberghes 
Title: Deputy Treasurer
The Northern Trust Company
Attn: Trade Securities Processing, C-1N
801 South Canal Street
Chicago, IL 60607
Fidelity Securities Fund: Fidelity Growth &
Income Portfolio. Reference Account# [*] 

Fax:                    
Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

FIDELITY COMMONWEALTH TRUST:  FIDELITY LARGE CAP STOCK FUND 

By:  /s/ Adrien Deberghes
Name: Adrien Deberghes 
Title: Deputy Treasurer
Brown Brothers Harriman & Co.
525 Washington Blvd
Jersey City NJ 07310
Attn: [*] 15th Floor
Corporate Actions 

Fax:                    
Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

FIDELITY HASTINGS STREET TRUST: FIDELITY SERIES GROWTH & INCOME FUND 

By:  /s/ Adrien Deberghes
Name: Adrien Deberghes 
Title: Deputy Treasurer
The Northern Trust Company
Attn: Trade Securities Processing, C-1N
801 South Canal Street
Chicago, IL 60607
Fidelity Securities Fund: Fidelity Growth &
Income Portfolio. Reference Account# [*]

Fax:                    
Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

FIDELITY HASTINGS STREET TRUST: FIDELITY ADVISOR SERIES GROWTH & INCOME FUND 

By:  /s/ Adrien Deberghes
Name: Adrien Deberghes 
Title: Deputy Treasurer
The Northern Trust Company
Attn: Trade Securities Processing, C-1N
801 South Canal Street
Chicago, IL 60607
Fidelity Securities Fund: Fidelity Growth &
Income Portfolio. Reference Account# [*]
Fax:                    
Email:                    

[Signature Page to Registration Rights A&R Letter Agreement]

Acknowledged and Agreed as 
of the date first written above:
PURCHASERS:

WOLVERINE FLAGSHIP FUND TRADING LIMITED
BY: WOLVERINE ASSET MANAGEMENT, LLC, ITS INVESTMENT MANAGER 

By:  /s/ Michael Adamski
Name: Michael Adamski 
Title: Chief Legal Officer
c/o Wolverine Asset Management, LLC
175 West Jackson Blvd, Ste 340
Chicago, IL 60604

Fax:    [*]                
Email:    [*]                

[Signature Page to Registration Rights A&R Letter Agreement]

Schedule A
	
	
	Purchaser

	Maxwell (Mauritius) Pte Ltd (“Temasek”)

	Total Energies Nouvelles Activités USA (“Total”)

	Pyramis Lifecycle Large Cap Stock Commingled Pool

	Variable Insurance Products Fund III:  Growth & Income Portfolio

	Fidelity Securities Fund:  Fidelity Growth & Income Portfolio

	Fidelity Commonwealth Trust:  Fidelity Large Cap Stock Fund

	Fidelity Hastings Street Trust: Fidelity Series Growth & Income Fund

	Fidelity Hastings Street Trust: Fidelity Advisor Series Growth & Income Fund

	Wolverine Flagship Fund Trading LimitedAmyris2014-Q210-QEx0402Global65ConvertibleSeniorNoteDue2019

   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.
THIS SECURITY AND THE SHARES OF COMMON STOCK ISSUABLE UPON CONVERSION OF THIS SECURITY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED EXCEPT IN ACCORDANCE WITH THE FOLLOWING SENTENCE.  BY ITS ACQUISITION HEREOF OR OF A BENEFICIAL INTEREST HEREIN, THE ACQUIRER:
		
	(1)
	REPRESENTS THAT IT AND ANY ACCOUNT FOR WHICH IT IS ACTING IS A “QUALIFIED INSTITUTIONAL BUYER” (WITHIN THE MEANING OF RULE 144A UNDER THE SECURITIES ACT) AND THAT IT EXERCISES SOLE INVESTMENT DISCRETION WITH RESPECT TO EACH SUCH ACCOUNT, AND

		
	(2)
	AGREES FOR THE BENEFIT OF AMYRIS, INC. (THE “COMPANY”) THAT IT WILL NOT OFFER, SELL, PLEDGE OR OTHERWISE TRANSFER THIS SECURITY OR ANY BENEFICIAL INTEREST HEREIN PRIOR TO THE DATE THAT IS THE LATER OF (X) ONE YEAR AFTER THE LAST ORIGINAL ISSUE DATE HEREOF OR SUCH SHORTER PERIOD OF TIME AS PERMITTED BY RULE 144 UNDER THE SECURITIES ACT OR ANY SUCCESSOR PROVISION THERETO, AND (Y) SUCH LATER DATE, IF ANY, AS MAY BE REQUIRED BY APPLICABLE LAW, EXCEPT:

		
	(A)
	TO THE COMPANY OR ANY SUBSIDIARY THEREOF, OR

		
	(B)
	PURSUANT TO A REGISTRATION STATEMENT WHICH HAS BECOME EFFECTIVE UNDER THE SECURITIES ACT, OR

    

		
	(C)
	TO A QUALIFIED INSTITUTIONAL BUYER IN COMPLIANCE WITH RULE 144A UNDER THE SECURITIES ACT, OR

		
	(D)
	PURSUANT TO AN EXEMPTION FROM REGISTRATION PROVIDED BY RULE 144 UNDER THE SECURITIES ACT OR ANY OTHER AVAILABLE EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT.

PRIOR TO THE REGISTRATION OF ANY TRANSFER IN ACCORDANCE WITH CLAUSE (2)(D) ABOVE, THE COMPANY AND THE TRUSTEE RESERVE THE RIGHT TO REQUIRE THE DELIVERY OF SUCH LEGAL OPINIONS, CERTIFICATIONS OR OTHER EVIDENCE AS MAY REASONABLY BE REQUIRED IN ORDER TO DETERMINE THAT THE PROPOSED TRANSFER IS BEING MADE IN COMPLIANCE WITH THE SECURITIES ACT AND APPLICABLE STATE SECURITIES LAWS.  NO REPRESENTATION IS MADE AS TO THE AVAILABILITY OF ANY EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT.1 

1The restricted legend shall be deemed removed from the face of this security without further action of the Company, the Trustee, or the Holders of this security at such time as the Company instructs the Trustee to remove such legend pursuant to Section 3.08 of the Indenture and upon such removal, the CUSIP No. shall be 03236M AC5.

        

AMYRIS, INC.
6.50% Convertible Senior Notes due 2019
No. R-1    U.S. $50,300,000
CUSIP NO.    03236M AB7
ISIN NO.    US03236MAB72
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 FIFTY MILLION THREE HUNDRED THOUSAND UNITED STATES DOLLARS (U.S. $50,300,000) (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 May 29, 2019.  The Principal Amount of Physical Notes and interest thereon, 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.  The Paying Agent will pay principal of any Note and interest thereon, as provided on the reverse hereof, in immediately available funds 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
Date: May 29, 2014

[Signature Page to Global Note (No. R-1)]

        

AMYRIS, INC.
6.50% Convertible Senior Notes due 2019
This Note is one of a duly authorized issue of Notes of the Company, designated as its 6.50% Convertible Senior Notes due 2019 (the “Notes”), initially limited in aggregate principal amount to $75,000,000 (or $90,000,000 if the Initial Purchaser exercises its option to purchase additional Notes pursuant to the Purchase Agreement), 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 May 29, 2014 (the “Indenture”) between the Company and Wells Fargo Bank, National Association, as Trustee (the “Trustee”), to which 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.  The Notes will bear interest at a rate of 6.50% per year.  Interest on the Notes will accrue from, and including, May 29, 2014, 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 November 15, 2014.  Pursuant to Section 8.03 of the Indenture, 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 May 1 or November 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 267.0370 shares of Common Stock per $1,000 Principal Amount of Notes (equivalent to an initial Conversion Price of approximately $3.74), subject to adjustment in certain events described in the Indenture.  Upon conversion, the Company will deliver shares of Common Stock and 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.
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.

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