Document:

Registration Rights Agreement

 Exhibit 4.04 
 REGISTRATION RIGHTS AGREEMENT 
 This Registration Rights
Agreement (this “Agreement”) is made and entered into as of February 27, 2012, by and among Amyris, Inc. a Delaware corporation (the “Company”), and the several purchasers signatory hereto (each a
“Purchaser” and collectively, the “Purchasers”). 
 This Agreement is made
pursuant to the Securities Purchase Agreement, dated as February 24, 2012 between the Company and each Purchaser (the “Purchase Agreement”) pursuant to which the Purchasers have purchased Convertible Senior Notes due 2017 (the
“Convertible Notes”) which are convertible into Common Stock (as defined below). 
 NOW,
THEREFORE, IN CONSIDERATION of the mutual covenants contained in this Agreement, and for other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, the Company and each of the Purchasers agree as follows:

 1. Definitions. Capitalized terms used and not otherwise defined herein that are defined in the
Purchase Agreement shall have the meanings given such terms in the Purchase Agreement. As used in this Agreement, the following terms shall have the following meanings: 

“Advice” has the meaning set forth in Section 6(c). 

“Affiliate” means, with respect to any person, any other person which directly or indirectly controls,
is controlled by, or is under common control with, such person. 
 “Agreement” has the meaning
set forth in the Preamble. 
 “Business Day” means a day, other than a Saturday or Sunday, on
which banks in New York City are open for the general transaction of business. 
 “Closing” has
the meaning set forth in the Purchase Agreement. 
 “Closing Date” has the meaning set forth in
the Purchase Agreement. 
 “Commission” means the Securities and Exchange Commission.

 “Common Stock” means the common stock of the Company, par value $0.0001 per share, and any
securities into which such common stock may hereinafter be reclassified. 
 “Company” has the
meaning set forth in the Preamble. 
 “Effective Date” means the date that the Registration
Statement filed pursuant to Section 2(a) is first declared effective by the Commission. 
 “Effectiveness Deadline” means, with respect to the Initial Registration Statement or the New Registration Statement, the ninetieth (90th) calendar day following the Closing Date (or, in the event the
Commission reviews and has written comments to the Initial Registration Statement or the New Registration Statement, the one hundred twentieth (120th) calendar day following the Closing Date); provided, however, that if the Company is notified by the
Commission that the Initial Registration Statement or the New Registration Statement will not be reviewed or is no longer subject to further 

 
review and comments, the Effectiveness Deadline as to such Registration Statement shall be the fifth (5th) Trading Day following the date on which the Company is so notified if such date precedes the dates otherwise
required above; provided, further, that if the Effectiveness Deadline falls on a Saturday, Sunday or other day that the Commission is closed for business, the Effectiveness Deadline shall be extended to the next Business Day on which the
Commission is open for business. 
 “Effectiveness Period” has the meaning set forth in
Section 2(b). 
 “Event” has the meaning set forth in Section 2(c).

 “Event Date” has the meaning set forth in Section 2(c). 

“Exchange Act” means the Securities Exchange Act of 1934, as amended, and the rules and regulations
promulgated thereunder. 
 “Filing Deadline” means, with respect to the
Initial Registration Statement required to be filed pursuant to Section 2(a), the twentieth (20th) calendar day following the Closing Date, provided, however, that if the Filing Deadline falls on a Saturday, Sunday or other day that the Commission is closed for business, the Filing
Deadline shall be extended to the next business day on which the Commission is open for business. 

“Holder” or “Holders” means the holder or holders, as the case may be, from time to
time of Registrable Securities. 
 “Indemnified Party” has the meaning set forth in
Section 5(c). 
 “Indemnifying Party” has the meaning set forth in
Section 5(c). 
 “Initial Registration Statement” means the initial Registration
Statement filed pursuant to Section 2(a) of this Agreement. 
 “Liquidated Damages”
has the meaning set forth in Section 2(c). 
 “Losses” has the meaning set
forth in Section 5(a). 
 “New Registration Statement” has the meaning set forth in
Section 2(a). 
 “Person” means an individual or corporation, partnership, trust,
incorporated or unincorporated association, joint venture, limited liability company, joint stock company, government (or an agency or subdivision thereof) or other entity of any kind. 

“Principal Market” means the Trading Market on which the Common Stock is primarily listed on and quoted
for trading, which, as of the Closing Date, shall be the NASDAQ Global Select Market. 

“Proceeding” means an action, claim, suit, investigation or proceeding (including, without limitation,
an investigation or partial proceeding, such as a deposition), whether commenced or threatened. 

“Prospectus” means the prospectus included in a 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 Securities 

  
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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 a 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. 

“Purchase Agreement” has the meaning set forth in the Recitals. 

“Purchaser” or “Purchasers” has the meaning set forth in the Preamble. 

“Registrable Securities” means all of (i) the Shares, and (ii) any securities issued or
issuable upon any stock split, dividend or other distribution, recapitalization or similar event with respect to the foregoing, provided, that the Holder has completed and delivered to the Company a Selling Stockholder Questionnaire; and
provided, further, that with respect to a particular Holder, such Holder’s Shares shall cease to be Registrable Securities upon the earliest to occur of the following: (A) a sale pursuant to a Registration Statement or Rule 144 under
the Securities Act (in which case, only such security sold by the Holder shall cease to be a Registrable Security); or (B) becoming eligible for resale by the Holder under Rule 144 without the requirement for the Company to be in compliance
with the current public information required thereunder and without volume or manner-of-sale restrictions, pursuant to a written opinion letter to such effect, addressed, delivered and acceptable to the Transfer Agent. 

“Registration Statements” means any one or more registration statements of the Company filed under the
Securities Act that covers the resale of any of the Registrable Securities pursuant to the provisions of this Agreement (including without limitation the Initial Registration Statement, the New Registration Statement and any Remainder Registration
Statements), amendments and supplements to such Registration Statements, including post-effective amendments, all exhibits and all material incorporated by reference or deemed to be incorporated by reference in such Registration Statements.

 “Remainder Registration Statement” has the meaning set forth in Section 2(a).

 “Rule 144” means Rule 144 promulgated by the Commission pursuant to the Securities Act, as
such Rule may be amended from time to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same effect as such Rule. 

“Rule 415” means Rule 415 promulgated by the Commission pursuant to the Securities Act, as such Rule may
be amended from time to time, or any similar rule or regulation hereafter adopted by the Commission having substantially the same effect as such Rule. 
 “Rule 424” means Rule 424 promulgated by the Commission pursuant to the Securities Act, as such Rule may be amended from time to time, or any similar rule or regulation hereafter adopted
by the Commission having substantially the same effect as such Rule. 
 “SEC Guidance” means
(i) any publicly-available written or oral guidance, comments, requirements or requests of the Commission staff and (ii) the Securities Act. 
 “Securities Act” means the Securities Act of 1933, as amended, and the rules and regulations promulgated thereunder. 

“Selling Stockholder Questionnaire” means a questionnaire in the form attached as Annex B hereto,
or such other form of questionnaire as may reasonably be proposed by a Purchaser and reasonably acceptable to the Company. 

  
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 “Shares” means the shares of Common Stock issued or
issuable to the Purchasers upon conversion of the Convertible Notes. 
 “Trading Day” means
(i) a day on which the Common Stock is listed or quoted and traded on its Principal Market (other than the OTC Bulletin Board), or (ii) if the Common Stock is not listed on a Trading Market (other than the OTC Bulletin Board), a day on
which the Common Stock is traded in the over-the-counter market, as reported by the OTC Bulletin Board, or (iii) if the Common Stock is not quoted on any Trading Market, a day on which the Common Stock is quoted in the over-the-counter market
as reported in the “pink sheets” by Pink Sheets LLC (or any similar organization or agency succeeding to its functions of reporting prices); provided, that in the event that the Common Stock is not listed or quoted as set forth in
(i), (ii) and (iii) hereof, then Trading Day shall mean a Business Day. 
 “Trading
Market” means whichever of the New York Stock Exchange, the American Stock Exchange, the NASDAQ Global Select Market, the NASDAQ Global Market, the NASDAQ Capital Market or OTC Bulletin Board on which the Common Stock is listed or quoted
for trading on the date in question. 
 2. Registration. 

(a) On or prior to the Filing Deadline, the Company shall prepare and file with the Commission a Registration Statement
covering the resale of all of the Registrable Securities not already covered by an existing and effective Registration Statement for an offering to be made on a continuous basis pursuant to Rule 415 or, if Rule 415 is not available for offers and
sales of the Registrable Securities, by such other means of distribution of Registrable Securities as the Holders may reasonably specify (the “Initial Registration Statement”). The Initial Registration Statement shall be on Form S-3
(except if the Company is then ineligible to register for resale the Registrable Securities on Form S-3, in which case such registration shall be on such other form available to register for resale the Registrable Securities as a secondary offering)
subject to the provisions of Section 2(e) and shall contain (except if otherwise required pursuant to written comments received from the Commission upon a review of such Registration Statement) the “Plan of Distribution”
section attached hereto as Annex A (which may be modified to respond to comments, if any, provided by the Commission). Notwithstanding the registration obligations set forth in this Section 2, in the event the Commission informs
the Company that all of the Registrable Securities cannot, as a result of the application of Rule 415, be registered for resale as a secondary offering on a single registration statement, the Company agrees to promptly (i) inform each of the
holders thereof and use its commercially reasonable efforts to file amendments to the Initial Registration Statement as required by the Commission and/or (ii) withdraw the Initial Registration Statement and file a new registration statement (a
“New Registration Statement”), in either case covering the maximum number of Registrable Securities permitted to be registered by the Commission, on Form S-3 or such other form available to register for resale the Registrable
Securities as a secondary offering; provided, however, that prior to filing such amendment or New Registration Statement, the Company shall be obligated to use its commercially reasonable efforts to advocate with the Commission for the
registration of all of the Registrable Securities in accordance with the SEC Guidance, including without limitation, the Manual of Publicly Available Telephone Interpretations D.29. Notwithstanding any other provision of this Agreement and subject
to the payment of liquidated damages in Section 2(c), if any SEC Guidance sets forth a limitation of the number of Registrable Securities permitted to be registered on a particular Registration Statement as a secondary offering (and
notwithstanding that the Company used diligent efforts to advocate with the Commission for the registration of all or a greater number of Registrable Securities), unless otherwise directed in writing by a Holder as to its Registrable Securities, the
number of Registrable Securities to be registered on such Registration Statement will first be reduced by Registrable Securities not acquired pursuant to the Purchase Agreement (whether pursuant to

  
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registration rights or otherwise), and second by Registrable Securities represented by Shares (applied, in the case that some Shares may be registered, to the Holders on a pro rata basis based on
the total number of unregistered Shares held by such Holders (or would be held by such Holders if the Convertible Notes held by such Holders were converted), subject to a determination by the Commission that certain Holders must be reduced first
based on the number of Shares held by such Holders). In the event the Company amends the Initial Registration Statement or files a New Registration Statement, as the case may be, under clauses (i) or (ii) above, the Company will use its
commercially reasonable efforts to file with the Commission, as promptly as allowed by Commission or SEC Guidance provided to the Company or to registrants of securities in general, one or more registration statements on Form S-3 or such other form
available to register for resale those Registrable Securities that were not registered for resale on the Initial Registration Statement, as amended, or the New Registration Statement (the “Remainder Registration Statements”).

 (b) The Company shall use its commercially reasonable efforts to cause each Registration Statement to be
declared effective by the Commission as soon as practicable and, with respect to the Initial Registration Statement or the New Registration Statement, as applicable, no later than the Effectiveness Deadline (including filing with the Commission a
request for acceleration of effectiveness in accordance with Rule 461 promulgated under the Securities Act), and shall use its commercially reasonable efforts to keep each Registration Statement continuously effective under the Securities Act until
the earlier of (i) such time as all of the Registrable Securities covered by such Registration Statement have been publicly sold by the Holders or (ii) the date that all Registrable Securities covered by such 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 (the “Effectiveness Period”). The Company shall telephonically request effectiveness of a
Registration Statement as of 5:00 P.M. New York City time on a Trading Day. The Company shall promptly notify the Holders via facsimile or electronic mail of a “.pdf” format data file of the effectiveness of a Registration Statement on the
same Trading Day that the Company telephonically confirms effectiveness with the Commission, which date of confirmation shall initially be the date requested for effectiveness of such Registration Statement. The Company shall, by 9:30 A.M. New York
City time on the first Trading Day after the Effective Date, file a final Prospectus with the Commission, as required by Rule 424(b). Failure to so notify the Holders on or before the second Trading Day after such notification or effectiveness or
failure to file a final Prospectus as aforesaid shall be deemed an Event under Section 2(c). 
 (c)
If: (i) the Initial Registration Statement is not filed with the Commission on or prior to the Filing Deadline, (ii) the Initial Registration Statement or the New Registration Statement, as applicable, is not declared effective by the
Commission (or otherwise does not become effective) for any reason on or prior to the Effectiveness Deadline or (iii) after its Effective Date, (A) such 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 Holders are not permitted to utilize the
Prospectus therein to resell such 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 Holders who are not affiliates are unable to sell 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 

  
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Date”), then in addition to any other rights the Holders 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 Holder 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 Holder pursuant to the Purchase Agreement for the Convertible Notes with respect to which any unregistered Registrable Securities are then held by
such Holder or would be held by such Holder if the Convertible Notes by such Holder 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
Holder pursuant to the Purchase Agreement for the Convertible Notes with respect to which any unregistered Registrable Securities are then held by such Holder or would be held by such Holder if the Convertible Notes by such Holder 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 Section 2(c)(iv) herein), (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 Section 2(c)(iv) herein) payable to a Holder exceed, in the aggregate, ten percent (10%) of the aggregate purchase price paid by such
Holder pursuant to the Purchase Agreement (twelve percent (12%) if the only Event is clause (iv)) and (2) in no event shall the 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 Holders 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 Holders pursuant to the Purchase Agreement. If the Company fails to pay any Liquidated Damages pursuant to this
Section 2(c) 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 Holder, 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 Holder from pursuing or obtaining any available remedies at law, specific performance or other equitable relief with respect to
this Section 2(c) in accordance with applicable law. The Company shall not be liable for Liquidated Damages under this Agreement as to any Registrable Securities which are not permitted by the Commission to be included in a Registration
Statement due solely to SEC Guidance from the time that it is determined that such Registrable Securities are not permitted to be registered until such time as the provisions of this Agreement as to the Remainder Registration Statements required to
be filed hereunder are triggered, in which case the provisions of this Section 2(c) shall once again apply, if applicable. 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 such Registration Statement. The Effectiveness Deadline for a 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 Securities Act (in which the Effectiveness Deadline would be extended with respect to Registrable Securities held by such Purchaser). 

  
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 (d) Each Holder agrees to furnish to the Company a completed Selling
Stockholder Questionnaire not more than ten (10) Trading Days following the date of this Agreement. At least ten (10) Trading Days prior to the first anticipated filing date of a Registration Statement for any registration under this
Agreement, the Company will notify each Holder of the information the Company requires from that Holder other than the information contained in the Selling Stockholder Questionnaire, if any, which shall be completed and delivered to the Company
promptly upon request and, in any event, within three (3) Trading Days prior to the applicable anticipated filing date. Each Holder further agrees that it shall not be entitled to be named as a selling securityholder in the Registration
Statement or use the Prospectus for offers and resales of Registrable Securities at any time, unless such Holder has returned to the Company a completed and signed Selling Stockholder Questionnaire and a response to any requests for further
information as described in the previous sentence. If a Holder of Registrable Securities returns a Selling Stockholder Questionnaire or a request for further information, in either case, after its respective deadline, the Company shall use its
commercially reasonable efforts to take such actions as are required to name such Holder as a selling security holder in the Registration Statement or any pre-effective or post-effective amendment thereto and to include (to the extent not
theretofore included) in the Registration Statement the Registrable Securities identified in such late Selling Stockholder Questionnaire or request for further information. Each Holder acknowledges and agrees that the information in the Selling
Stockholder Questionnaire or request for further information as described in this Section 2(d) will be used by the Company in the preparation of the Registration Statement and hereby consents to the inclusion of such information in the
Registration Statement. 
 (e) In the event that Form S-3 is not available for the registration of the resale of
Registrable Securities hereunder, the Company shall (i) register the resale of the Registrable Securities on Form S-1 or another appropriate form reasonably acceptable to the Holders and (ii) undertake to register the Registrable
Securities on Form S-3 promptly after such form is available, provided that the Company shall maintain the effectiveness of the Registration Statement then in effect until such time as a Registration Statement on Form S-3 covering the
Registrable Securities has been declared effective by the Commission. 
 3. Registration Procedures

 In connection with the Company’s registration obligations hereunder, the Company shall: 

(a) Not less than five (5) Trading Days prior to the filing of each Registration Statement and not less than one
(1) Trading Day prior to the filing of any related Prospectus or any amendment or supplement thereto (except for Annual Reports on Form 10-K, and Quarterly Reports on Form 10-Q and Current Reports on Form 8-K and any similar or successor
reports), (i) furnish to the Holder copies of such Registration Statement, Prospectus or amendment or supplement thereto, as proposed to be filed, which documents will be subject to the review of such Holder (it being acknowledged and agreed
that if a Holder does not object to or comment on the aforementioned documents within such five (5) Trading Day or one (1) Trading Day period, as the case may be, then the Holder shall be deemed to have consented to and approved the use of
such documents) and (ii) use commercially reasonable efforts to cause its officers and directors, counsel and independent registered public accountants to respond to such inquiries as shall be necessary, in the reasonable opinion of respective
counsel to each Holder, to conduct a reasonable investigation within the meaning of the Securities Act. The Company shall not file any Registration Statement or amendment or supplement thereto in a form to which a Holder reasonably objects in good
faith, provided that, the Company is notified of such objection in writing within the five (5) Trading Day or one (1) Trading Day period described above, as applicable. 

  
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 (b) (i) Prepare and file with the Commission such amendments (including
post-effective amendments) and supplements, to each Registration Statement and the Prospectus used in connection therewith as may be necessary to keep such Registration Statement continuously effective as to the applicable Registrable Securities for
its Effectiveness Period; (ii) cause the related Prospectus to be amended or supplemented by any required Prospectus supplement (subject to the terms of this Agreement), and, as so supplemented or amended, to be filed pursuant to Rule 424;
(iii) respond as promptly as reasonably practicable to any comments received from the Commission with respect to each Registration Statement or any amendment thereto and, as promptly as reasonably possible, provide the Holders true and complete
copies of all correspondence from and to the Commission relating to such Registration Statement that pertains to the Holders as “Selling Stockholders” but not any comments that would result in the disclosure to the Holders of material and
non-public information concerning the Company; and (iv) comply with the provisions of the Securities Act and the Exchange Act with respect to the disposition of all Registrable Securities covered by a Registration Statement until such time as
all of such Registrable Securities shall have been disposed of (subject to the terms of this Agreement) in accordance with the intended methods of disposition by the Holders thereof as set forth in such Registration Statement as so amended or in
such Prospectus as so supplemented; provided, however, that in the event the Company informs the Holders in writing that it does not satisfy the conditions specified in Rule 172 and, as a result thereof, the Holders are required to deliver a
Prospectus in connection with any disposition of Registrable Securities, the Company shall deliver to the Holders a copy of the Prospectus in electronic format and each such Holder shall be responsible for the delivery of the Prospectus to the
Persons to whom such Holder sells any of the Registrable Securities, and each Holder agrees to dispose of Registrable Securities in compliance with the “Plan of Distribution” described in the Registration Statement and otherwise in
compliance with applicable federal and state securities laws. In the case of amendments and supplements to a Registration Statement which are required to be filed pursuant to this Agreement (including pursuant to this Section 3(b)) by
reason of the Company filing a report on Form 10-K, Form 10-Q or Form 8-K or any analogous report under the Exchange Act, the Company shall have incorporated such report by reference into such Registration Statement, if applicable, or shall file
such amendments or supplements with the Commission on the same day on which the Exchange Act report which created the requirement for the Company to amend or supplement such Registration Statement was filed. 

(c) Notify the Holders (which notice shall, pursuant to clauses (iii) through (v) hereof, be accompanied by an
instruction to suspend the use of the Prospectus until the requisite changes have been made) as promptly as reasonably practicable (and, in the case of (i)(A) below, not less than one (1) Trading Day prior to such filing) and (if requested by
any such Person) confirm such notice in writing no later than one (1) Trading Day following the day: (i)(A) when a Prospectus or any Prospectus supplement or post-effective amendment to a Registration Statement is proposed to be filed;
(B) when the Commission notifies the Company whether there will be a “review” of such Registration Statement and whenever the Commission comments in writing on any Registration Statement (in which case the Company shall provide to
each of the Holders true and complete copies of all comments that pertain to the Holders as a “Selling Stockholder” or to the “Plan of Distribution” and all written responses thereto, but not information that the Company believes
would constitute material and non-public information); and (C) with respect to each Registration Statement or any post-effective amendment, when the same has become effective; (ii) of any request by the Commission or any other Federal or
state governmental authority for amendments or supplements to a Registration Statement or Prospectus or for additional information that pertains to the Holders as “Selling Stockholders” or the “Plan of Distribution”;
(iii) of the issuance by the Commission or any other federal or state governmental authority of any stop order suspending the effectiveness of a Registration Statement covering any or all of the Registrable Securities or the initiation of any
Proceedings for that purpose; (iv) of the receipt by the Company of any notification with respect to the suspension of the qualification or exemption from qualification of any of 

  
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the Registrable Securities for sale in any jurisdiction, or the initiation or threatening of any Proceeding for such purpose; and (v) of the occurrence of any event or passage of time that
makes the financial statements included in a Registration Statement ineligible for inclusion therein or any statement made in such Registration Statement or Prospectus or any document incorporated or deemed to be incorporated therein by reference
untrue in any material respect or that requires any revisions to such Registration Statement, Prospectus or other documents so that, in the case of such Registration Statement or the Prospectus, as the case may be, it will not contain any untrue
statement of a material fact or omit to state any material fact required to be stated therein or necessary to make the statements therein (in the case of any Prospectus, form of prospectus or supplement thereto, in light of the circumstances under
which they were made), not misleading. 
 (d) Use commercially reasonable efforts to avoid the issuance of, or,
if issued, obtain the withdrawal of (i) any order suspending the effectiveness of a Registration Statement, or (ii) any suspension of the qualification (or exemption from qualification) of any of the Registrable Securities for sale in any
jurisdiction, as soon as practicable. 
 (e) If requested by a Holder, furnish to such Holder, without charge,
at least one conformed copy of each Registration Statement and each amendment thereto and all exhibits to the extent requested by such Person (including those previously furnished or incorporated by reference) promptly after the filing of such
documents with the Commission; provided, that the Company shall have no obligation to provide any document pursuant to this clause that is available on the Commission’s EDGAR system. 

(f) Prior to any resale of Registrable Securities by a Holder, use its commercially reasonable efforts to register or
qualify or cooperate with the selling Holders in connection with the registration or qualification (or exemption from the registration or qualification) of such Registrable Securities for the resale by the Holder under the securities or Blue Sky
laws of such jurisdictions within the United States as any Holder reasonably requests in writing, to keep each registration or qualification (or exemption therefrom) effective during the Effectiveness Period and to do any and all other acts or
things reasonably necessary to enable the disposition in such jurisdictions of the Registrable Securities covered by each Registration Statement; provided, that the Company shall not be required to qualify generally to do business in any
jurisdiction where it is not then so qualified, subject the Company to any material tax in any such jurisdiction where it is not then so subject or file a general consent to service of process in any such jurisdiction. 

(g) If requested by a Holder, cooperate with such Holder to facilitate the timely preparation and delivery of
certificates representing Registrable Securities to be delivered to a transferee pursuant to the Registration Statement, which certificates shall be free, to the extent permitted by the Purchase Agreement and under law, of all restrictive legends,
and to enable such Registrable Securities to be in such denominations and registered in such names as any such Holders may reasonably request. 
 (h) Following the occurrence of any event contemplated by Section 3(c), as promptly as reasonably practicable, prepare a supplement or amendment, including a post-effective amendment, to the
affected Registration Statements or a supplement to the related Prospectus or any document incorporated or deemed to be incorporated therein by reference, and file any other required document so that, as thereafter delivered, no Registration
Statement nor any Prospectus will contain an untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the statements therein (in the case of any Prospectus, form of prospectus or
supplement thereto, in light of the circumstances under which they were made), not misleading. If the Company notifies the Holders in accordance with clauses (iii) through (v) of Section 3(c) above to suspend the use of any
Prospectus until the requisite changes to such Prospectus have been made, then the Holders shall suspend 

  
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use of such Prospectus. The Company will use its commercially reasonable efforts to ensure that the use of the Prospectus may be resumed as promptly as is practicable. The Company shall be
entitled to exercise its right under this Section 3(h) to suspend the availability of a Registration statement and Prospectus, subject to the payment of partial Liquidated Damages otherwise required pursuant to Section 2(c),
for a period not to exceed forty (40) calendar days (which need not be consecutive days) in any twelve (12) month period. 
 (i) The Company may require each selling Holder to furnish to the Company a certified statement as to (i) the number of shares of Common Stock beneficially owned by such Holder and any Affiliate
thereof, (ii) any Financial Industry Regulatory Authority (“FINRA”) affiliations, (iii) any natural persons who have the power to vote or dispose of the common stock and (iv) any other information as may be requested
by the Commission, FINRA or any state securities commission. During any periods that the Company is unable to meet its obligations hereunder with respect to the registration of Registrable Securities because any Holder fails to furnish such
information within three (3) Trading Days of the Company’s request, any Liquidated Damages that are accruing at such time as to such Holder only shall be tolled and any Event that may otherwise occur solely because of such delay shall be
suspended as to such Holder only, until such information is delivered to the Company. 
 (j) The Company shall
cooperate with any registered broker through which a Holder proposes to resell its Registrable Securities in effecting a filing with FINRA pursuant to FINRA Rule 5110 as requested by any such Holder and the Company shall pay the filing fee required
for the first such filing within two (2) Business Days of the request therefor. 
 4. Registration
Expenses. All fees and expenses incident to the Company’s performance of or compliance with its obligations under this Agreement (excluding any underwriting discounts and selling commissions and all legal fees and expenses of legal counsel
for any Holder) shall be borne by the Company whether or not any Registrable Securities are sold pursuant to a Registration Statement. The fees and expenses referred to in the foregoing sentence shall include, without limitation, (i) all
registration and filing fees (including, without limitation, fees and expenses (A) with respect to filings required to be made with any Trading Market on which the Common Stock is then listed for trading, (B) with respect to compliance
with applicable state securities or Blue Sky laws (including, without limitation, fees and disbursements of counsel for the Company in connection with Blue Sky qualifications or exemptions of the Registrable Securities and determination of the
eligibility of the Registrable Securities for investment under the laws of such jurisdictions as requested by the Holders) and (C) if not previously paid by the Company in connection with Section 3(j) above, with respect to any
filing that may be required to be made by any broker through which a Holder intends to make sales of Registrable Securities with FINRA pursuant to the FINRA Rule 5110, so long as the broker is receiving no more than a customary brokerage commission
in connection with such sale, (ii) printing expenses (including, without limitation, expenses of printing certificates for Registrable Securities and of printing prospectuses if the printing of prospectuses is reasonably requested by the
Holders of a majority of the Registrable Securities included in the Registration Statement), (iii) messenger, telephone and delivery expenses, (iv) fees and disbursements of counsel for the Company, (v) Securities Act liability
insurance, if the Company so desires such insurance, and (vi) fees and expenses of all other Persons retained by the Company in connection with the consummation of the transactions contemplated by this Agreement. In addition, the Company shall
be responsible for all of its internal expenses incurred in connection with the consummation of the transactions contemplated by this Agreement (including, without limitation, all salaries and expenses of its officers and employees performing legal
or accounting duties), the expense of any annual audit and the fees and expenses incurred in connection with the listing of the Registrable Securities on any securities exchange as required hereunder. In no event shall the Company be responsible for
any underwriting, broker or similar fees or commissions of any Holder or, except to the extent provided for in the Purchase Agreement, any legal fees or other costs of the Holders, except as provided in the immediately succeeding

  
 10 

 
sentence. The Holders shall have the right to select one legal counsel to review and oversee any registration pursuant to this Agreement (“Legal Counsel”) which shall be Goodwin
Procter LLP or such other counsel designated by the Holders, and the cost thereof shall be borne by the Company. 
 5. Indemnification. 
 (a) Indemnification by the
Company. The Company shall, notwithstanding any termination of this Agreement, indemnify, defend and hold harmless each Holder, the officers, directors, agents, partners, members, managers, stockholders, Affiliates and employees of each of them,
each Person who controls any such Holder (within the meaning of Section 15 of the Securities Act or Section 20 of the Exchange Act) and the officers, directors, partners, members, managers, stockholders, agents and employees of each such
controlling Person, to the fullest extent permitted by applicable law, from and against any and all losses, claims, damages, liabilities, costs (including, without limitation, reasonable costs of preparation and investigation and reasonable
attorneys’ fees) and expenses (collectively, “Losses”), as incurred, that arise out of or are based upon (i) any untrue or alleged untrue statement of a material fact contained in any Registration Statement, any Prospectus
or any form of prospectus or in any amendment or supplement thereto or in any preliminary prospectus, or arising out of or relating to any omission or alleged omission to state a material fact required to be stated therein or necessary to make the
statements therein (in the case of any Prospectus or form of prospectus or supplement thereto, in light of the circumstances under which they were made) not misleading, or (ii) any violation or alleged violation by the Company of the Securities
Act, Exchange Act or any state securities law or any rule or regulation thereunder, in connection with the performance of its obligations under this Agreement, except to the extent, but only to the extent, that (A) such untrue statements,
alleged untrue statements, omissions or alleged omissions are based solely upon information regarding such Holder furnished in writing to the Company by such Holder expressly for use therein, or to the extent that such information relates to such
Holder or such Holder’s proposed method of distribution of Registrable Securities and was reviewed and approved in writing by such Holder expressly for use in the Registration Statement, such Prospectus or such form of Prospectus or in any
amendment or supplement thereto (it being understood that each Holder has approved Annex A hereto for this purpose) or (B) in the case of an occurrence of an event of the type specified in Section 3(c)(iii)-(v),
related to the use by a Holder of an outdated or defective Prospectus after the Company has notified such Holder in writing that the Prospectus is outdated or defective and prior to the receipt by such Holder of the Advice contemplated and defined
in Section 6(c) below, to the extent that following the receipt of the Advice the misstatement or omission giving rise to such Loss would have been corrected or (C) to the extent that any such Losses arise out of the
Purchaser’s (or any other indemnified Person’s) failure to send or give a copy of the Prospectus or supplement (as then amended or supplemented), if required, pursuant to Rule 172 under the Securities Act (or any successor rule) to the
Persons asserting an untrue statement or alleged untrue statement or alleged untrue statement or omission or alleged omission at or prior to the written confirmation of the sale of Registrable Securities to such Person if such statement or omission
was corrected in such Prospectus or supplement. The Company shall notify the Holders promptly of the institution, threat or assertion of any Proceeding arising from or in connection with the transactions contemplated by this Agreement of which the
Company is aware. Such indemnity shall remain in full force and effect regardless of any investigation made by or on behalf of an Indemnified Party (as defined in Section 5(c)) and shall survive the transfer of the Registrable Securities
by the Holders. 
 (b) Indemnification by Holders. Each Holder shall, severally and not jointly,
indemnify and hold harmless the Company, its directors, officers, agents and employees, each Person who controls the Company (within the meaning of Section 15 of the Securities Act and Section 20 of the Exchange Act), and the directors,
officers, agents or employees of such controlling Persons, to the fullest extent permitted by applicable law, from and against all Losses, as incurred, arising out of or are based solely upon any untrue or alleged untrue statement of a material fact
contained in any Registration 

  
 11 

 
Statement, any Prospectus, or any form of prospectus, or in any amendment or supplement thereto or in any preliminary prospectus, or arising out of or relating to any omission or alleged omission
of a material fact required to be stated therein or necessary to make the statements therein (in the case of any Prospectus, or any form of prospectus or supplement thereto, in light of the circumstances under which they were made) not misleading
(i) to the extent that such untrue statements or omissions are based solely upon information regarding such Holder furnished in writing to the Company by such Holder expressly for use therein or (ii) to the extent that such information
relates to such Holder or such Holder’s proposed method of distribution of Registrable Securities and was reviewed and approved in writing by such Holder expressly for use in a Registration Statement (it being understood that the Holder has
approved Annex A hereto for this purpose), such Prospectus or such form of Prospectus or in any amendment or supplement thereto or (iii) in the case of an occurrence of an event of the type specified in
Section 3(c)(iii)-(vi), to the extent related to the use by such Holder of an outdated or defective Prospectus after the Company has notified such Holder in writing that the Prospectus is outdated or defective and prior to the
receipt by such Holder of the Advice contemplated in Section 6(c). In no event shall the liability of any selling Holder hereunder be greater in amount than the dollar amount of the net proceeds received by such Holder upon the sale of
the Registrable Securities giving rise to such indemnification obligation. 
 (c) Conduct of Indemnification
Proceedings. If any Proceeding shall be brought or asserted against any Person entitled to indemnity hereunder (an “Indemnified Party”), such Indemnified Party shall promptly notify the Person from whom indemnity is sought (the
“Indemnifying Party”) in writing, and the Indemnifying Party shall have the right to assume the defense thereof, including the employment of counsel reasonably satisfactory to the Indemnified Party and the payment of all reasonable
fees and expenses incurred in connection with defense thereof; provided, that the failure of any Indemnified Party to give such notice shall not relieve the Indemnifying Party of its obligations or liabilities pursuant to this Agreement,
except (and only) to the extent that it shall be finally determined by a court of competent jurisdiction (which determination is not subject to appeal or further review) that such failure shall have materially and adversely prejudiced the
Indemnifying Party. 
 An Indemnified Party shall have the right to employ separate counsel in any such
Proceeding and to participate in the defense thereof, but the fees and expenses of such counsel shall be at the expense of such Indemnified Party or Parties unless: (1) the Indemnifying Party has agreed in writing to pay such fees and expenses;
(2) the Indemnifying Party shall have failed promptly to assume the defense of such Proceeding and to employ counsel reasonably satisfactory to such Indemnified Party in any such Proceeding; or (3) the named parties to any such Proceeding
(including any impleaded parties) include both such Indemnified Party and the Indemnifying Party, and such Indemnified Party shall have been advised by counsel that a conflict of interest exists if the same counsel were to represent such Indemnified
Party and the Indemnifying Party (in which case, if such Indemnified Party notifies the Indemnifying Party in writing that it elects to employ separate counsel at the expense of the Indemnifying Party, the Indemnifying Party shall not have the right
to assume the defense thereof and such counsel shall be at the expense of the Indemnifying Party); provided, that the Indemnifying Party shall not be liable for the fees and expenses of more than one separate firm of attorneys at any time for
all Indemnified Parties. The Indemnifying Party shall not be liable for any settlement of any such Proceeding effected without its written consent, which consent shall not be unreasonably withheld, delayed or conditioned. No Indemnifying Party
shall, without the prior written consent of the Indemnified Party, effect any settlement of any pending Proceeding in respect of which any Indemnified Party is a party, unless such settlement includes an unconditional release of such Indemnified
Party from all liability on claims that are the subject matter of such Proceeding and such settlement does not include any non-monetary limitation on the actions of any Indemnified Party or any of its affiliates or any admission of fault or
liability on behalf of any such Indemnified Party. 

  
 12 

 Subject to the terms of this Agreement, all fees and expenses of the
Indemnified Party (including reasonable fees and expenses to the extent incurred in connection with investigating or preparing to defend such Proceeding in a manner not inconsistent with this Section 5) shall be paid to the Indemnified
Party, as incurred, within twenty (20) Trading Days of written notice thereof to the Indemnifying Party; provided, that the Indemnified Party shall promptly reimburse the Indemnifying Party for that portion of such fees and expenses
applicable to such actions for which such Indemnified Party is finally judicially determined to not be entitled to indemnification hereunder). The failure to deliver written notice to the Indemnifying Party within a reasonable time of the
commencement of any such action shall not relieve such Indemnifying Party of any liability to the Indemnified Party under this Section 5, except to the extent that the Indemnifying Party is materially and adversely prejudiced in its
ability to defend such action. 
 (d) Contribution. If a claim for indemnification under
Section 5(a) or 5(b) is unavailable to an Indemnified Party or insufficient to hold an Indemnified Party harmless for any Losses, then each Indemnifying Party, in lieu of indemnifying such Indemnified Party, shall contribute to
the amount paid or payable by such Indemnified Party as a result of such Losses, in such proportion as is appropriate to reflect the relative fault of the Indemnifying Party and Indemnified Party in connection with the actions, statements or
omissions that resulted in such Losses as well as any other relevant equitable considerations. The relative fault of such Indemnifying Party and Indemnified Party shall be determined by reference to, among other things, whether any action in
question, including any untrue or alleged untrue statement of a material fact or omission or alleged omission of a material fact, has been taken or made by, or relates to information supplied by, such Indemnifying Party or Indemnified Party, and the
parties’ relative intent, knowledge, access to information and opportunity to correct or prevent such action, statement or omission. The amount paid or payable by a party as a result of any Losses shall be deemed to include, subject to the
limitations set forth in this Agreement, any reasonable attorneys’ or other reasonable fees or expenses incurred by such party in connection with any Proceeding to the extent such party would have been indemnified for such fees or expenses if
the indemnification provided for in this Section 5 was available to such party in accordance with its terms. 
 The parties hereto agree that it would not be just and equitable if contribution pursuant to this Section 5(d) were determined by pro rata allocation or by any other method of allocation that
does not take into account the equitable considerations referred to in the immediately preceding paragraph. Notwithstanding the provisions of this Section 5(d), (A) no Holder shall be required to contribute, in the aggregate, any
amount in excess of the amount by which the net proceeds actually received by such Holder from the sale of the Registrable Securities subject to the Proceeding exceeds the amount of any damages that such Holder has otherwise been required to pay by
reason of such untrue or alleged untrue statement or omission or alleged omission and (B) no contribution will be made under circumstances where the maker of such contribution would not have been required to indemnify the Indemnified Party
under the fault standards set forth in this Section 5. No person guilty of fraudulent misrepresentation (within the meaning of Section 11(f) of the Securities Act) shall be entitled to contribution from any Person who was not guilty
of such fraudulent misrepresentation. 
 The indemnity and contribution agreements contained in this Section 5 are
in addition to any liability that the Indemnifying Parties may have to the Indemnified Parties and are not in diminution or limitation of the indemnification provisions under the Purchase Agreement. 

6. Miscellaneous. 
 (a) Remedies. In the event of a breach by the Company or by a Holder of any of their obligations under this Agreement, each Holder or the Company, as the case may be, in addition to being entitled
to exercise all rights granted by law and under this Agreement, including recovery of 

  
 13 

 
damages, will be entitled to specific performance of its rights under this Agreement. The Company and each Holder agree that monetary damages would not provide adequate compensation for any
losses incurred by reason of a breach by it of any of the provisions of this Agreement and hereby further agrees that, in the event of any action for specific performance in respect of such breach, it shall waive the defense that a remedy at law
would be adequate. 
 (b) Compliance. Each Holder covenants and agrees that in the event the Company
informs such Holder in writing that it does not satisfy the conditions specified in Rule 172 and, as a result thereof, such Holder is required to deliver a Prospectus in connection with any disposition of Registrable Securities, it will comply with
the prospectus delivery requirements of the Securities Act as applicable to it (unless an exemption therefrom is available) in connection with sales of Registrable Securities pursuant to the Registration Statement and shall sell the Registrable
Securities only in accordance with a method of distribution described in the Registration Statement 
 (c)
Discontinued Disposition. By its acquisition of Registrable Securities, each Holder agrees that, upon receipt of a notice from the Company of the occurrence of any event of the kind described in Section 3(c)(iii)-(v), such
Holder will forthwith discontinue disposition of such Registrable Securities under a Registration Statement until it is advised in writing (the “Advice”) by the Company that the use of the applicable Prospectus (as it may have been
supplemented or amended) may be resumed. The Company will use its commercially reasonable efforts to ensure that the use of the Prospectus may be resumed as promptly as is practicable. The Company agrees and acknowledges that any periods during
which the Holder is required to discontinue the disposition of the Registrable Securities hereunder shall be subject to the provisions of Section 2(c). 

(d) No Inconsistent Agreements. Neither the Company nor any of its Subsidiaries has entered, as of the date
hereof, nor shall the Company or any of its Subsidiaries, on or after the date hereof, enter into any agreement with respect to its securities, that would have the effect of impairing the rights granted to the Holders in this Agreement or otherwise
conflicts with the provisions hereof. 
 (e) Amendments and Waivers. The provisions of this Agreement,
including the provisions of this sentence, may not be amended, modified or supplemented, or waived unless the same shall be in writing and signed by the Company and each Holder. Notwithstanding the foregoing, a waiver or consent to depart from the
provisions hereof with respect to a matter that relates exclusively to the rights of Holders and that does not directly or indirectly affect the rights of other Holders may be given by Holders of all of the Registrable Securities to which such
waiver or consent relates; provided, however, that the provisions of this sentence may not be amended, modified, or supplemented except in accordance with the provisions of the immediately preceding sentence. 

(f) Notices. Any and all notices or other communications or deliveries required or permitted to be provided
hereunder shall be delivered as set forth in the Purchase Agreement. 
 (g) Successors and Assigns. This
Agreement shall inure to the benefit of and be binding upon the successors and permitted assigns of each of the parties and shall inure to the benefit of each Holder. Nothing in this Agreement, express or implied, is intended to confer upon any
party other than the parties hereto or their respective successors and assigns any rights, remedies, obligations, or liabilities under or by reason of this Agreement, except as expressly provided in this Agreement. The Company may not assign its
rights (except by merger or in connection with another entity acquiring all or substantially all of the Company’s assets) or obligations hereunder without the prior written consent of all the Holders of the then outstanding Registrable
Securities. Each Holder may assign its respective rights hereunder in the manner and to the Persons as permitted under the Purchase Agreement; provided in each case that (i) the Holder agrees in writing with the transferee or assignee to assign
such rights and related 

  
 14 

 
obligations under this Agreement, and for the transferee or assignee to assume such obligations, and a copy of such agreement is furnished to the Company within a reasonable time after such
assignment, (ii) the Company is, within a reasonable time after such transfer or assignment, furnished with written notice of the name and address of such transferee or assignee and the securities with respect to which such registration rights
are being transferred or assigned, (iii) at or before the time the Company received the written notice contemplated by clause (ii) of this sentence, the transferee or assignee agrees in writing with the Company to be bound by all of the
provisions contained herein and (iv) the transferee is an “accredited investor,” as that term is defined in Rule 501 of Regulation D. 
 (h) Execution and Counterparts. This Agreement may be executed in two or more counterparts, each of which when so executed shall be deemed to be an original and, all of which taken together shall
constitute one and the same Agreement and shall become effective when counterparts have been signed by each party and delivered to the other party, it being understood that both parties need not sign the same counterpart. In the event that any
signature is delivered by facsimile transmission or by e-mail delivery of a “.pdf” format data file, such signature shall create a valid and binding obligation of the party executing (or on whose behalf such signature is executed) with the
same force and effect as if such facsimile or “.pdf” signature were the original thereof. 
 (i)
Governing Law. All questions concerning the construction, validity, enforcement and interpretation of this Agreement shall be determined in accordance with the provisions of the Purchase Agreement. 

(j) Cumulative Remedies. The remedies provided herein are cumulative and not exclusive of any other remedies
provided by law. 
 (k) Severability. If any term, provision, covenant or restriction of this Agreement
is held by a court of competent jurisdiction to be invalid, illegal, void or unenforceable, the remainder of the terms, provisions, covenants and restrictions set forth herein shall remain in full force and effect and shall in no way be affected,
impaired or invalidated, and the parties hereto shall use their good faith reasonable efforts to find and employ an alternative means to achieve the same or substantially the same result as that contemplated by such term, provision, covenant or
restriction. It is hereby stipulated and declared to be the intention of the parties that they would have executed the remaining terms, provisions, covenants and restrictions without including any of such that may be hereafter declared invalid,
illegal, void or unenforceable. 
 (l) Headings. The headings in this Agreement are for convenience only
and shall not limit or otherwise affect the meaning hereof. 
 [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK] 

  
 15 

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 AMYRIS, INC.

		
	 By:
	 	 /s/ John Melo

	 Name:
	 	 John Melo

	 Title:
	 	 President and Chief Executive Officer

 [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK] 

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 PURCHASERS:

	
	 Fidelity Advisor Series I: Fidelity Advisor

	 Equity Income Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Variable Insurance Products Fund: Equity

	 Income Portfolio

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Devonshire Trust: Fidelity Equity

	 Income Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Destiny Portfolios: Fidelity

	 Advisor Diversified Stock Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Variable Insurance Products Fund III:

	 Growth & Income Portfolio

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Advisors Series I: Fidelity Advisor

	 Growth & Income Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Securities Fund: Fidelity Growth &

	 Income Portfolio

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Commonwealth Trust: Fidelity

	 Large Cap Stock Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Advisor Series I: Fidelity Advisor

	 Large Cap Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Variable Insurance Products Fund III:

	 Balanced Portfolio

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Advisor Series I: Fidelity Advisor

	 Dividend Growth Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Securities Fund: Fidelity Dividend

	 Growth Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Rutland Square Trust II: Strategic

	 Advisers Core Multi-Manager Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 IN WITNESS WHEREOF, the parties have executed this Registration Rights
Agreement as of the date first written above. 
  

			
	 Fidelity Rutland Square Trust II: Strategic

	 Advisers Core Fund

		
	 By:
	 	 /s/ Adrien Deberghes

		 	 (signature)

 

			
	 Name:
	 	 Adrien Deberghes

	 Title:
	 	 Deputy Treasurer

		
	 Address:
	 	 Andrew Boyd

		 	 Fidelity Investments

		 	 82 Devonshire St., VI3H

		 	 Boston, MA 02109

		
	 Tel:
	 	 (617) 563-5144

	 Fax:
	 	 (617) 385-2833

	 E-mail Address:
	 	 andrew.boyd@fmr.com

 ANNEX A 
 PLAN OF DISTRIBUTION 
 We are registering the shares of common
stock previously issued to the selling stockholders and issuable upon conversion of the Convertible Notes previously issued to the selling stockholders to permit the resale of these shares of common stock by the holders of the common stock and
Convertible Notes from time to time after the date of this prospectus. We will not receive any of the proceeds from the sale by the selling stockholders of the shares of common stock. We will bear all fees and expenses incident to our obligation to
register the shares of common stock. 
 The selling stockholders may sell all or a portion of the shares of
common stock beneficially owned by them and offered hereby from time to time directly or through one or more underwriters, broker-dealers or agents. If the shares of common stock are sold through underwriters or broker-dealers, the selling
stockholders will be responsible for underwriting discounts or commissions or agent’s commissions. The shares of common stock may be sold in one or more transactions at fixed prices, at prevailing market prices at the time of the sale, at
varying prices determined at the time of sale, or at negotiated prices. The selling stockholders will act independently of us in making decisions with respect to the timing, manner and size of each sale. These sales may be effected in transactions,
which may involve crosses or block transactions, 
  

	 	•	 	 on any national securities exchange or quotation service on which the securities may be listed or quoted at the time of sale;

  

	 	•	 	 in the over-the-counter market; 

  

	 	•	 	 in transactions otherwise than on these exchanges or systems or in the over-the-counter market; 

 

	 	•	 	 through the writing of options, whether such options are listed on an options exchange or otherwise; 

 

	 	•	 	 ordinary brokerage transactions and transactions in which the broker-dealer solicits purchasers; 

 

	 	•	 	 block trades in which the broker-dealer will attempt to sell the shares as agent but may position and resell a portion of the block as principal to
facilitate the transaction; 

  

	 	•	 	 purchases by a broker-dealer as principal and resale by the broker-dealer for its account; 

 

	 	•	 	 an exchange distribution in accordance with the rules of the applicable exchange; 

 

	 	•	 	 privately negotiated transactions; 

  

	 	•	 	 short sales; 

	 	•	 	 through the distribution of the common stock by any selling stockholders to its partners, members or stockholders; 

 

	 	•	 	 through one or more underwritten offerings on a firm commitment or best efforts basis; 

 

	 	•	 	 sales pursuant to Rule 144; 

  

	 	•	 	 broker-dealers may agree with the selling stockholders to sell a specified number of such shares at a stipulated price per share;

  

	 	•	 	 a combination of any such methods of sale; and 

  

	 	•	 	 any other method permitted pursuant to applicable law. 

If the selling stockholders effect such transactions by selling shares of common stock to or through underwriters,
broker-dealers or agents, such underwriters, broker-dealers or agents may receive commissions in the form of discounts, concessions or commissions from the selling stockholders or commissions from purchasers of the shares of common stock for whom
they may act as agent or to whom they may sell as principal (which discounts, concessions or commissions as to particular underwriters, broker-dealers or agents may be in excess of those customary in the types of transactions involved). In
connection with sales of the shares of common stock or otherwise, the selling stockholders may enter into hedging transactions with broker-dealers, which may in turn engage in short sales of the shares of common stock in the course of hedging in
positions they assume. The selling stockholders may also sell shares of common stock short and deliver shares of common stock covered by this prospectus to close out short positions and to return borrowed shares in connection with such short sales.
The selling stockholders may also loan or pledge shares of common stock to broker-dealers that in turn may sell such shares. 
 The selling stockholders may pledge or grant a security interest in some or all of the shares of common stock owned by them and, if they default in the performance of their secured obligations, the
pledgees or secured parties may offer and sell the shares of common stock from time to time pursuant to this prospectus or any amendment to this prospectus under Rule 424(b)(3) or other applicable provision of the Securities Act amending, if
necessary, the list of selling stockholders to include the pledgee, transferee or other successors in interest as selling stockholders under this prospectus. The selling stockholders also may transfer and donate the shares of common stock in other
circumstances in which case the transferees, donees, pledgees or other successors in interest will be the selling beneficial owners for purposes of this prospectus. 

The selling stockholders and any broker-dealer participating in the distribution of the shares of common stock may be
deemed to be “underwriters” within the meaning of the Securities Act, and any commission paid, or any discounts or concessions allowed to, any such broker-dealer may be deemed to be underwriting commissions or discounts under the
Securities Act. At the time a particular offering of the shares of common stock is made, a prospectus supplement, if required, will be distributed which will set forth the aggregate amount of shares of common stock being offered and the terms of the
offering, including the name or names of any broker-dealers or agents, any discounts, commissions and other terms constituting compensation from the selling stockholders and any discounts, commissions or concessions allowed or reallowed or paid to

 
broker-dealers. The selling stockholders may indemnify any broker-dealer that participates in transactions involving the sale of the shares of common stock against certain liabilities, including
liabilities arising under the Securities Act. 
 Under the securities laws of some states, the shares of common
stock may be sold in such states only through registered or licensed brokers or dealers. In addition, in some states the shares of common stock may not be sold unless such shares have been registered or qualified for sale in such state or an
exemption from registration or qualification is available and is complied with. 
 There can be no assurance
that any selling stockholder will sell any or all of the shares of common stock registered pursuant to the registration statement, of which this prospectus forms a part. 

The selling stockholders and any other person participating in such distribution will be subject to applicable provisions
of the Exchange Act and the rules and regulations thereunder, including, without limitation, Regulation M of the Exchange Act, which may limit the timing of purchases and sales of any of the shares of common stock by the selling stockholders and any
other participating person. Regulation M may also restrict the ability of any person engaged in the distribution of the shares of common stock to engage in market-making activities with respect to the shares of common stock. All of the foregoing may
affect the marketability of the shares of common stock and the ability of any person or entity to engage in market-making activities with respect to the shares of common stock. 

We will pay all expenses of the registration of the shares of common stock pursuant to the registration rights agreement,
estimated to be $             in total, including, without limitation, SEC filing fees and expenses of compliance with state securities or “Blue Sky” laws;
provided, however, that a selling stockholder will pay all underwriting discounts and selling commissions, if any. We will indemnify the selling stockholders against liabilities, including some liabilities under the Securities Act, in
accordance with the registration rights agreement, or the selling stockholders will be entitled to contribution. We may be indemnified by the selling stockholders against civil liabilities, including liabilities under the Securities Act, that may
arise from any written information furnished to us by the selling stockholder specifically for use in this prospectus, in accordance with the registration rights agreement, or we may be entitled to contribution. 

Once sold under the registration statement, of which this prospectus forms a part, the shares of common stock will be
freely tradable in the hands of persons other than our affiliates. 

 ANNEX B 
 AMYRIS, INC. 
 SELLING STOCKHOLDER NOTICE AND QUESTIONNAIRE 

The undersigned holder of shares of the common stock, par value $0.01 per share, of Amyris, Inc. (the
“Company”) understands that the Company intends to file with the Securities and Exchange Commission a registration statement on Form S-3 (the “Resale Registration Statement”) for the registration and the resale
under Rule 415 of the Securities Act of 1933, as amended (the “ Securities Act”), of the Registrable Securities in accordance with the terms of the Registration Rights Agreement. All capitalized terms not otherwise defined herein
shall have the meanings ascribed thereto in the Registration Rights Agreement. 
 In order to sell or otherwise
dispose of any Registrable Securities pursuant to the Resale Registration Statement, a holder of Registrable Securities generally will be required to be named as a selling stockholder in the related prospectus or a supplement thereto (as so
supplemented, the “Prospectus”), deliver the Prospectus to purchasers of Registrable Securities (including pursuant to Rule 172 under the Securities Act) and be bound by the provisions of the Registration Rights Agreement (including
certain indemnification provisions, as described below). Holders must complete and deliver this Notice and Questionnaire in order to be named as selling stockholders in the Prospectus.  

Certain legal consequences arise from being named as a selling stockholder in the Resale Registration Statement and the
Prospectus. Holders of Registrable Securities are advised to consult their own securities law counsel regarding the consequences of being named or not named as a selling stockholder in the Resale Registration Statement and the Prospectus.

 NOTICE 
 The undersigned holder (the “Selling Stockholder”) of Registrable Securities hereby gives notice to the Company of its intention to sell or otherwise dispose of Registrable Securities
owned by it and listed below in Item (3), unless otherwise specified in Item (3), pursuant to the Resale Registration Statement. The undersigned, by signing and returning this Notice and Questionnaire, understands and agrees that it will be bound by
the terms and conditions of this Notice and Questionnaire and the Registration Rights Agreement. 
 The
undersigned hereby provides the following information to the Company and represents that such information is accurate and complete: 
 QUESTIONNAIRE 
  

	1.	 Name. 

  

	 	(a)	 Full Legal Name of Selling Stockholder: 

  

					
		 	
                 
                                
	 	

	 	(b)	 Full Legal Name of Registered Holder (if not the same as (a) above) through which Registrable Securities Listed in Item 3 below are held:

  

			
	
                 
                                
	 	

  

	 	(c)	 Full Legal Name of Natural Control Person (which means a natural person who directly or indirectly alone or with others has power to vote or dispose
of the securities covered by the questionnaire): 

  

			
	
                 
                                
	 	

  

	2.	Address for Notices to Selling Stockholder: 

  

 
  

 
  

 

Telephone:                     
                                         
                                         
                                         
                                         
                                         
          

Fax:                      
                                         
                                         
                                         
                                         
                                         
                      
 Contact Person:                              
                                         
                                         
                                         
                                         
                                  

			
	 E-mail address of Contact Person:
	  	  

  

	3.	 Beneficial Ownership of Registrable Securities: 

 

	 	(a)	 Type and Number of Registrable Securities beneficially owned: 

 

			
	
                 
                                
	 	
	
                 
                                
	 	
	
                 
                                
	 	

  

	 	(b)	 Number of shares of Common Stock to be registered pursuant to this Notice for resale: 

 

			
	
                 
                                
	 	
	
                 
                                
	 	
	
                 
                                
	 	

  

	4.	Broker-Dealer Status: 

  

	 	(a)	 Are you a broker-dealer? 

 Yes   ̈    No   ̈ 

 

	 	(b)	 If “yes” to Section 4(a), did you receive your Registrable Securities as compensation for investment banking services to the Company?

Yes   ̈    No   ̈ 

 Note:  If no, the Commission’s staff has indicated that you should be
identified as an underwriter in the Registration Statement. 
  

	 	(c)	 Are you an affiliate of a broker-dealer? 

 Yes   ̈    No   ̈ 

Note:  If yes, provide a narrative explanation below: 

 

			
	
                 
                                
	 	
	
                 
                                
	 	

  

	 	(d)	 If you are an affiliate of a broker-dealer, do you certify that you bought the Registrable Securities in the ordinary course of business, and at the
time of the purchase of the Registrable Securities to be resold, you had no agreements or understandings, directly or indirectly, with any person to distribute the Registrable Securities? 

Yes   ̈    No   ̈ 
 Note:  If no, the Commission’s staff has indicated that you should
be identified as an underwriter in the Registration Statement. 
  

	5.	 Beneficial Ownership of Other Securities of the Company Owned by the Selling Stockholder. 

Except as set forth below in this Item 5, the undersigned is not the beneficial or registered owner of any securities of the
Company other than the Registrable Securities listed above in Item 3. 
 Type and amount of other securities
beneficially owned: 
  
  

 
  

 
  

 
  

 

	6.	Relationships with the Company: 

 Except as set forth below, neither the undersigned nor any of its affiliates, officers, directors or principal equity holders (owners of 5% of more of the equity securities of the undersigned) has held
any position or office or has had any other material relationship with the Company (or its predecessors or affiliates) during the past three years. 
 State any exceptions here: 
  

 
  

 

			
	
                 

	 	

  
  

 

			
	
                 

	 	

  

	7.	Plan of Distribution: 

The undersigned has reviewed the form of Plan of Distribution attached as Annex A to the Registration Rights Agreement, and hereby
confirms that, except as set forth below, the information contained therein regarding the undersigned and its plan of distribution is correct and complete. 
 State any exceptions here: 
  

 
  

 

			
	
                 

	 	

  
  

 
  

			
	
                 

	 	

 *********** 
 The undersigned agrees to promptly notify the Company of any inaccuracies or changes in the information provided herein that may occur subsequent to the date hereof and prior to the effective date of any
applicable Resale Registration Statement. All notices hereunder and pursuant to the Registration Rights Agreement shall be made in writing, by hand delivery, confirmed or facsimile transmission, first-class mail or air courier guaranteeing overnight
delivery at the address set forth below. In the absence of any such notification, the Company shall be entitled to continue to rely on the accuracy of the information in this Notice and Questionnaire. 

By signing below, the undersigned consents to the disclosure of the information contained herein in its answers to Items (1) through
(7) above and the inclusion of such information in the Resale Registration Statement and the Prospectus. The undersigned understands that such information will be relied upon by the Company in connection with the preparation or amendment of any
such Registration Statement and the Prospectus. 
 By signing below, the undersigned acknowledges that it understands its
obligation to comply, and agrees that it will comply, with the provisions of the Exchange Act and the rules and regulations thereunder, particularly Regulation M in connection with any offering of Registrable Securities pursuant to the Resale
Registration Statement. The undersigned also acknowledges that it understands that the answers to this Questionnaire are furnished for use in connection with Registration Statements filed pursuant to the Registration Rights Agreement and any
amendments or supplements thereto filed with the Commission pursuant to the Securities Act. 
 By returning this Questionnaire,
the undersigned will be deemed to be aware of the foregoing interpretation. 
 I confirm that, to the best of my knowledge and
belief, the foregoing statements (including, without limitation the answers to this Questionnaire) are correct. 

 IN WITNESS WHEREOF the undersigned, by authority duly given, has caused this Questionnaire
to be executed and delivered either in person or by its duly authorized agent. 
  

											
	 Dated:
	 	  
	 		 	 Beneficial Owner:
	 	  

					
		 		 		 	 By:
	 	  

		 		 		 		 	 Name:
	 	
		 		 		 		 	 Title:First Amendment to Amended and Restated Investors' Rights Agreement

 Exhibit 4.06 
 AMYRIS, INC. 
 AMENDMENT NO. 1 TO AMENDED AND RESTATED INVESTORS’
RIGHTS AGREEMENT 
 This Amendment No. 1 to the Amended and Restated Investors’ Rights Agreement (this
“Amendment”) is made and entered into as of February 23, 2012, by and among Amyris, Inc., a Delaware corporation (the “Company”), the Investors and the Common Holders. 

RECITALS 
 WHEREAS, the Company, the Investors and the Common Holders are parties to that certain Amended and Restated Investors’ Rights Agreement dated June 21, 2010 (the “Rights
Agreement”). Capitalized terms used in this Amendment and not otherwise defined herein have the meanings ascribed to them in the Rights Agreement. 
 WHEREAS, the Company, the Investors and the Common Holders desire to make certain amendments to the Rights Agreement and add certain parties thereto. 

WHEREAS, pursuant to Section 3.7 of the Rights Agreement, the Rights Agreement may be amended with the written consent of the
(i) Company, and (ii) the holders of a majority of the Registrable Securities currently outstanding (together, the “Requisite Majority”). 
 WHEREAS, the undersigned parties constitute the Requisite Majority. 
 NOW,
THEREFORE, the parties hereby agree as follows: 
 1. AMENDMENT OF SECTION 1.1(c) OF THE RIGHTS AGREEMENT.
Section 1.1(c) of the Rights Agreement shall be deleted in its entirety and replaced with the following: 
 “The term
“Holder” means (i) any Investor having purchased more than 5% of the Preferred Stock sold by the Company, (ii) except with respect to Sections 1.2, 1.12, 1.13 and Section 2 hereof, the Common Holders owning or
having the right to acquire Registrable Securities or any assignee thereof in accordance with Section 1.13 hereof, (iii) each “Purchaser” as such term is defined in that certain Securities Purchase Agreement dated as of
February 22, 2012 by and among the Company and the Purchasers identified therein (each a “Purchaser”), and (iv) an additional Investor hereto (to be identified to each Purchaser by written notice via electronic mail from
the Secretary of the Company and to execute a counterpart signature page hereto prior to such party becoming an Investor and a Holder hereunder, the “Note Investor”) that purchases (a) promissory note(s) convertible into Common
Stock with a principal amount of up to $30,000,000 in a private placement by the Company to be completed on or prior to February 29, 2012 (the “Convertible Notes”).” 

2. AMENDMENT OF SECTION 1.1(f) OF THE RIGHTS AGREEMENT. Section 1.1(f) of the Rights Agreement shall be deleted in its
entirety and replaced with the following: 

 “The term “Registrable Securities” means: (i) any Common Stock issued or
issuable upon conversion of the Preferred Stock of the Company, (ii) other than with respect to Sections 1.2, 1.12, 1.13 and Section 2 hereof, any Common Stock of the Company held by the Common Holders, (iii) the Common Shares,
as defined in that certain Stock Transfer Agreement, dated December 24, 2009, by and among the Company, certain holders of the Company’s Preferred Stock and certain holders of the Company’s Common Stock, (iv) shares of Common
Stock issued pursuant to that certain Securities Purchase Agreement dated as of February 22, 2012 by and among the Company and the Purchasers, (v) Common Stock issued or issuable upon conversion of the Convertible Notes; and (vi) any
Common Stock of the Company issued as (or issuable upon the conversion or exercise of any warrant, right or other security that is issued as) a dividend or other distribution with respect to, or in exchange for, or in replacement of, the securities
set forth in subsection (i), (ii), (iii) or (iv) hereof, excluding, however, any Registrable Securities which (A) have previously been registered or which have been sold to the public either pursuant to a registration statement or
Rule 144, (B) which have been sold in a private transaction in which the transferor’s rights under this Agreement are not assigned, or (C) held by a Holder (together with its affiliates) if, as reflected on the Company’s list of
stockholders, such Holder (together with its affiliates) holds less than 1% of the Company’s outstanding Common Stock (treating all shares of Preferred Stock on an as converted basis)” 

3. AMENDMENT OF SECTION 1.12 OF THE RIGHTS AGREEMENT. Section 1.12 of the Rights Agreement shall be amended such that
the following sentence at the end of the Section shall be deleted in its entirety: 
 “The Company shall not be obligated to
effect any registration pursuant to this Section 1.12 if the Company delivers to the Holders requesting registration under this Section 1.12 an opinion, in form and substance reasonably acceptable to such Holders, of counsel reasonably
satisfactory to such Holders, that all Registrable Securities so requested to be registered may be sold or transferred pursuant to Rule 144 under the Act.” 
 4. AMENDMENT OF SECTION 1.15 OF THE RIGHTS AGREEMENT. Section 1.15 of the Rights Agreement shall be deleted in its entirety and replaced with the following: 

“No Holder shall be entitled to exercise any right provided for in this Section 1 after February 23, 2017.”

 5. AMENDMENT OF SECTION 3.5 OF THE RIGHTS AGREEMENT. Section 3.5 of the Rights Agreement shall be amended
such that the following words are added to the end of the Section: 
 “Notwithstanding anything to the contrary in this
Agreement, in the event the Company is required to provide notice to Holders pursuant to the terms of this Agreement, the Company shall only be required to provide such notice to those Holders who hold shares of record of the Company’s capital
stock at the time such notice is required to be provided by the Company.” 

 6. ADDITION OF PARTIES TO RIGHTS AGREEMENT. Effective upon the execution of
this Amendment, each Purchaser shall each become a party to the Rights Agreement as an “Investor”, and in connection therewith they shall each execute a counterpart signature page to the Rights Agreement in substantially the form attached
hereto as Exhibit A. Effective immediately following both notification to the Purchasers with respect to the identity of the Note Holder as contemplated by Section 1.1(c) as amended hereby and execution of a counterpart signature page by
the Note Investor, Note Investor shall become a party to the Rights Agreement as an “Investor.” 
 7. FULL FORCE
AND EFFECT. Except as expressly modified by this Amendment, the terms of the Rights Agreement shall remain in full force and effect. 
 8. GOVERNING LAW. This Amendment shall be governed by and construed under the internal laws of the State of California as applied to agreements among California residents entered into and to
be performed entirely within California, without reference to principles of conflict of laws or choice of laws. 
 9.
INTEGRATION. This Amendment and the Rights Agreement and the documents referred to herein and therein and the exhibits and schedules thereto, 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. 

10. COUNTERPARTS; FACSIMILE. This Amendment may be executed in two (2) 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 the signature page by such method
will be deemed to have the same effect as if the original signature had been delivered to the other parties. 

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

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

			
	COMPANY:
	
	AMYRIS, INC.
		
	By:	 	 /s/ John Melo

		 	John Melo, Chief Executive Officer

 [SIGNATURE PAGE TO AMENDMENT
NO. 1 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT] 

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

			
	INVESTORS:
	
	KPCB HOLDINGS, INC., AS NOMINEE
		
	By:	 	 /s/ John Doerr

	Name:	 	  

	Title:	 	  

 [SIGNATURE PAGE TO AMENDMENT
NO. 1 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT] 

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

			
	INVESTORS:
	
	KHOSLA VENTURES II, L.P.
		
	By:	 	 /s/ Samir Kaul

	Name:	 	 Samir Kaul

	Title:	 	  

	
	KHOSLA VENTURES III, LP
		
	By:	 	 /s/ Samir Kaul

	Name:	 	 Samir Kaul

	Title:	 	  

 [SIGNATURE PAGE TO AMENDMENT
NO. 1 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT] 

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

			
	INVESTORS:
	
	TOTAL GAS & POWER USA, SAS
		
	By:	 	 /s/ Arnaud Chaperon

	Name:	 	 Arnaud Chaperon

	Title:	 	 Chairman

 [SIGNATURE PAGE TO AMENDMENT
NO. 1 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT] 

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

			
	INVESTORS:
	
	MAXWELL (MAURITIUS) PTE LTD
		
	By:	 	 /s/ Jonathan Ang

	Name:	 	 Jonathan Ang

	Title:	 	 Authorised Signatory

 [SIGNATURE PAGE TO AMENDMENT
NO. 1 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT] 

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

			
	INVESTORS:
	
	NAXYRIS S.A.
		
	By:	 	 /s/ S. Reckinger

	Name:	 	 S. Reckinger

	Title:	 	 Director

 [SIGNATURE PAGE TO AMENDMENT
NO. 1 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT] 

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

			
	COMMON HOLDERS
	
	 /s/ John Melo

	 John Melo

		
	 Address:
	 	  

		 	  

		 	  

 [SIGNATURE PAGE TO AMENDMENT
NO. 1 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT] 

 EXHIBIT A 

Counterpart Signature Page to Amended and Restated Investors’ Rights Agreement 

 IN WITNESS WHEREOF, the parties have executed this Amended and Restated Investors’
Rights Agreement as of the date first above written. 
 INVESTOR: 

        [              
              ] 
 [SIGNATURE
PAGE TO AMENDMENT NO. 1 TO AMYRIS, INC. AMENDED AND RESTATED INVESTORS’
RIGHTS AGREEMENT]

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