Exhibit 10.7

This FIRST SUPPLEMENTAL INDENTURE, dated as of September 25, 2009 (this
“Supplemental Indenture”), is made by and among VERENIUM CORPORATION, a Delaware
corporation (the “Company”), and WELLS FARGO BANK, NATIONAL ASSOCIATION, as
Trustee (the “Trustee”), under the Indenture referred to herein. Capitalized
terms used herein and not otherwise defined herein shall have the meanings
ascribed to them in the Indenture referred to below.

W I T N E S S E T H:

WHEREAS, the Company and the Trustee are parties to an Indenture dated as of
September 1, 2009 (the “Indenture”), providing for the issuance of 9.00%
Convertible Senior Secured Notes due 2027 (herein called the “Securities”);

WHEREAS, the Company on or about September 9, 2009 effected a one-for-twelve
reverse stock split of its common stock whereby each twelve shares of the
Company’s common stock that were issued and outstanding or held in treasury at
5:00 PM eastern time on such date (the “Effective Time”) were automatically
combined into one share, subject to the elimination of fractional shares (the
“Stock Split”);

WHEREAS, upon the Stock Split, pursuant to Section 10.06(a)(4) of the Indenture,
the Conversion Rate of the Securities automatically adjusted at the Effective
Time from the prior Conversion Rate of 1,250 shares of common stock per $1,000
principal amount of Securities to the post Stock Split Conversion Rate of
104.1667 shares of common stock per $1,000 principal amount of Securities which
results in an initial Conversion Price of $9.60 per share of common stock;

WHEREAS, pursuant to Section 2.19 of the Indenture, the Company desires to issue
additional Securities (the “Additional Securities”) on the same terms and
conditions (except for any difference in the issue price therefor and interest
accrued prior to the date of issuance thereof) and with the same CUSIP number as
the Securities initially issued under the Indenture;

WHEREAS, Section 9.01(vii) of the Indenture provides that the Company and the
Trustee may amend the Indenture and the Securities without the consent or
affirmative vote of any Holders of the Securities for the purposes specified
therein, and Section 2.19 of the Indenture provides that the Company may issue
the Additional Securities without the consent or affirmative vote of any Holders
of the Securities;

WHEREAS, this Supplemental Indenture has been duly authorized by all necessary
corporate action on the part of the Company;

WHEREAS, the Trustee is authorized to execute and deliver this Supplemental
Indenture; and

WHEREAS, all things necessary to make this Supplemental Indenture a valid
supplemental indenture and agreement according to its terms have been done.

NOW, THEREFORE, in consideration of the premises and for other good and valuable
consideration, the receipt and sufficiency of which is hereby acknowledged, the
Company and the Trustee mutually covenant and agree as follows for the equal and
ratable benefit of the Holders of the Securities:

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ARTICLE 1

INDENTURE UPDATES

SECTION 1.1 Conversion of Securities. In accordance with Section 10.06 of the
Indenture, at and after the Effective Time, the Holder of each Security then
outstanding shall have the right, during the period such Security shall be
convertible as specified in Article X of the Indenture, to convert such Security
into a number of shares of common stock of the Company equal to the Conversion
Rate post Stock Split, which for the avoidance of doubt, shall be equal to
104.1667 shares of common stock per $1,000 principal amount of Securities which
results in a corresponding Conversion Price of $9.60 per share of common stock.

SECTION 1.2 Increase in Outstanding Securities. In accordance with Section 2.19
of the Indenture, the Securities have been reopened and an additional aggregate
principal amount of Securities equal to $893,000 which results in an aggregate
principal amount of outstanding Securities after the issuance of the Additional
Securities of $13,707,000. Such Additional Securities were issued on the same
terms and conditions (except for any difference in the issue price therefor) and
with the same CUSIP number as the Securities initially issued under the
Indenture and will form the same series with the Securities initially issued
under the Indenture. The Securities initially issued under the Indenture and the
Additional Securities rank equally and ratably and will be treated as a single
series of debt securities for all purposes under the Indenture.

SECTION 1.3 Update Fundamental Change Make-Whole Table.

(a) Pursuant to clause (iii) of the proviso to Section 10.16(B) of the
Indenture, in connection with the Stock Split, the Make-Whole Applicable
Increase table provided in Section 10.16(B) is hereby replaced with the table
set forth immediately below:

 

    Effective Date “Applicable
Price   October 1,
2009   April 1,
2010   October 1,
2010   April 1,
2011   October 1,
2011   April 1,
2012 $ 7.20   31.87   25.49   19.12   12.75   6.37   0.00 $ 8.40   26.98   21.58
  16.19   10.79   5.40   0.00 $ 9.75   20.34   16.27   12.20   8.14   4.07  
0.00 $ 11.10   15.31   12.25   9.19   6.12   3.06   0.00 $ 12.45   11.38   9.10
  6.83   4.55   2.28   0.00 $ 13.80   8.21   6.57   4.93   3.28   1.64   0.00 $
15.15   5.61   4.49   3.37   2.24   1.12   0.00 $ 16.50   3.43   2.75   2.06  
1.37   0.69   0.00 $ 17.85   1.59   1.27   0.95   0.63   0.32   0.00 $ 19.20  
0.00   0.00   0.00   0.00   0.00   0.00”

(b) Pursuant to clause (iii) of the proviso to Section 10.16(B) of the
Indenture, in connection with the Stock Split, clause (ii) of the proviso to
Section 10.16(B) of the Indenture is replaced in its entirety as follows:

 

2.

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“(ii) if the actual Applicable Price of such Make-Whole Fundamental Change is
greater than $19.20 per share (subject to adjustment as provided in
Section 10.16(B)(iii)), or if the actual Applicable Price of such Make-Whole
Fundamental Change is less than $7.20 per share (subject to adjustment as
provided in Section 10.16(B)(iii)), then the Make-Whole Applicable Increase
shall be equal to zero (0);”

SECTION 1.4 Trustee’s Acceptance. The Trustee hereby accepts this Supplemental
Indenture and agrees to perform the same under the terms and conditions set
forth in the Indenture.

ARTICLE 2

MISCELLANEOUS

SECTION 2.1 Effectiveness of Supplemental Indenture. Upon the execution and
delivery of this Supplemental Indenture by the Company and the Trustee and an
authenticated Global Note reflecting the increase in the aggregate principal
amount of the Securities, the Indenture shall be supplemented in accordance
herewith, and this Supplemental Indenture shall form a part of the Indenture for
all purposes, and every Holder of Securities heretofore or hereafter
authenticated and delivered under the Indenture shall be bound hereby.

SECTION 2.2 Indenture Remains in Full Force and Effect. Except as supplemented
hereby, all provisions in the Indenture shall remain in full force and effect.

SECTION 2.3 Indenture and Supplemental Indenture Construed Together. This
Supplemental Indenture is an indenture supplemental to and in implementation of
the Indenture, and the Indenture and this Supplemental Indenture shall
henceforth be read and construed together.

SECTION 2.4 Confirmation and Preservation of Indenture. The Indenture as
supplemented by this Supplemental Indenture is in all respects confirmed and
preserved.

SECTION 2.5 Severability. In case any provision in this Supplemental Indenture
shall be invalid, illegal or unenforceable, the validity, legality and
enforceability of the remaining provisions shall not in any way be affected or
impaired thereby.

SECTION 2.6 Headings. The Article and Section headings of this Supplemental
Indenture have been inserted for convenience of reference only, are not to be
considered part of this Supplemental Indenture and shall in no way modify or
restrict any of the terms or provisions hereof.

SECTION 2.7 Benefits of Supplemental Indenture, etc. Nothing in this
Supplemental Indenture, express or implied, shall give to any person, other than
the parties hereto and their successors hereunder and the Holders of the
Securities, any benefit of any legal or equitable right, remedy or claim under
the Indenture, this Supplemental Indenture or the Securities.

SECTION 2.8 Certain Duties and Responsibilities of the Trustee. In entering into
this Supplemental Indenture, the Trustee shall be entitled to the benefit of
every provision of the Indenture relating to the conduct or affecting the
liability or affording protection to the Trustee, whether or not elsewhere
herein so provided.

SECTION 2.9 Counterparts. The parties may sign any number of copies of this
Supplemental Indenture. Each signed copy shall be an original, but all of them
together represent the same agreement.

 

3.

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SECTION 2.10 Governing Law. The laws of the State of New York, without regard to
principles of conflicts of law, shall govern this Supplemental Indenture.

SECTION 2.11 The Trustee. The Trustee shall not be responsible in any manner
whatsoever for or in respect of the validity or sufficiency of this Supplemental
Indenture or for or in respect of the recitals contained herein (other than the
seventh recital), all of which recitals are made solely by the Company.

[Signature Pages Follow]

 

4.

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IN WITNESS WHEREOF, the parties have caused this Supplemental Indenture to be
duly executed as of the date first written above.

 

COMPANY: VERENIUM CORPORATION

By:

 

/s/ Gerald M. Haines II

Name:

 

Gerald M. Haines II

Title:

 

Executive Vice President

THE TRUSTEE: WELLS FARGO BANK, NATIONAL ASSOCIATION

By:

 

/s/ Lynn M. Steiner

Name:

 

Lynn M. Steiner

Title:

 

Vice President