Document:

Amendment to Employment Agreement -- James E. Levine

 Exhibit 10.58 
 AMENDMENT TO 
 EMPLOYMENT AGREEMENT 

THIS AMENDMENT TO EMPLOYMENT AGREEMENT
(the “Amendment”) is effective as of March 31, 2011 (the “Effective Date”), and as of the Effective Date amends the Employment Agreement dated April 24, 2009 by and between
VERENIUM CORPORATION (hereinafter the “Company”), and James Levine (hereinafter “Executive”) (the “Employment Agreement”).

 RECITALS 
 WHEREAS, the Company and Executive wish to amend the Employment Agreement as of the Effective Date to reflect the Executive’s (1) new duties and
responsibilities as the Company’s President and Chief Executive Officer, and (2) revised compensation arrangement and other terms of employment; 
 NOW, THEREFORE, the Company and Executive, in consideration of the mutual promises set forth herein, agree that the Employment Agreement is amended as
of the Effective Date as follows: 
 ARTICLE 1 
 AMENDMENTS 
 1.1 Section 2. Section 2 of the
Employment Agreement is hereby amended and restated in its entirety as follows: 
 “2. Duties and
Responsibilities. During the Term of this Agreement, you shall have, and you agree to carry out to the best of your ability, the duties and responsibilities of President and Chief Executive Officer. You shall have such executive
responsibilities and duties as are assigned by the Board of Directors of the Company (the “Board”) and are consistent with the positions of President and Chief Executive Officer. In the performance of your duties and
responsibilities hereunder, you shall regularly report to the Board. You agree to devote your full business time, attention and energies to the business and interests of the Company during the Term of this Agreement and you will not accept any
outside position without the prior written consent of the Board, except that you may serve on up to a maximum of two boards of directors provided that you have approval of the Board’s Compensation Committee and provided that your time spent in
such service is reasonable and does not detract from the performance of your duties to the Company. You warrant that you are free to enter into and fully perform this Agreement and are not subject to any employment, confidentiality, non-competition
or other agreement which would restrict your performance under this Agreement. As soon as practicable following the Effective Date, you will be appointed to serve in the class of directors whose terms expire at the Company’s 2013 annual
stockholders’ meeting. In connection with the termination of your employment by the Company as President and Chief Executive Officer, you shall resign from the Board effective simultaneously with the effective date of such termination, unless
otherwise requested by the remaining Board members. 

  
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 You consent and agree to permanently relocate your primary residence to the San Diego,
California area, which relocation is anticipated will occur sometime on or around June 2011 (the applicable relocation date is the “Relocation Date”). From and following the Relocation Date, you shall fulfill your duties and
responsibilities to the Company hereunder primarily from the Company’s office located in San Diego, California; provided, however, that the Company may from time to time require you to travel temporarily to other locations in connection with
the Company’s business. You hereby acknowledge that your relocation to the San Diego, California area does not trigger any right by you to resign your employment for “Good Reason.”” 

1.2 Section 3(a). The first sentence of Section 3(a) of the Employment Agreement is hereby amended and restated
in its entirety to read as follows: 
 “Commencing on the Effective Date, and during the Term of this Agreement, the Company
will pay you a base salary at not less than the biweekly rate of $15,000.00 (“Base Salary”), minus withholdings as required by law or other deductions authorized by you, which amount shall be paid to you in periodic
installments in accordance with the Company’s payroll practices then in effect.” 
 1.3
Section 3(b). The first sentence of Section 3(b) of the Employment Agreement is hereby amended and restated in its entirety to read as follows: 
 “For each calendar year during the Term of this Agreement, you will be eligible to receive an annual performance-based incentive bonus, based upon the achievement of milestones set by the Board, with
a target bonus of 60% percent of the Base Salary earned during such period (the “Bonus”).” 

1.4 Section 3(e). Section 3(e) of the Employment Agreement is hereby amended and restated in its entirety to read
as follows: 
 “(e) Stock Options and Restricted Stock. The Company granted a stock option to you on
February 24, 2011 to purchase up to 164,491 shares of the Company’s common stock with an exercise price of $3.31 per share, subject to vesting and the other terms and conditions set forth in the stock option grant notice and agreement
previously provided to you. All Company stock option and restricted stock awards previously granted to you shall continue in effect from and following the Effective Date in accordance with their existing terms. You may be eligible to receive
additional grants of Company stock option and restricted stock awards in the sole discretion and subject to the approval of the Compensation Committee of the Board.” 
 1.5 Section 3(j). A new Section 3(j) is hereby added to the Employment Agreement as follows: 
 “(j) Relocation Expenses. The Company agrees to reimburse the reasonable and customary costs of relocation of your primary residence from Boston, Massachusetts to

  
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San Diego, California, under terms and conditions to be determined in good faith and pursuant to the mutual agreement of you and the Company.” 

1.6 Effective Date and Term of Amended Employment Agreement. With respect to application of the amendments to the
Employment Agreement that are set forth in this Amendment, all references to the “Effective Date” contained in the amended Employment Agreement are with respect to the date of March 31, 2011, and all references to the
“Term” of the Employment Agreement are with respect to the period of employment commencing on March 31, 2011. 
 ARTICLE 2 
 GENERAL PROVISIONS 

2.1 Impact of Amendment. Except as expressly amended by this Amendment, the terms of the Employment Agreement remain in
full force and effect. 
 2.2 Governing Law. The validity, interpretation, construction and performance of this
Amendment and the amended Employment Agreement and the rights of the parties thereunder shall be interpreted and enforced under the law of the Commonwealth of Massachusetts. 
 2.3 Validity. The invalidity or unenforceability of any provision of this Amendment or the Employment Agreement shall not affect the validity or enforceability of any other provision of this
Amendment or the Employment Agreement, which shall remain in full force and effect. 
 2.4 Controlling Document.
In case of conflict between any of the terms and condition of this Amendment and the Employment Agreement herein referred to, the terms and conditions of this Amendment shall control. 

2.5 Executive Acknowledgment. Executive acknowledges (a) that he has consulted with or has had the opportunity to
consult with independent counsel of his own choice concerning this Amendment, and has been advised to do so by the Company, and (b) that he has read and understands the Amendment, is fully aware of its legal effect, and has entered into it
freely based on his own judgment. 
 2.6 Counterparts. This Amendment may be executed in one or more counterparts,
all of which taken together shall constitute one and the same document. 
 [Remainder of Page Intentionally Left Blank]

  
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 Executed by the parties hereto on the date(s) set forth below: 

 
  

									
	EXECUTIVE	 		 	VERENIUM CORPORATION
					
	By:	 	/s/ James Levine	 		 	By:	 	/s/ Dr. James Cavanaugh
		 	James Levine	 		 		 	Dr. James Cavanaugh
		 		 		 		 	Chairman of the Board of Directors
					
	Date:	 	March 4, 2011	 		 	Date:	 	March 4, 2011

  
 4Amendment to Employment Agreement -- Jeffrey G. Black

 Exhibit 10.59 
 AMENDMENT TO 
 EMPLOYMENT AGREEMENT 

THIS AMENDMENT TO EMPLOYMENT AGREEMENT
(the “Amendment”) is effective as of March 31, 2011 (the “Effective Date”), and as of the Effective Date amends the Employment Agreement dated December 17, 2008 by and between
VERENIUM CORPORATION (hereinafter the “Company”), and Jeffrey Black (hereinafter “Executive”) (the “Employment Agreement”).

 RECITALS 
 WHEREAS, the Company and Executive wish to amend the Employment Agreement as of the Effective Date to reflect the Executive’s (1) new duties and
responsibilities as the Company’s Senior Vice President and Chief Financial Officer, and (2) revised compensation arrangement; 
 NOW, THEREFORE, the Company and Executive, in consideration of the mutual promises set forth herein, agree that the Employment Agreement is amended as
of the Effective Date as follows: 
 ARTICLE 1 
 AMENDMENTS 
 1.1 Section 2. Section 2 of the
Employment Agreement is hereby amended and restated in its entirety as follows: 
 “2. Duties and
Responsibilities. During the Term of this Agreement, you shall have, and you agree to carry out to the best of your ability, the duties and responsibilities of Senior Vice President and Chief Financial Officer. You shall have such
responsibilities and duties as are assigned by the President and Chief Executive Officer (“CEO”) and/or the Board of Directors of the Company (the “Board”) and are consistent with the position of
Senior Vice President and Chief Financial Officer. In the performance of your duties and responsibilities hereunder, you shall regularly report to the CEO. You agree to devote your full business time, attention and energies to the business and
interests of the Company during the Term of this Agreement and you will not accept any outside position without the prior written consent of the CEO or the Board, except that you may serve on up to a maximum of two boards of directors provided that
you have approval of the CEO or the Board’s Compensation Committee and provided that your time spent in such service is reasonable and does not detract from the performance of your duties to the Company. You warrant that you are free to enter
into and fully perform this Agreement and are not subject to any employment, confidentiality, non-competition or other agreement which would restrict your performance under this Agreement. You shall fulfill your duties and responsibilities to the
Company hereunder primarily from the Company’s office located in San Diego, California provided, however, that the Company may from time to time require you to travel temporarily to other locations in connection with the Company’s
business.” 

  
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 1.2 Section 3(a). The first sentence of Section 3(a) of the
Employment Agreement is hereby amended and restated in its entirety to read as follows: 
 “During the Term of this
Agreement, the Company will pay you a base salary at not less than the bi-weekly rate of $10,769.23 (“Base Salary”), minus withholdings as required by law or other deductions authorized by you, which amount shall be paid to
you in periodic installments in accordance with the Company’s payroll practices then in effect.” 
 1.3
Section 3(i). A new Section 3(i) is hereby added to the Employment Agreement as follows: 
 “(i) Stock
Options and Restricted Stock. The Company granted a stock option to you on February 24, 2011 to purchase up to 42,626 shares of the Company’s common stock with an exercise price of $3.31 per share, subject to vesting and the other
terms and conditions set forth in the stock option grant notice and agreement previously provided to you. All Company stock option and restricted stock awards previously granted to you shall continue in effect from and following the Effective Date
in accordance with their existing terms. You may be eligible to receive additional grants of Company stock option and restricted stock awards in the sole discretion and subject to the approval of the Compensation Committee of the Board.”

 1.4 Effective Date and Term of Amended Employment Agreement. With respect to application of the amendments to
the Employment Agreement that are set forth in this Amendment, all references to the “Effective Date” contained in the amended Employment Agreement are with respect to the date of March 31, 2011, and all references to the
“Term” of the Employment Agreement are with respect to the period of employment commencing on March 31, 2011. 
 ARTICLE 2 
 GENERAL PROVISIONS 

2.1 Impact of Amendment. Except as expressly amended by this Amendment, the terms of the Employment Agreement remain in
full force and effect. 
 2.2 Governing Law. The validity, interpretation, construction and performance of this
Amendment and the amended Employment Agreement and the rights of the parties thereunder shall be interpreted and enforced under the law of the Commonwealth of Massachusetts. 
 2.3 Validity. The invalidity or unenforceability of any provision of this Amendment or the Employment Agreement shall not affect the validity or enforceability of any other provision of this
Amendment or the Employment Agreement, which shall remain in full force and effect. 
 2.4 Controlling Document.
In case of conflict between any of the terms and condition of this Amendment and the Employment Agreement herein referred to, the terms and conditions of this Amendment shall control. 

  
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 2.5 Executive Acknowledgment. Executive acknowledges (a) that he has
consulted with or has had the opportunity to consult with independent counsel of his own choice concerning this Amendment, and has been advised to do so by the Company, and (b) that he has read and understands the Amendment, is fully aware of
its legal effect, and has entered into it freely based on his own judgment. 
 2.6 Counterparts. This Amendment
may be executed in one or more counterparts, all of which taken together shall constitute one and the same document. 
 Executed by the parties
hereto on the date(s) set forth below: 
  

									
	EXECUTIVE	 		 	VERENIUM CORPORATION
					
	By:	 	/s/ Jeffrey Black	 		 	By:	 	/s/ Dr. James Cavanaugh
		 	Jeffrey Black	 		 		 	Dr. James Cavanaugh
		 		 		 		 	Chairman of the Board of Directors
					
	Date:	 	March 4, 2011	 		 	Date:	 	March 4, 2011

  
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