Amendment No. 1 to the Third Amended and Restated Registration Rights Agreement



 Exhibit 4.3 
 AMENDMENT NO. 1 
 TO 

THIRD AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT 
 This Amendment No. 1 (this “Amendment”) to that certain Third Amended and Restated Registration Rights Agreement, dated as of August 31, 2010, by and among Mascoma Corporation,
a Delaware corporation (the “Corporation”), and the Investors and Key Stockholders named therein (the “Registration Rights Agreement”), is made as of January 7, 2011, by and among the Corporation, Diamond
Alternative Energy, LLC, a Delaware limited liability company (“Valero”), and the holders of Registrable Securities (as defined in the Registration Rights Agreement) listed on the signature pages hereto (“Rights
Holders”). 
 WHEREAS, in connection with the Corporation’s sale and issuance of shares of the Corporation’s
Series D Preferred Stock, par value $0.001 per share (the “Series D Preferred Stock”) and warrant to purchase shares of Series D Preferred Stock to Valero pursuant to that certain Series D Preferred Stock and Warrant Purchase
Agreement, by and between the Corporation and Valero, dated as of even date herewith (the “Valero Purchase Agreement”), the Rights Holders desire to amend the Registration Rights Agreement as set forth in this Amendment, and consent
to the grant of registration rights to Valero through the addition of Valero as a party to the Registration Rights Agreement in the capacity of an Investor; 
 WHEREAS, Section 14 of the Registration Rights Agreement provides that the Corporation may not enter into an agreement with any holder or prospective holder of any securities of the Corporation that
would grant such holder the right to demand registration of shares of the Corporation’s capital stock, or to include such shares in a registration statement that would reduce the number of shares includable by the Holders (as defined in the
Registration Rights Agreement) without the consent of the Holders of at least a majority of Registrable Securities held by the Holders (the “Requisite Holders”); 

WHEREAS, Section 17(c) of the Registration Rights Agreement provides that the Registration Rights Agreement may be amended with the
written consent of the Corporation and the holders of at least a majority in interest of voting power of the then outstanding Registrable Securities issued (collectively, the “Requisite Rights Holders,” and together with the
Requisite Holders, the “Requisite Parties”); and 
 WHEREAS, the Rights Holders party hereto hold a sufficient
number of Registrable Securities to constitute the Requisite Parties. 
 NOW, THEREFORE, in consideration of the premises and
the mutual covenants contained in this Amendment and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows: 

1. Consent to Addition of Valero to the Registration Rights Agreement. The Requisite Parties hereby consent to the addition of
Valero as a party to the Registration Rights Agreement in the capacity of an Investor, and agree that Valero shall have all of the rights granted to an Investor in the Registration Rights Agreement, including without limitation, demand registration
rights and piggyback registration rights with respect to its Registrable 







 
Securities. Valero, by its signature to this Amendment, hereby agrees that it is becoming a party to the Registration Rights Agreement, as amended hereby, in the capacity of an Investor.

 2. Certain Defined Terms. All capitalized terms used herein and not defined herein shall have the meanings given to
such terms in the Registration Rights Agreement, as amended hereby. 
 3. Amendment to Registration Rights Agreement.
Section 17(e) of the Registration Rights Agreement is amended and restated in its entirety to read as set forth below: 

“All notices hereunder shall be given in accordance with Section 4.03 of the Note Conversion Agreement, Section 7.09 of
the Share Purchase Agreement, or Section 13 of the Series D Preferred Stock and Warrant Purchase Agreement, dated as of January 7, 2011, by and between the Corporation and Diamond Alternative Energy, LLC, a Delaware limited liability
company, as applicable.” 
 4. Governing Law. This Amendment shall be governed by, and construed and enforced in
accordance with, the substantive laws of the State of Delaware without regard to its principles of conflicts of laws. 
 5.
Counterparts. This Amendment may be executed in one or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. 

[Signature Page to Follow] 

  
 2 








 IN WITNESS WHEREOF, the undersigned parties have executed this Amendment No. 1 to Third
Amended and Restated Registration Rights Agreement as an instrument under seal as of the date first written above. 
  

					
	MASCOMA CORPORATION
		
	By:	 	 /s/ William J. Brady

		 	Name:	 	William J. Brady
		 	Title:	 	Chief Executive Officer



  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 








 
					
	DIAMOND ALTERNATIVE ENERGY, LLC
		
	By:	 	 /s/ S. Eugene Edwards

		 	Name:	 	S. Eugene Edwards
		 	Title:	 	Executive Vice President


 



 

  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	ATLAS VENTURE FUND VII, L.P.
	By:	 	 Atlas Venture Associates VII, L.P.,
 Its General Partner

	By:	 	 Atlas Venture Associates VII, Inc.,
 Its General Partner

		
	By:	 	 /s/ Kristen Laguerre

	Name:	 	Kristen Laguerre
	Title:	 	VP


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 








 BLUESTEM GROWTH & INCOME FUND III, LLC 

			
	By: Bluestem Capital Company, LLC
		
	By:	 	 /s/ Sandy Horst

	Name:	 	Sandy Horst
	Title:	 	CFO

 BLUESTEM
SELECT OPPORTUNITIES FUND, LLC 

			
	By: Bluestem Capital Company, LLC
		
	By:	 	 /s/ Sandy Horst

	Name:	 	Sandy Horst
	Title:	 	CFO


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	FLAGSHIP VENTURES FUND 2004, L.P.
		
	By:	 	 its General Partner

Flagship Ventures General Partner LLC

		
	By:	 	 /s/ [ILLEGIBLE]

		 	Manager


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	GC ENTREPRENEURS FUND IV, L.P.
	By General Catalyst Partners IV, L.P.,
		 	its General Partner
	By General Catalyst GP IV, LLC,
		 	its General Partner
		
	By:	 	 /s/ William J. Fitzgerald

	Name:	 	William J. Fitzgerald
	Title:	 	Member and Chief Financial Officer
	
	GENERAL CATALYST GROUP IV, L.P.
	By General Catalyst Partners IV, L.P.,
		 	its General Partner
	By General Catalyst GP IV, LLC,
		 	its General Partner
		
	By:	 	 /s/ William J. Fitzgerald

	Name:	 	William J. Fitzgerald
	Title:	 	Member and Chief Financial Officer


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









									
	 BLACKROCK INVESTMENT MANAGEMENT (UK) LIMITED, 
 by its nominee, HARE & CO.
	 	
					
	By:	 	 /s/ JOSHUA FREEDMAN
	 		 	DATE:	 	06 JANUARY 2011
	Name:	 	JOSHUA FREEDMAN	 		 		 	
	Title:	 	FUND MANAGER - BLACKROCK	 		 		 	
					
		 	 /s/ Poppy Allonby
	 		 		 	
		 	POPPY ALLONBY	 		 		 	
		 	FUND MANAGER - BLACKROCK	 		 		 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	KPCB HOLDINGS, INC.
		
	By:	 	 /s/ ERIC KELLER

	Name:	 	ERIC KELLER
	Title:	 	PRESIDENT


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	MALAYSIAN LIFE SCIENCES CAPITAL FUND
		
	By:	 	 /s/ Roger Wyse

	Name:	 	Roger Wyse
	Title:	 	Co-Chairman


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	MPC INVESTMENT LLC
		
	By:	 	 /s/ Clifford C. Cook

	Name:	 	Clifford C. Cook
	Title:	 	Manager
	
	






  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	PIPER JAFFRAY & CO.
		
	By:	 	 /s/ Robert P. Rinek

	Name:	 	Robert P. Rinek
	Title:	 	Managing Director


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	SUNOPTA INC.
		
	By:	 	 /s/ Steven R
Bromley                    5/1/11

	Name:	 	Steven R Bromley
	Title:	 	President & CEO


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 








 
			
	VPVP CLEANTECH HOLDINGS 2006, L.L.C.
		
	By:	 	 VantagePoint Venture Partners 2006 (Q), L.P.,
 Its Sole Member

	By:	 	 VantagePoint Venture Associates 2006, L.L.C.,
 Its Managing Member

		
	By:	 	 /s/ Alan E. Salzman

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member
	
	VANTAGEPOINT CLEANTECH PARTNERS, L.P.
		
	By:	 	VantagePoint CleanTech Associates, L.L.C., Its General Partner
		
	By:	 	 /s/ Alan E. Salzman

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member



  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	GENERAL MOTORS VENTURES LLC
		
	By:	 	 /s/ Jon Lauckner

	Name:	 	Jon Lauckner
	Title:	 	President


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	KHOSLA VENTURES I, L.P.
		
	By:	 	Khosla Ventures Associates I, LLC, a Delaware limited liability company and general partner of Khosla Ventures I, LP
		
	By:	 	VK Services, LLC, a Delaware limited liability company and manager of Khosla Ventures Associates I, LLC
		
	By:	 	 /s/ Vinod Khosla

	Name:	 	Vinod Khosla
	Title:	 	Member


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	PINNACLE VENTURES II-A, L.P.
	PINNACLE VENTURES II-B, L.P.
	PINNACLE VENTURES II-C, L.P.
	PINNACLE VENTURES II-R, L.P.
		
	By:	 	Pinnacle Ventures Management II, L.L.C., Their general partner
		
	By:	 	  

	Name:	 	Robert N. Savoie
	Title:	 	Chief Financial Officer

 PINNACLE VENTURES EQUITY FUND I AFFILIATES, L.P. 
 PINNACLE VENTURES EQUITY FUND I, L.P. 
 PINNACLE VENTURES EQUITY FUND I-O, L.P.

  

			
	By:	 	 Pinnacle Ventures Equity Management I, L.L.C.,
 Their general partner


  

			
	By:	 	  

	Name:	 	Robert N. Savoie
	Title:	 	Chief Financial Officer


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









	
	  

	R. Jeremy Grantham


  

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	Barbara D. Rybeck


  

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	BERSHAW & CO.
	C/O CITIBANK CANADA, SECURITIES CAGE
		
	By:	 	  

	Name:	 	
	Title:	 	


  

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	BOWEN BIO-ENERGY, LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	BOWEN ENGINEERING CORPORATION
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









	
	  

	Bradley D. Spindler


  

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	 BRANT INVESTMENTS LIMITED
 99480027
	 	
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	
			
		 		 	c/s
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	
		
	 BRANT INVESTMENTS LIMITED
 99480072
	 	
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	
			
		 		 	c/s
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	


  

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	Brian J. Stater


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









	
	  

	Bruce A. Jamerson


  

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	CANACCORD GENUITY CORP.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 








 CANACCORD GENUITY CORPORATION 
 ITF PETER J CHANDLER AC# 139-264S-4 (RRSP) 
  

			
	By:	 	  

	Name:	 	
	Title:	 	
	
	 CANACCORD GENUITY CORPORATION
 ITF PETER J CHANDLER AC# 139-264M-2

		
	By:	 	  

	Name:	 	
	Title:	 	


  

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	CRM HOLDINGS, LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









	
	  

	David Mann


  

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	DAVID NODA AND KAY M. NISHIYAMA
	(as joint tenants with right of survivorship)
	
	  

	David Noda
	
	  

	Kay M. Nishiyama


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









	
	  

	Dean W. Rybeck


  

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	Eric Lemelson


  

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	FAGEN, INC.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









					
	JAYVEE & CO. INVF0004002	 	
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	
			
		 		 	c/s
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	
		
	JAYVEE & CO. INVF0013002	 	
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	
			
		 		 	c/s
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









					
	 JAYVEE & CO.
 on behalf of MACKENZIE FINANCIAL CORP.

			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	
			
		 		 	c/s
			
	By:	 	  
	 	
	Name:	 		 	
	Title:	 		 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









	
	  

	Larry Hannah


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	LOWE’S LTD., L.P.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

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	PURDUE RESEARCH FOUNDATION
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









	
	  

	Robert L. Bowen


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement 









			
	ROCH ENTERPRISES, L.P.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

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	Rod Fuller


  

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	STACK, LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

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	Susan Williams


  

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	Terry L. Bowen


  

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	Todd Noffke


  

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	Wendy Strub


  

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	WILDSTOIC LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

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	WILSEY INVEST LTD.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

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 TRIMARK RESOURCES FUND 
 (formerly, TRIMARK CANADIAN RESOURCES FUND), 
 by its Manager, INVESCO TRIMARK LTD.

 (formerly AIM FUNDS MANAGEMENT INC.) 
  

					
	By:	 	  
	 	
	Name:	 	Theodor Heldman
	Title:	 	VP & Chief Financial Officer, Funds
			
		 		 	c/s
			
	By:	 	  
	 	
	Name:	 	David C. Warren
	Title:	 	Chief Admin Officer, NA Retail


  

Signature Page to Amendment No. 1 to Third A&R Registration Rights Agreement