Amendment No. 2 to the Third Amended and Restated Registration Rights Agreement



 Exhibit 4.4 
 AMENDMENT NO. 2 
 TO 

THIRD AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT 
 This Amendment No. 2 (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, as amended (the “Registration Rights Agreement”), is made as of June 1, 2011, by and among the Corporation,
Pinnacle Ventures, L.L.C., a Delaware limited liability company (“Pinnacle”), 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 term loan facility to be entered into by and among the Corporation,
certain subsidiaries of the Corporation, and Pinnacle pursuant to the Amended and Restated Loan and Security Agreement, dated as of an even date herewith, and the warrant to purchase shares of the Corporation’s Common Stock to be issued to
Pinnacle pursuant to that certain Warrant Purchase Agreement, by and among the Corporation and Pinnacle, dated as of even date herewith, the Rights Holders desire to amend the Registration Rights Agreement as set forth in this Amendment; 

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. 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. 
 2. Amendment to Registration Rights Agreement.
(a) Section 1(e) of the Registration Rights Agreement is amended in relevant part to read as set forth below: 







 “(e) The term “Registrable Securities” means (1) the Common Stock
issuable upon conversion of Preferred Stock, (2) the Common Stock purchased by an Investor pursuant to Section 9(b) of the Third Amended and Restated Stockholders Agreement, dated of even date herewith (the “Stockholders
Agreement”), by and among the Corporation, the Investors and certain stockholders of the Corporation (or Common Stock for or into which New Securities (as therein defined) purchased by the Investor pursuant to such Section 9(b) may be
exercised or converted), (3) any Common Stock of the Corporation issued as a dividend or other distribution with respect to, or in exchange for or in replacement of, such Preferred Stock or Common Stock, (4) any Common Stock of the
Corporation issuable upon conversion, exercise or exchange of convertible securities, warrants, options or similar rights issued as a dividend or other distribution with respect to, or in exchange or in replacement of, such Preferred Stock or Common
Stock, (5) the Common Stock held by the Key Stockholders, (6) Common Stock issued or issuable under the Share Purchase Agreement, (7) Common Stock issued upon exercise of the warrant issued or issuable to SunOpta Inc., a Canadian
company (“SunOpta”) under the Share Purchase Agreement (the “SunOpta Warrant”), or (8) Common Stock issued or issuable to Pinnacle under a certain Warrant Purchase Agreement dated as of May
    , 2011 (the “Pinnacle Common Warrant”) by and among the Corporation and Pinnacle Ventures II Equity Holdings, L.L.C., a Delaware limited liability company; provided, however, that shares of Common Stock that
are Registrable Securities shall cease to be Registrable Securities (i) when such shares are eligible for sale pursuant to an effective registration statement under the Act or Rule 144 under the Act or (ii) upon a transfer of such shares
to a person or entity that is not entitled to the rights provided hereunder.” 
 (b) Section 2 of the Registration
Rights Agreement is amended in relevant part to read: “The foregoing notwithstanding, (a) the Corporation shall not be obligated to effect a registration pursuant to this Section 2 that would become effective less than six months
after the effective date of any prior registration effected by the Corporation pursuant to this Section 2; (b) the Corporation shall not be obligated to effect a registration pursuant to this Section 2 unless such registration would
include at least twenty percent (20%) of the aggregate of the shares of Common Stock issuable upon conversion of the outstanding shares of Preferred Stock and the shares of Common Stock issued to SunOpta under the Share Purchase Agreement and
upon exercise of the SunOpta Warrant and the aggregate price to the public of Registrable Securities to be included in such registration statement for the account of selling Holders is reasonably anticipated to exceed $5,000,000; (c) the
Corporation shall not be obligated to effect a registration pursuant to this Section 2 during the period starting with the date that is ninety (90) days prior to the Corporation’s estimated date of filing of, and ending on a date that
is one hundred eighty (180) days following the effective date of, a registration statement pertaining to an underwritten public offering of securities for the account of the Corporation, provided that (i) the Corporation delivers notice to
the Holders within 30 days of its receipt of the written request from the Holders, (ii) the Corporation is actively employing in good faith its best efforts to cause such registration statement to become effective and (iii) the
Corporation’s estimate of the date of filing such registration statement is made in good faith; (d) if the Corporation shall furnish to the Holders a certificate signed by the President of the Corporation stating that in the good faith
judgment of the Board of Directors it would be detrimental to the Corporation or its stockholders for a registration statement to be filed in the near future, then the Corporation’s obligation to use


  
 2 








 
its best efforts to file a registration statement shall be deferred for a period not to exceed three (3) months, provided, however, that the Corporation may not obtain a
deferral pursuant to this clause (d) more than once in any twelve (12) month period; (e) the Corporation may postpone a registration pursuant to this Section 2 for such period of time as may be required to permit the use of
regular audited year-end figures with supplemental short period figures for a period not exceeding three months, unless the Holders agree to bear the costs of any special audit required by the underwriters; and for all purposes of this
Section 2, shares of Preferred Stock or Common Stock held by Pinnacle (collectively, “Warrant Shares”) as a result of the exercise or conversion of (i) a certain warrant issued to Pinnacle by the Corporation on
October 6, 2006, (ii) a certain warrant issued to Pinnacle by the Corporation on February 5, 2008, or (iii) the Pinnacle Common Warrant shall not be considered Registrable Securities hereunder.” 

3. 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. 
 4. 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] 

  
 3 








 IN WITNESS WHEREOF, the undersigned parties have executed this Amendment No. 2 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. 2 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. 2 to Third A&R Registration Rights Agreement









			
	DIAMOND ALTERNATIVE ENERGY, LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 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:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Barbara D. Rybeck


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









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

		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	 BLUESTEM GROWTH & INCOME FUND III, LLC
 By: Bluestem Capital Company, LLC

		
	By:	 	  

	Name:	 	
	Title:	 	
	
	 BLUESTEM SELECT OPPORTUNITIES FUND, LLC
 By: Bluestem Capital Company, LLC

		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	BOWEN BIO-ENERGY, LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	BOWEN ENGINEERING CORPORATION
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Bradley D. Spindler


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









					
	 BRANT INVESTMENTS LIMITED
 99480027

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

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


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Brian J. Stater


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Bruce A. Jamerson


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	CANACCORD GENUITY CORP.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 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:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	CRM HOLDINGS, LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	David Mann


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









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

	
	  

	David Noda
	
	  

	Kay M. Nishiyama


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Dean W. Rybeck


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Eric Lemelson


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	FAGEN, INC.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









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

Flagship Ventures General Partner LLC

		
	By:	 	 /s/ Noubar B. Afeyan

		 	Manager


  

Signature Page to Amendment No. 2 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. 2 to Third A&R Registration Rights Agreement 









			
	GENERAL MOTORS VENTURES LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 








 BLACKROCK INVESTMENT MANAGEMENT (UK) LIMITED, 

by its nominee, HARE & CO. 
  

			
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 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. 2 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. 2 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. 2 to Third A&R Registration Rights Agreement 









			
	KPCB HOLDINGS, INC.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Larry Hannah


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	LOWE’S LTD., L.P.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	MALAYSIAN LIFE SCIENCES CAPITAL FUND
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	MPC INVESTMENT LLC
		
	By:	 	 /s/ D.L. Whikehart

	Name:	 	D.L. Whikehart
	Title:	 	Director, Product Supply

 



 

  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	PIPER JAFFRAY & CO.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	PURDUE RESEARCH FOUNDATION
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	R. Jeremy Grantham


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	 Robert L. Bowen



  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	ROCH ENTERPRISES, L.P.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Rod Fuller


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	STACK, LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	SUNOPTA INC.
		
	By:	 	 /s/ Jeremy N. Kendall

	Name:	 	
	Title:	 	CHAIRMAN


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Susan Williams


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Terry L. Bowen


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Todd Noffke


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	VANTAGEPOINT CLEANTECH PARTNERS, L.P.
	By:	 	 VantagePoint CleanTech Associates, L.L.C.,
 Its General Partner

		
	By:	 	  

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member
	
	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:	 	  

	Name:	 	Alan E. Salzman
	Title:	 	Managing Member


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









	
	  

	Wendy Strub


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	WILDSTOIC LLC
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 









			
	WILSEY INVEST LTD.
		
	By:	 	  

	Name:	 	
	Title:	 	


  

Signature Page to Amendment No. 2 to Third A&R Registration Rights Agreement 








 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. 2 to Third A&R Registration Rights Agreement