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(12) United States Patent (10) Patent No.: US 9,169,486 B2 Burk Et Al

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(12) United States Patent (10) Patent No.: US 9,169,486 B2 Burk Et Al US009 1694.86B2 (12) United States Patent (10) Patent No.: US 9,169,486 B2 Burk et al. (45) Date of Patent: Oct. 27, 2015 (54) MICROORGANISMS FOR PRODUCING 2003, OO87381 A1 5/2003 Gokarn BUTADIENE AND METHODS RELATED 2003,0224363 A1 12/2003 Park et al. THERETO 2003/0233218 A1 12/2003 Schilling 2004/OOO9466 A1 1/2004 Maranas et al. (75) Inventors: Mark J. Burk, San Diego, CA (US); 3.92. !: A. 3.38: Eas al Anthony Burgard Bellefonte, PA 2004/0152159 A1 8/2004 CauseyaSSO etca. al. (US); Robin E. Osterhout, San Diego, 2005/0042736 A1 2/2005 San et al. CA (US); Jun Sun, San Diego, CA (US); 2005, 0079482 A1 4/2005 Maranas et al. Priti Pharkya, San Diego, CA (US) 2006/004.6288 A1 3/2006 Ka-Yiu et al. 2006, OO73577 A1 4/2006 Ka-Yiu et al. (73) Assignee: Genomatica, Inc., San Diego, CA (US) 2009/00477182007/O184539 A1 2/20098, 2007 SanBlaschek et al. et al. (*) Notice: Subject to any disclaimer, the term of this 39887. A. 23. Ewsi al. patent is extended or adjusted under 35 2010.0003716 A1 1/2010 Cervin et al. U.S.C. 154(b) by 0 days. 2010.0184171 A1 7, 2010 Jantama et al. 2010/0304453 A1 12/2010 Trawicket al. 2010/0330635 Al 12/2010 Burgard et al. (21) Appl. No.: 13/527,440 2011/0008861 A1 1/2011 Berry et al. 2011/0300597 A1* 12/2011 Burk et al. .................... 435/167 (22) Filed: Jun. 19, 2012 2012/0225466 A1 9, 2012 Burk et al. 2013, OO11891 A1 1/2013 Burk et al. (65) Prior Publication Data US 2013/0011891 A1 Jan. 10, 2013 FOREIGN PATENT DOCUMENTS WO WO O2/O55995 T 2002 O O WO WO O2/O61115 8, 2002 Related U.S. Application Data WO WOO3/106998 12/2003 WO WO 2004/018621 3, 2004 (60) Provisional application No. 61/500,130, filed on Jun. WO WO 2005/047498 5, 2005 22, 2011, provisional application No. 61/502.264, WO WO 2006/031424 3, 2006 filed on Jun. 28, 2011. WO WO 2006/034156 3, 2006 WO WO 2007 141208 12/2007 (51) Int. Cl. WO WO 2008/08O124 T 2008 CI2N L/20 (2006.01) WO WO 2008/115840 9, 2008 CI2P 5/02 (2006.01) WO WO 2008/131286 10, 2008 CI2N 15/52 (2006.01) (Continued) CI2P 7/04 (2006.01) OTHER PUBLICATIONS CI2P 7/16 (2006.01) (52) U.S. Cl. Adams et al., “Oxidoreductase-Type Enzymes and Redox Proteins CPC ................. CI2N 15/52 (2013.01); C12P5/026 Involved in Fermentative Metabolisms of Hyperthermophilic (2013.01); CI2P 7/04 (2013.01); C12P 7/16 Archaea," Archaea. Adv. Protein Chem, 48: 101-180 (1996). (2013.01) Andersson et al., “Effect of different carbon sources on the produc (58) Field of Classification Search tion of Succinic acid using metabolically engineered Escherichia CPC ................ C12P 5/02; C12P 5700; C12P1/04; coli,” Biotechnol. Prog. 23(2):381-388 (2007). C12P 7/16; C12N 9/88; C12N 1/20; C12N Aoshima and Igarashi. “A novel oxaloSuccinate-forming enzyme 9/0006; C12N 15/52; C12N 15/74; C12N involved in the reductive carboxylation of 2-oxoglutarate 9/001; C12N 15/8243; C12R 1/01; C07C flignolater thermophilus TK-6.” Mol. Microbiol. 62:748-759 297 60; C07C 11/167; C07C31/12: C12Q 1/04 Aoshima and Igarashi, "Nondecarboxylating and Decarboxylating See application file for complete search history. Isocitrate Dehydrogenases: OxaloSuccinate Reductase as an Ances tral Form of Isocitrate Dehydrogenase.” J. Bacteriol. 190:2050-2055 (56) References Cited (2008). Aoshima et al., “A novel biotin protein required for reductive U.S. PATENT DOCUMENTS carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6. Mol. Microbiol. 51:791-798 5,413,922 A 5/1995 Matsuyama et al. (2004). 5,830,716 A 11/1998 Kojima et al. (Continued) 5,849,970 A 12/1998 Fall et al. 5,958,745 A 9/1999 Gruys et al. 6,117,658 A 9, 2000 Dennis et al. Primary Examiner — Iqbal H Chowdhury 6,455.284 B1 9, 2002 Gokarn et al. (74) Attorney, Agent, or Firm — Jones Day 7,127.379 B2 10/2006 Palsson et al. 7,223,567 B2 5, 2007 Ka-Yiu et al. 7,244,610 B2 7/2007 San et al. (57) ABSTRACT 23:2. R: 292 s al. al The invention provides non-naturally occurring microbial 7.309,597 B2 1/2007 O organisms having abutadiene or crotyl alcohol pathway. The 7947483 B2 5/2011 Burgard et al. invention additionally provides methods of using such organ 2002/0012939 A1 1/2002 Palsson isms to produce butadiene or crotyl alcohol. 2002/0168654 A1 11/2002 Maranas et al. 2003/0059792 A1 3/2003 Palsson et al. 16 Claims, 24 Drawing Sheets US 9,169.486 B2 Page 2 (56) References Cited Cox et al., “Development of a metabolic network design and optimi Zation framework incorporating implementation constraints: A Suc cinate production case study.” Metab. 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Dobbek et al., “Crystal Structure of a Carbon Monoxide Aoshima et al., “A novel enzyme, citryl-CoA synthetase, catalysing Dehydrogenase Reveals a Ni-4Fe-5S Cluster.” Science 293: 1281 the first step of the citrate cleavage reaction in Hydrogenobacter 1285 (2001). thermophilus TK-6.” Mol. Micrbiol. 52:751-761 (2004). Dorner and Boll, J. "Properties of 2-Oxoglutarate:Ferredoxin Aoshima, M.. “Novel enzyme reactions related to the tricarboxylic Oxidoreductase from Thauera aromatica and Its Role in Enzymatic acid cycle: phylogenetic? functional implications and biotechnologi Reduction of the Aromatic Ring.” Bacteriol. 184 (14), 3975-83 (2002). cal applications.” Appl. Microbiol. Biotechnol. 75:249-255 (2007). Drake and Daniel, “Physiology of the thermophilic acetogen Arikawa et al., “Soluble fumarate reductase isoenzymes from Sac Moorella thermoacetica.” Res. 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Bernhard et al., "Functional and structural role of the cytochrome b Edwards and Palsson, "Metabolic flux balance analysis and the in Subunit of the membrane-bound hydrogenase complex of silico analysis of Escherichia coli K-12 gene deletions.” BMC Alcaligenes eutrophus H16.” Eur, J. Biochem. 248, 179-186 (1997). Bioinform. 1:1 (2000). Bisswanger, “Substrate Specificity of the Pyruvate Dehydrogenase Edwards and Palsson, “The Escherichia coli MG 1655 in silico Meta Complex from Escherichia Coli.” H., J. Biol. Chem. 256:815-82 bolic Genotype: Its Definition, Characteristics, and Capabilities.” (1981). Proc. Natl. Acad. Sci. U.S.A. 97(10):5528-5533 (2000). Edwards et al., “Metabolic modelling of microbes: the flux-balance Blaschkowski et al., “Routes of Flavodoxin and Ferredoxin Reduc approach.” Environ. Microbiol. 4(3):133-140 (2002). tion in Escherichia coli.” Eur, J. Biochem. 123:563-569 (1982). Edwards et al., “In Silico Predictions of Escherichia coli metabolic Bock et al., “Purification and Characterization of Two Extremely capabilities are Consistent with Experimental Data.” Nat. Biotechnol. Thermostable Enzymes, Phosphate Acetyltransferase and Acetate 19(2):125-130 (2001). Kinase, from the Hyperthermophilic Eubacterium Thermotoga mari Eikmanns et al., “The phosphoenolpyruvate carboxylae gene of time.” J. Bacteriol. 181: 1861-1867 (1999). Corynebacterium glutamicum: Molecular cloning, nucleotide Bott and Dimroth, “Likebsiella pneumonia genes for citrate lyase and sequence, and expression.” Mol. Gen. Genet. 218:330-339 (1989). citrate lyase ligase: localization, sequencing, and expression.” Mol. Eisen et al., “The complete genome sequence of Chlorobium tepidum Microbiol. 14:347-356 (1994). TLS, a photosynthetic, anaerobic, green-sulfur bacterium.” PNAS Bott, "Anaerobic citrate metabolism and its regulation in 99(14): 9509-14 (2002). enterobacteria.” Arch. 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