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(12) United States Patent (10) Patent No.: US 8,906,665 B2 Berry Et Al

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(12) United States Patent (10) Patent No.: US 8,906,665 B2 Berry Et Al USOO8906665B2 (12) United States Patent (10) Patent No.: US 8,906,665 B2 Berry et al. (45) Date of Patent: Dec. 9, 2014 (54) METHODS AND COMPOSITIONS FOR THE (58) Field of Classification Search RECOMBINANT BIOSYNTHESIS OF EATTY CPC ........................ C12P 7/649; C12Y 602/01003 ACDS AND ESTERS USPC ....................... 435/183,252.3, 134:536/23.2 See application file for complete search history. (71) Applicants: David Arthur Berry, Brookline, MA (US); Noubar Boghos Afeyan, (56) References Cited Lexington, MA (US); Frank Anthony Skrally, Watertown, MA (US); Christian U.S. PATENT DOCUMENTS Perry Ridley, Acton, MA (US); Dan 4,720.457 A 1/1988 Armstrong et al. Eric Robertson, Belmont, MA (US); 5,000,000 A 3/1991 Ingram et al. Regina Wilpiszeski, Cambridge, MA 5,162,516 A 11/1992 Ingram et al. (US); Martha Sholl, Haverhill, MA 5,304.475 A 4, 1994 Kim et al. (US) 6,429,006 B1 8, 2002 Porro et al. 6,632,631 B1 10/2003 Shuster et al. 6,699,696 B2 3/2004 Woods et al. (72) Inventors: David Arthur Berry, Brookline, MA 7,026,527 B2 4/2006 Falco et al. (US); Noubar Boghos Afeyan, 7,122,331 B1 10/2006 Eisenreich et al. Lexington, MA (US); Frank Anthony 8,048,654 B2 11/2011 Berry et al. Skrally, Watertown, MA (US); Christian 2005/0014241 A1 1/2005 Chen Perry Ridley, Acton, MA (US); Dan 2005, 012401.0 A1 6/2005 Short et al. Eric Robertson, Belmont, MA (US); 2005/0239 179 A1 10/2005 Skrally et al. Regina Wilpiszeski, Cambridge, MA 2011/0020883 A1 1/2011 Roessler et al. (US); Martha Sholl, Haverhill, MA FOREIGN PATENT DOCUMENTS (US) WO WO 2007/084477 1, 2007 (73) Assignee: Joule Unlimited Technologies, Inc., WO WO 2007/136762 11, 2007 WO WO 2007/139925 12/2007 Bedford, MA (US) WO WO 2008/119082 10, 2008 WO WO 2009/009391 1, 2009 (*) Notice: Subject to any disclaimer, the term of this WO WO 2009/062190 5/2009 patent is extended or adjusted under 35 WO WO 2009,076.559 6, 2009 U.S.C. 154(b) by 71 days. WO WO 2009,111513 9, 2009 WO WO 2010/O19813 2, 2010 Appl. No.: 13/765,211 WO WO 2010/021711 2, 2010 (21) WO WO 2010/O22090 2, 2010 WO WO 2010/033921 3, 2010 (22) Filed: Feb. 12, 2013 WO WO 2010/044960 4/2010 (65) Prior Publication Data OTHER PUBLICATIONS US 2013/O14330.6 A1 Jun. 6, 2013 European Patent Office, Search Report and Opinion, European Patent Application No. 13195355.6, Feb. 3, 2014, five pages. Related U.S. Application Data Kaku, N. et al., “Effects of overexpression of Escherichia coli kate and bet genes on the tolerance for salt stress in a freshwater (63) Continuation of application No. 13/243,165, filed on cyanobacterium Synechocuccus sp. PCC 7942.” Plant Science, 2000, Sep. 23, 2011, now Pat. No. 8,399.227, which is a pp. 281-288, vol. 159. continuation of application No. 12/876,056, filed on State Intellectual Property Office of the People's Republic of China, Sep. 3, 2010, now Pat. No. 8,048,654, which is a Third Office Action, Chinese Patent Application No. 200980114073. continuation of application No. PCT/US2009/035937, 0, Apr. 15, 2014, six pages. filed on Mar. 3, 2009. State Intellectual Property Office of the People's Republic of China, Second Office Action, Chinese Patent Application No. (60) Provisional application No. 61/121,532, filed on Dec. 20098.0114073.0, Aug. 15, 2013, seven pages. 10, 2008, provisional application No. 61/033,411, filed on Mar. 3, 2008, provisional application No. (Continued) 61/033,402, filed on Mar. 3, 2008, provisional application No. 61/353,145, filed on Jun. 9, 2010. Primary Examiner — Tekchand Saidha (74) Attorney, Agent, or Firm — Fenwick & West LLP: (51) Int. C. Chang B. Hong, Esq. CI2N L/20 (2006.01) CI2N 9/00 (2006.01) (57) ABSTRACT CI2N 15/79 (2006.01) The present disclosure identifies methods and compositions CI2P 7/64 (2006.01) for modifying photoautotrophic organisms, such that the (52) U.S. C. organisms efficiently convert carbon dioxide and light into CPC ................. CI2N 15/79 (2013.01); Y02E 50/17 compounds Such as esters and fatty acids. In certain embodi (2013.01); CI2P 7/649 (2013.01); C12Y ments, the compounds produced are secreted into the medium 602/01003 (2013.01); Y02E 50/13 (2013.01) used to culture the organisms. USPC ........ 435/252.3; 435/134: 435/183; 435/232; 536/23.2 20 Claims, 5 Drawing Sheets US 8,906.665 B2 Page 2 (56) References Cited 217-223 (abstract only) Online Retrieved Nov. 28, 2009 Retrieved from the internet (URL:http://pcp.oxfordjournals.org/cgi/content/ OTHER PUBLICATIONS abstract? 43.2/217-. Liu, X. et al., “Production and Secretion of Fatty Acids in Genetically Engineered Cyanobacteria.” Proceedings of the National Academy of Cho, H. et al., “Defective Export of a Periplasmic Enzyme Disrupts Sciences USA Early Edition, Mar. 29, 2010, six pages. Online Regulation of Fatty Acid Synthesis.” The Journal of Biological Retrieved from the Internet <URL:http://www.pnas.org/content/ Chemistry, 1995, pp. 4216-4219, vol. 270, No. 9. early/2010/07/01/100 1946 107.full.pdf>. Cho, H. et al., “Escherichia coli Thioesterase I, Molecular Cloning Liu, X. et al., “Supporting Information: SI Materials and Methods. and Sequencing of the Structural Gene and Identification as a Growth of an SD Culture Started from a Single Cell Descended Periplasmic Enzyme.” The Journal of Biological Chemistry, May 5, Colony.” Proceedings of the National Academy of Sciences USA, 2010, ten pages. Online Retrieved from the Internet: <URL:http:// 1993, vol. 268, pp. 9238-9245, No. 13. www.pnas.org/content/suppl/2010/03/26/100 1946 107. Chollet, R. et al., “The AcrAB-ToIC Pump Is Involved in Macrollide DCSupplemental/pnas. 100 1946 107 SI.pdf>. Resistance but Not in Telithromycin Efflux in Enterobacter Lloyd, A. et al., “Topology of the Escherichia coli uhpT Sugar aerogenes and Escherichia coli, 'Antimicrobial Agents and Chemo Phosphate Transporter Analyzed by Using Tnpho A Fusions,” Jour therapy, Sep. 2004, pp. 3621-3624, vol. 48. nal of Bacteriology, Apr. 1990, pp. 1688-1693, vol. 172, No. 4. Cohen, N. et al., “Functional Expression of Rat GLUT 1 Glucose Lopez-Maury, L., "A Two-component Signal Transduction System Transporter in Dictyostelium discoideum,” Biochem. J., 1996, pp. Involved in Nickel Sensing in the Cyanobacterium Synechocystis sp. 971-975, vol. 3.15. PCC 6803.” Molecular Microbiology, 2002, pp. 247-256, vol.43, No. Deng, M. et al., “Ethanol Synthesis by Genetic Engineering in 1. Marrakchi, H. et al., “Mechanistic Diversity and Regulation of Type Cyanobacteria.” Applied and Environmental Microbiology, Feb. II Fatty Acid Synthesis.” Biochemical Society Transactions, 2002, 1999, pp. 523-528, vol. 65, No. 2. pp. 1050-1055, vol. 30. European Patent Office. Examination Report, European Patent Nielsen, D.R. et al., “Engineering Alternative Butanol Production Application No. 09717082.3, Feb. 14, 2013, four pages. Platforms in Heterologous Bacteria.” Metabolic Engineering, Jul. European Patent Office. Examination Report, European Patent 2009, pp. 262-273, vol. 11. Application No. 09820965.3, Feb. 18, 2013, five pages. PCT International Search Report and Written Opinion, PCT Appli European Patent Office, Supplementary Search Report and Opinion, cation No. PCT/US2009/035937, Aug. 3, 2009, fifteen pages. European Patent Application No. 09820965.3, Feb. 22, 2012, seven PCT International Search Report and Written Opinion, PCT Appli pageS. cation No. PCT/US2009/055949, Mar. 15, 2010, seven pages. Frigaard, N-U. et al., “Gene Inactivation in the Cyanobacterium Qi. Q. et al., "Application of the Synechococcus nirA Promoter to Synechococcus sp. PCC 7002 and the Green Sulfur Bacterium Establish an Inducible Expression System for Engineering the Chlorobium tepidum Using in Vitro-made DNA Constructs and Synechocystis Tocopherol Pathway.” Applied and Environmental Natural Transformation.” Methods in Molecular Biology, 2004, pp. Microbiology, Oct. 2005, pp. 5678-5684, vol. 71, No. 10. 325-340, vol. 274. Rock, C. et al., “Increased Unsaturated Fatty Acid Production Asso Genin, S. et al., “Ralstonia solanacearum: Secrets of a Major Patho ciated with a Suppressor of the fabA6(Ts) Mutation in Escherichia gen Unveiled by Analysis of Its Genome.” Molecular Plant Pathol coli,” Journal of Bacteriology, 1996, pp. 5382-5387, vol. 178, No. 18. ogy, 2002, pp. 111-118, vol. 3, No. 3. State Intellectual Property Office of the People's Republic of China, Ho, N. et al., “Genetically Engineered Saccharomyces Yeast Capable First Office Action, Chinese Patent Application No. 200980114073. of Effective Cofermentation of Glucose and Xylose.” Applied and 0, Dec. 5, 2012, fourteen pages. Environmental Microbiology, 1998, pp. 1852-1859, vol. 64, No. 5. Steen, E. et al., “Microbial Production of Fatty-acid-derived Fuels Inokuma, K. et al., "Characterization of Enzymes Involved in the and Chemicals from Plant Biomass.” Nature, Jan. 28, 2010, pp. Ethanol Production of Moorella sp. HUC22-1.” Archives of 559-562, vol. 463. Microbiology, 2007, pp. 37-45, vol. 188. Stoveken, T. et al., “The Wax Ester Synthase/Acyl Coenzyme Iwai. M. et al., “Improved Genetic Transformation of the A:Diacylglycerol Acyltransferase from Acinetobacter sp. Strain Thermophilic Cyanobacterium, Thermosynechococcus elongatus ADP1: Characterization of a Novel Type of Acyltransferase.” Journal BP-1.” Plant and Cell Physiology, 2004, pp. 171-175, vol. 45, No. 2. of Bacteriology, Feb. 2005, pp. 1369-1376, vol. 187, No. 4. Kalscheuer, R. et al., “A Novel Bifunctional Wax Ester Synthase? Tsukagoshi, N. et al., “Entry into and Release of Solvents by Acyl-CoA: Diacyglycerol Acyltransferase Mediates Wax Ester and Escherichia coli in an Organic-Aqueous Two-Liquid-Phase System Triacylglycerol Biosynthesis in Acinetobacter calcoaceticus ADP1.” and Substrate Specificity of the AcrAB-ToIC Solvent-Extruding Journal of Biological Chemistry, 2003, pp.
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