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Pygal Application No. 61/209.917, Filed on Mar. CNENEEEN USOO8404465B2 (12) UnitedO States Patent (10) Patent No.: US 8.404,465 B2 Baynes et al. (45) Date of Patent: *Mar. 26, 2013 (54) BIOLOGICAL SYNTHESIS OF 2006.01601 38 A1 7, 2006 Church 6-AMINOCAPROCACID FROM 3.28 2. A 3.92 ElaC CARBOHYDRATE FEEDSTOCKS 2007/025.4341 A1 11/2007 Raemakers-Franken 2007,0269870 A1 11/2007 Church (75) Inventors: Brian M. Baynes, Cambridge, MA 2008, OO6461.0 A1 3/2008 Lipovsek (US); John Michael Geremia, 2008/0287320 A1 1 1/2008 Baynes Somerville, MA (US); Shaun M. 2009,008784.0 A1 4/2009 Baynes Lippow, Somerville, MA (US) 2009,0246838 A1 10, 2009 Zelder FOREIGN PATENT DOCUMENTS (73) Assignee: Celexion, LLC, Cambridge, MA (US) JP 2002223 770 8, 2008 c WO WO9507996 3, 1995 (*) Notice: Subject to any disclaimer, the term of this WO WOO166573 9, 2001 patent is extended or adjusted under 35 WO WOO3106691 12/2003 U.S.C. 154(b) by 225 days. WO WO2004O13341 2, 2004 WO WO2007099029 9, 2007 This patent is Subject to a terminal dis- WO WO2007101867 9, 2007 claimer. WO WO2O08092.720 9, 2008 WO WO2008127283 10, 2008 WO WO2009/046375 4/2009 (21) Appl. No.: 12/661,125 WO WO2009.113853 9, 2009 WO WO2009.113855 9, 2009 (22) Filed: Mar 11, 2010 WO WO2009,151728 12/2009 (65) Prior Publication Data OTHER PUBLICATIONS US 2012/O3O1950 A1 Nov. 29, 2012 Chica et al. Curr Opin Biotechnol. Aug. 2005:16(4):378-84.* Sen et al. Appl Biochem Biotechnol. Dec. 2007: 143(3):212-23.* Related U.S. Application Data Witkowski et al. Biochemistry. Sep. 7, 1999;38(36): 11643-50.* (60) Pygal application No. 61/209.917, filed on Mar. DonoghueCNENEEEN", and Trudgill “The metabolism of cyclohexanolON." by s 1-7. (51) Int. Cl Howell et al., “Identification of Enzymes Homologous to Isocitrate we Dehydrogenase That are Involved in Coenzyme B and Leucine W. 3.08: Biosynthesis in Methanoarchaea'. J. Bacteriol., 2000, vol. 182, No. CI2N IS/00 (2006.01) 17, pp. 5013-35016. C7H 2L/04 (2006.01) Goodlove et al., “Cloning and sequence analysis of the fermentative -. alcohol-dehydrogenase-encoding gene of Escherichia coli. Gene, (52) U.S. Cl. ..................... 435/135; 435/183; 435/320.1; 1989, vol. 85, No. 1, pp. 209-214. 536/23.2 Tanaka et al., “Metabolism of cyclohexanol by Pseudomonas sp.” (58) Field of Classification Search ............... ... ... None Hakko Kagaku Kaishi (1977), 55(2), 62-7. See application file for complete search history. Fujii T. et al., “Cloning and characterization of pcd encoding delta piperideine-6-carboxylate dehydrogenase from Flavobacterium (56) References Cited lutescens IF03084.” J. Biochem. 2000, 128(3):391-7. Hudson et al. "An LL-Diaminopimelate Aminotransferase Defines a U.S. PATENT DOCUMENTS Novel Variant of the Lysine Biosynthesis Pathway in Plants' Plant 3,485,821 A 12/1969 Sheehan Physiol. 140(1) 292-301, 2006. 4400,468 A 8, 1983 Faber 4,683, 195 A 7, 1987 Mullis (Continued) 4,725,542 A 2f1988 Barer 4,730,040 A 3/1988 Vagt et al. $93. A 3. 1999 Primary Examiner — Christian Fronda 5.258,393 A 1/1993 (74) Attorney, Agent, or Firm — Jennifer A. Camacho; 53.73073 A 12, 1993. Frost Natalie Salem; Greenberg Traurig, LLP 5,487.987 A 1, 1996 Frost 5,616,496 A 4, 1997 Frost 5,629, 190 A 5, 1997 Petre (57) ABSTRACT 5,994.478 A 11/1999 ASrar 6,180,388 B1 1/2001 Crouzet Provided herein are methods for the productionproducti off difunc 33 R 1.583 powicz tional alkanes in microorganisms. Also provided are enzymes 6,794, 165 B2 9/2004 Cheng and nucleic acids encoding Such enzymes, associated with the 7,189,543 B2 3/2007 Nishi difunctional alkane production from carbohydrates feed 7,323,320 B2 1/2008 Oleinikov stocks in microorganisms. The invention also provides 23, E: 1939 E. recombinant microorganisms and metabolic pathways for the 2002/027666 Al 9, 2002 Brzostowicz production of difunctional alkanes. 2003, OO87403 A1 5/2003 Cheng 2004.0053382 A1 3/2004 Senkpeil 2006, OO84152 A1 4/2006 Pompeius 6 Claims, 10 Drawing Sheets US 8.404,465 B2 Page 2 OTHER PUBLICATIONS Howell et al., “Alpha-keto acid chain elongation reactions involved in the biosynthesis of coenzyme B (7-mercaptoheptanoyl threonine Miyazaki T. et al. “Alpha-Aminoadipate aminotransferase from an phosphate) in methanogenic Archaea'. Biochemistry, 1998, vol. 37. extremely thermophilic bacterium. Thermus thermophilus' 2004, Microbiology, 150:2327-2334. No. 28, pp. 10108101.17. Kim et al. “Characterization of (R)-2-Hydroxyisocaproate Iwaki et al. “Identification of a Transcriptional Activator (ChnR) and Dehydrogenase and a Family III Coenzyme a Transferase Involved in a 6-Oxohexanoate Dehydrogenase (ChnE) in the Cyclohexanol Cata Reduction of L-Leucine to Isocaproate by Clostridium difficile' bolic Pathway in Acinetobacter sp. Strain NCIMB 98.71 and Local Applied and Environmental Microbiology, 2006, vol. 72, pp. 6062 ization of the Genes That Encode Them”. Applied and Environmental 6069 Microbiology, 1999, p. 5158-5162, vol. 65, No. 11. Andi B. et al. "Stabilization and characterization of histidine-tagged Jia Yet al. "Kinetics and product analysis of the reaction catalysed by homocitrate synthase from Saccharomyces cerevisiae.” Archives of recombinant homoaconitase from Thermus thermophilus.” Biochem Biochemistry and Biophysics (2004), 421 (2): 243-254. J. (2006) 396(3):479-85. Atsumi, Shota et al., “Non-fermentative pathways for synthesis of Jones Prather, Kristala L., et al., “De novo biosynthetic pathways: branched-chain higher alcohols as biofuels' Nature, vol. 451, pp. 86-90, 2008. rational design of microbial chemical factories' Current Opinion in Caspi, Ron, et al., “The MetaCyc database of metabolic pathways and Biotechnology, vol. 19, pp. 468-474, 2008. enzymes and the BioCyc collection of pathways/genome databases' Kingsbury J.M. et al. “Novel chimeric spermidine synthase-sac Nucleic Acids Research, vol. 36, D623-D631, 2008. charopine dehydrogenase gene (SPE3-LYS9) in the human pathogen de la Plaza M. et al. "Biochemical and molecular characterization Cryptococcus neoformans' Eukaryotic Cell, 3(3), pp. 752-763, of ketoisovalerate decarboxylase, an enzyme involved in the for 2004. mation of aldehydes from amino acids by Lactococcus lactis” FEMS Lin Y. et al. “Complete kinetic mechanism of homoisocitrate Microbiology Letters 238, pp. 367-374, 2004. dehydrogenase from Saccharomyces cerevisiae.” Biochemistry De Las Rivas B. et al. 'Gene cloning, expression, and functional (2007) 46 (3): 890-898. characterization of an ornithine decarboxylase protein from Serratia Niu, Wei et al., “Benzene-free synthesis of adipic acid” Biotechnol. liquefaciens IF 165” J. Microbial. Biotechnol., 17(3), pp. 408-413, Prog., vol. 18, pp. 201-211, 2002. 2007. Yan H. et al. “Cloning, sequencing and characterization of the Drevland et al., “Methanogen Homoaconitase Catalyzes Both O-aminoadipate reductase gene (LYS2) from Saccharomycopsis Hydrolyase Reactions in Coenzyme B Biosynthesis”, Journal of fibuligera” Yeast, 24, pp. 189-199, 2007. Biological Chemistry, vol. 283, pp. 28888-28896, 2008. Zhang et al., “Expanding metabolism for synthesis of nonnatural Fotheringham Ian, "Engineering biosynthetic pathways: new routes alcohols' P.N.A.S. 2008, vol. 105, No. 52, pp. 20653-20658. for chiral amino acids' Current opinion in Biology, vol. 4, pp. 120 Zheng, et al. “Purification of the Azotobacter vinelandiinifV-en 124, 2000. coded homocitrate synthase'. J. Bacteriol., 1997, vol. 179, No. 18. Goh D.L. M. et al. “Characterization of the human gene encoding pp. 5963-5966. O-aminoadipate aminotransferase (AADAT)' Molecular Genetics and Metabolism, 76, pp. 172-180, 2002. * cited by examiner U.S. Patent Mar. 26, 2013 Sheet 1 of 10 US 8.404,465 B2 f U.S. Patent Mar. 26, 2013 Sheet 2 of 10 US 8.404,465 B2 O O ºººZ?un61–\,^^^ U.S. Patent Mar. 26, 2013 Sheet 3 of 10 US 8.404,465 B2 U.S. Patent US 8.404,465 B2 o*J» U.S. Patent US 8.404,465 B2 O U.S. Patent Mar. 26, 2013 Sheet 6 of 10 US 8.404,465 B2 LIG ºº:: OUHO,"D~~~~ U.S. Patent Mar. 26, 2013 Sheet 7 of 10 US 8.404,465 B2 U.S. PatentN^~~~NBZO ?u?uæAepeoO N^~~~~oNMar. 26, 2013 Sheet 8 of 10 US 8.404,465 B2 U.S. Patent Mar. 26, 2013 Sheet 9 of 10 US 8.404,465 B2 9?unôl [OOUZO2 <–O GO3?eoeue?uadÅxOupÁ?OO ºº:: U.S. Patent US 8.404,465 B2 •× US 8,404,465 B2 1. 2 BIOLOGICAL SYNTHESIS OF In other embodiments, the microorganism also includes a 6-AMINOCAPROCACID FROM nucleic acid encoding a polypeptide that catalyzes a Substrate CARBOHYDRATE FEEDSTOCKS to product conversion Such as: i) 6-amino-3-hydroxyhexanoyl-CoA to 6-aminohexanoyl RELATED APPLICATIONS 5 CoA or ii) 6-aminohexanoyl-CoA to 6-aminocaproic acid. This application claims the benefit of U.S. Provisional In a second aspect, the invention provides in part a recom Application No. 61/209,917, filed Mar. 11, 2009, which binant microorganism producing 6-aminocaproic acid from application is hereby incorporated by reference in its entirety. lysine, and the recombinant microorganism includes at least 10 one nucleic acid encoding a polypeptide that catalyzes a FIELD OF INVENTION Substrate to product conversion Such as: i) lysine to beta-lysine, Aspects of the invention relate to methods for the produc ii) beta-lysine to 3,6-diaminohexanoyl-CoA, tion of difunctional alkanes in microorganisms. In particular, iii) 3,6-diaminohexanoyl-CoA to 6-aminohex-2-enoyl aspects of the invention describe enzymes, and nucleic acids 15 CoA, encoding Such enzymes, associated with the difunctional iv) 6-aminohex-2-enoyl-CoA to 6-aminohex-2-enoic acid, alkane production from carbohydrates feedstocks in micro O organisms. More specifically, aspects of the invention V) 6-aminohex-2-enoic acid to 6-aminocaproic acid.
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