WO 2017/015368 Al 2 6 January 2017 (26.01.2017) P O P C T

WO 2017/015368 Al 2 6 January 2017 (26.01.2017) P O P C T

(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization II International Bureau (10) International Publication Number (43) International Publication Date WO 2017/015368 Al 2 6 January 2017 (26.01.2017) P O P C T (51) International Patent Classification: Plaza 721/2340, 974 Centre Road, PO Box 291 5 Wilming C12N 1/19 (2006.01) C12N 9/00 (2006.01) ton, US 19805 (US). C12P 7/64 (2006.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 16/043 133 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 20 July 20 16 (20.07.2016) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/195,340 22 July 2015 (22.07.2015) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/195,338 22 July 2015 (22.07.2015) US (84) Designated States (unless otherwise indicated, for every (71) Applicant: E I DU PONT DE NEMOURS AND COM¬ kind of regional protection available): ARIPO (BW, GH, PANY [US/US]; Chestnut Run Plaza, 974 Centre Road, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, P.O. Box 2915, Wilmington, Delaware 19805 (US). TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (72) Inventors: ZHU, Quinn Qun; 544 Revere Road, West DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, Chester, Pennsylvania 19382 (US). FAN, Xiaochun; 175 LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, Pratt Lane, West Chester, Pennsylvania 19382 (US). SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, HONG, Seung-PYO; 9 Pierson's Ridge, Hockessin, GW, KM, ML, MR, NE, SN, TD, TG). Delaware 19707 (US). BOUGIOUKOU, Despina; 230 Published: Presidential Drive, Wilmington, Delaware 19807 (US). XIE, Dongming; 33 Renee Lane, Newark, Delaware — with international search report (Art. 21(3)) 1971 1 (US). DHAMANKAR, Himanshu H.; 258 Presid — with sequence listing part of description (Rule 5.2(a)) ential Drive, Apt. D, Greenville, Delaware 19807 (US). (74) Agent: CHESIRE, Dennis; E.I. du Pont de Nemours and Company, Legal Patent Records Center, Chestnut Run (54) Title: HIGH LEVEL PRODUCTION OF LONG-CHAIN DICARBOXYLIC ACIDS WITH MICROBES FIG. 1 © (57) Abstract: Recombinant microbial cells comprising an engineered LCDA production pathway that comprises at least one up- o regulated long-chain acyl-CoA synthetase (ACoS) are disclosed. These recombinant microbial cells are capable of producing one or more long-chain dicarboxylic acid (LCDA) products from a long-chain fatty acid-comprising substrate. Methods of using recombin ant microbial cells to produce LCDAs are also disclosed. TITLE HIGH LEVEL PRODUCTION OF LONG-CHAIN DICARBOXYLIC ACIDS WITH MICROBES This application claims the benefit of U.S. Provisional Application Nos. 62/1 95,340 (filed July 22, 201 6) and 62/1 95,338 (filed July 22, 201 6), which are both incorporated herein by reference in their entirety. FIELD OF INVENTION The present disclosure is in the field of molecular biology. For example, the disclosure pertains to microbes, such as yeast, genetically engineered to produce long- chain dicarboxylic acids (LCDA) from fatty acid-comprising substrates. REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named CL6467WOPCT_SequenceListing_ST25 created on July 18 , 2016, and having a size of 480 kilobytes and is filed concurrently with the specification. The sequence listing contained in this ASCII-formatted document is part of the specification and is herein incorporated by reference in its entirety. BACKGROUND Dicarboxylic acids comprising ten or more carbon atoms can be referred to as long-chain dicarboxylic acids (LCDAs). LCDAs are useful as constituent monomers for various synthetic materials such as polyamides (nylons), polyurethanes, and polyesters. Other uses of LCDAs include, for example, production of certain polycarbonates, powder coatings, fragrances, personal care items, food additives, solvents, cleaning additives, hot-melt adhesives, lubricants, insecticides and fungicides. LCDAs can also be used as plasticizers for engineering plastics and as corrosion inhibitors in metal processing technology, for example. Quantities of LCDAs suitable for carrying out commercial applications such as described above are generally not found in nature. Certain LCDAs, such as dodecanedioic acid (DDDA), can be prepared via various synthetic processes. However, biological processes such as microbial fermentation could also be useful for producing LCDAs. Feedstocks containing oil or free fatty acids, for example, may be suitable as substrates for fermenting LCDA products. Efforts to ferment LCDAs with yeast biocatalysts have been undertaken (U.S. Pat. Appl. Publ. Nos. 2004/0146999, 2010/0041 5 , 201 3/0267012, 2014/0228586). Fatty acids can be activated in yeast for use in beta-oxidation and other downstream pathways, thereby drawing fatty acids away from pathways of omega- oxidation. Thus, some yeast biocatalysts have been modified to exhibit reduced fatty acid activation, such as by down-regulating expression of long-chain fatty acyl-CoA synthetase, to augment fermentation of LCDA products via omega-oxidation (e.g., see U.S. Pat. Appl. Publ. Nos. 2014/0228586 and 2013/0267012). The above disclosures notwithstanding, it has now surprisingly been found that increasing fatty acid activation in yeast by up-regulating long-chain fatty acyl-CoA synthetase allows for high LCDA production. Thus, microbial biocatalysts engineered for high levels of LCDA production are disclosed herein. SUMMARY OF INVENTION In one embodiment, the disclosure concerns a recombinant microbial cell comprising an engineered LCDA production pathway that comprises up-regulation of a polynucleotide sequence encoding a long-chain acyl-CoA synthetase (ACoS enzyme), wherein the microbial cell is capable of producing one or more long-chain dicarboxylic acid (LCDA) products from a long-chain fatty acid-comprising substrate. Another embodiment concerns a recombinant microbial cell, comprising: (i) up-regulation of a polynucleotide sequence encoding a cytochrome P450 monooxygenase (CYP enzyme) and/or up-regulation of a polynucleotide sequence encoding a cytochrome P450 reductase (CPR enzyme), (ii) up-regulation of a polynucleotide sequence encoding a long-chain acyl- CoA synthetase (ACoS enzyme), and (iii) down-regulation of an endogenous polynucleotide sequence encoding a peroxisome biogenesis factor-3, wherein the microbial cell is capable of producing one or more long-chain dicarboxylic acid (LCDA) products from a long-chain fatty acid-comprising substrate. Another embodiment concerns a method of producing a long-chain dicarboxylic acid (LCDA). This method comprises: a) contacting a recombinant microbial cell as disclosed herein with a long-chain fatty acid-comprising substrate, wherein the microbial cell synthesizes an LCDA from the substrate; and b) optionally recovering the LCDA of step (a). BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCES FIG. 1: Lipid metabolic pathways, including fatty acid beta-oxidation and omega- oxidation aspects of lipid metabolism, are depicted. Dashed lines/arrows indicate low or weak activity in Y. lipolytica. FIG. 2 : Strategies are shown for engineering . lipolytica to produce LCDA from oil, oil-derived fatty acids, and/or fatty acid esters. FIG. 3 : Phylogenetic tree of candidate acyl-CoA synthetases from S. cerevisiae, Y. lipolytica and C. tropicalis. Certain abbreviations used in this figure: FAA1 and FAA2 denote S. cerevisiae Faal p and Faa2p, respectively. YA-1 denotes YIFaal p. Α -" denotes "YIACoS-". Refer to Example 1. FIG. 4 : LCDA production by strain D0145 in flask assay. DCA, dicarboxylic acid. Refer to Example 2 . FIG. 5A: Plasmid construct pZP2-YIACoS-3Ps (SEQ ID NO:63). FIG. 5B: Plasmid construct pZP2-YIACoS-5Ps (SEQ ID NO:64). FIG. 5C: Plasmid construct pZP2-YIACoS-6Ps (SEQ ID NO:65). FIG. 5D: Plasmid construct pZP2-YIACoS-1 0Ps (SEQ ID NO:66). FIG. 5E: Plasmid construct pZKL7A-FYIFAAs (SEQ ID NO:67). FIG. 5F: Plasmid construct pZP2-YIACoS-5PS3s (SEQ ID NO:68). FIG. 6A: SDS-PAGE analysis of soluble and insoluble fractions of E . coli cells transformed to over-express putative fatty acyl CoA synthetases. Lanes 1, 2 , 3 , 4 , 5 , 6 : samples from E . coli cells over-expressing YIACoS-3P (SEQ ID NO:39), YIACoS-5P (SEQ ID NO:42), YIAC0S-6P (SEQ ID NO:44), YIACoS-10P (SEQ ID NO:49), YIFAA (SEQ ID NO:36), or YIACoS-5PS3 (SEQ ID NO:56), respectively. Lane C : sample from E . coli cells transformed with the pET23d vector alone (negative control). Lane M : protein markers. Refer to Example 5 . FIG. 6B: SDS-PAGE of lysates of E . coli cells before and after IPTG-induced over-expression of putative fatty acyl CoA synthetases. Lanes 1, 2 , 3 , 4 : samples from E . coli cells over-expressing YIACoS-3P (SEQ ID NO:39), YIACoS-5P (SEQ ID NO:42), YIAC0S-6P (SEQ ID NO:44), or YIACoS-1 0P (SEQ ID NO:49), respectively. Lane C : sample from E . coli cells transformed with the pET23d vector alone (negative control). Lane M : protein markers. Refer to Example 5 . FIG. 7A: A diagram is shown depicting the lineage of certain strains listed in Table 7 .

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