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(12) Patent Application Publication (10) Pub. No.: US 2016/0319313 A1 SUN Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2016/0319313 A1 SUN Et Al US 201603.1931.3A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0319313 A1 SUN et al. (43) Pub. Date: Nov. 3, 2016 (54) MICROORGANISMS AND METHODS FOR continuation of application No. 12/940,021, filed on THE COPRODUCTION 1,4-BUTANEDIOL Nov. 4, 2010, now Pat. No. 8,530,210. AND GAMMA-BUTYROLACTONE (60) Provisional application No. 61/264,598, filed on Nov. (71) Applicant: Genomatica, Inc., San Diego, CA (US) 25, 2009. Publication Classification (72) Inventors: Jun SUN, San Diego, CA (US); Mark J. BURK, San Diego, CA (US); (51) Int. Cl. Anthony P. BURGARD, Bellefonte, CI2P I 7/04 (2006.01) CA (US); Robin E. OSTERHOUT, CI2N 15/52 (2006.01) San Diego, CA (US); Wei NIU, CI2P 7/18 (2006.01) Lincoln, NE (US); John D. (52) U.S. Cl. TRAWICK, La Mesa, CA (US); CPC .................. CI2P 17/04 (2013.01); C12P 7/18 Robert HASELBECK, San Diego, CA (2013.01); C12N 15/52 (2013.01) (US) (57) ABSTRACT (21) Appl. No.: 14/954,487 The invention provides non-naturally occurring microbial organisms comprising 1,4-butanediol (14-BDO) and (22) Filed: Nov. 30, 2015 gamma-butyrolactone (GBL) pathways comprising at least one exogenous nucleic acid encoding a 14-BDO and GBL pathway enzyme expressed in a Sufficient amount to produce Related U.S. Application Data 14-BDO and GBL. The invention additionally provides (63) Continuation of application No. 13/936,878, filed on methods of using Such microbial organisms to produce Jul. 8, 2013, now Pat. No. 9,222,113, which is a 14-BDO and GBL. Patent Application Publication Nov. 3, 2016 Sheet 1 of 8 US 2016/0319313 A1 Patent Application Publication Nov. 3, 2016 Sheet 2 of 8 US 2016/0319313 A1 3. 2-2 2-3 8. Sai assics Stras a Passics × |×******************* 2-4 Sai assis FG. 2 Patent Application Publication Nov. 3, 2016 Sheet 3 of 8 US 2016/0319313 A1 FG. 3 Patent Application Publication Nov. 3, 2016 Sheet 4 of 8 US 2016/0319313 A1 BC, 250 Aer Seri-anaero x Araer 130 d 3 f Patent Application Publication Nov. 3, 2016 Sheet 5 of 8 US 2016/0319313 A1 edia, Fitriests, gii OSS: Ce: Recycle Soyert Recycie & 38. etc. Sepatatio? to Y Y-1'co is- <S --S C interia, nutrients, glucose Ce: Recycle &as sea 3) FG. 5 Patent Application Publication Nov. 3, 2016 Sheet 8 of 8 US 2016/0319313 A1 *... : FG. 9 US 2016/03193 13 A1 Nov. 3, 2016 MCROORGANISMS AND METHODS FOR ments includes the non-enzymatic lactonization of THE COPRODUCTION 14-BUTANEDIOL 4-hydroxybutyryl-phosphate or 4-hydroxybutyryl-CoA to AND GAMMA-BUTYROLACTONE form GBL. 0001. This application is a continuation of U.S. Non BRIEF DESCRIPTION OF THE DRAWINGS provisional application Ser. No. 13/936,878, filed Jul. 8, 2013, which is a continuation of U.S. Non-provisional 0008 FIGS. 1A and 1B show exemplary pathways for application Ser. No. 12/940,021, filed Nov. 4, 2010, now co-production of 14-BDO and GBL. Enzymes for transfor issued U.S. Pat. No. 8,530,210, issued Sep. 10, 2013, which mation of identified Substrates to products include: A) Suc claims the benefit of priority of U.S. Provisional Application cinyl-CoA reductase (aldehyde forming), B) alpha-ketoglu No. 61/264,598, filed Nov. 25, 2009, the entire contents of tarate decarboxylase, C) 4-hydroxybutyrate dehydrogenase, which are each incorporated herein by reference. D) 4-hydroxybutyrate reductase, E) 1,4-butanediol dehydro genase, F) Succinate reductase, G) Succinyl-CoA transferase, BACKGROUND OF THE INVENTION H) Succinyl-CoA hydrolase, I) succinyl-CoA synthetase (or Succinyl-CoA ligase), J) glutamate dehydrogenase, K) glu 0002 The instant application contains a Sequence Listing tamate transaminase, L) glutamate decarboxylase, M) which has been submitted in ASCII format via EFS-Web and 4-aminobutyrate dehydrogenase, N) 4-aminobutyrate is hereby incorporated by reference in its entirety. Said transaminase, O) 4-hydroxybutyrate kinase, P) phospho ASCII copy, created on Nov. 30, 2015, is named 12956 trans-4-hydroxybutyrylase, Q) 4-hydroxybutyryl-CoA 386-999 Sequence Listing and is 5,588 bytes in size. reductase (aldehyde forming), R) 4-hydroxybutyryl-phos 0003. The present invention relates generally to biosyn phate reductase, S) Succinyl-CoA reductase (alcohol form thetic processes, and more specifically to organisms having ing), T) 4-hydroxybutyryl-CoA transferase, U) 4-hydroxy 1,4-butanediol and gamma-butyrolactone biosynthetic capa butyryl-CoA hydrolase, V) 4-hydroxybutyryl-CoA bility. synthetase (or 4-hydroxybutyryl-CoA ligase), W) 4-hy 0004 1,4-Butanediol (14-BDO) is a polymer intermedi droxybutyryl-CoA reductase (alcohol forming), X) alpha ate and industrial solvent with a global market of about 3 ketoglutarate reductase, Y) 5-hydroxy-2-oxopentanoate billion lb/year. 14-BDO is currently produced from petro dehydrogenase, Z) 5-hydroxy-2-oxopentanoate decarboxy chemical precursors, primarily acetylene, maleic anhydride, lase, AA) 5-hydroxy-2-oxopentanoate dehydrogenase (de and propylene oxide. For example, acetylene is reacted with carboxylation), AB) 4-hydroxybutyrate lactonase, AC) non 2 molecules of formaldehyde in the Reppe synthesis reaction enzymatic 4-hydroxybutyryl-phosphate lactonization, and (Kroschwitz and Grant, Encyclopedia of Chem. Tech. John AD) non-enzymatic 4-hydroxybutyryl-CoA lactonization. Wiley and Sons, Inc., New York (1999)), followed by 0009 FIG. 2 shows the production of 4-HB in glucose catalytic hydrogenation to form 1,4-butanediol. Down minimal medium using E. coli Strains harboring plasmids stream, 14-BDO can be further transformed; for example, by expressing various combinations of 4-HB pathway genes. oxidation to gamma-butyrolactone (GBL) or hydrogenolysis (a) 4-HB concentration in culture broth; (b) succinate con to tetrahydrofuran (THF). These compounds have varied centration in culture broth; (c) culture OD, measured at 600 uses as polymer intermediates, solvents, and additives, and nm. Clusters of bars represent the 24 hour, 48 hour, and 72 have a combined market of nearly 2 billion lb/year. hour (if measured) timepoints. The codes along the X-axis 0005 Gamma-butyrolactone (GBL) is a chemical inter indicate the strain/plasmid combination used. The first index mediate and common solvent with a global market of about refers to the host strain: 1, MG1655 lacI’: 2, MG1655 0.5 billion lb/year. GBL has wide applications. GBL serves Agabl) lacI: 3, MG 1655 AgabD AaldA lacI. The second as a chemical intermediate in the manufacture of pyrroli index refers to the plasmid combination used: 1, pZE13 dones that are widely used in the pharmaceutical industry. It 0004-0035 and pZA33-0036: 2, p7E13-0004-0035 and can be used in the production of pesticides, herbicides and pZA33-0010n: 3, p.ZE13-0004-0008 and pZA33-0036; 4, plant growth regulators. GBL is also used as an aroma pZE13-0004-0008 and pZA33-0010n; 5, Control vectors compound, as a stain remover, as a Superglue remover, as a pZE13 and pZA33. paint stripper, and as a solvent in some wet aluminum 0010 FIG. 3 shows the production of 4-HB from glucose electrolytic capacitors. Currently, GBL is mainly synthe in E. coli Strains expressing O-ketoglutarate decarboxylase sized through 14-BDO from crude oil and/or natural gas from Mycobacterium tuberculosis. Strains 1-3 contain derived feedstocks by the Reppe acetylene chemistry. pZE13-0032 and pZA33-0036. Strain 4 expresses only the empty vectors pZE13 and pZA33. Host strains are as fol 0006 Microbial organisms and methods for effectively lows: 1 and 4, MG1655 lacI’: 2, MG1655 AgabD lacI: 3, co-producing commercial quantities of 14-BDO and GBL MG1655 Agabd AaldA lacI. The bars refer to concentra are described herein and include related advantages. tion at 24 and 48 hours. SUMMARY OF INVENTION (0011 FIG. 4 shows the production of BDO from 10 mM 4-HB in recombinant E. coli strains. Numbered positions 0007. The invention provides non-naturally occurring correspond to experiments with MG1655 lacI containing microbial organisms containing 1,4-butanediol (14-BDO) pZA33-0024, expressing cat? from P gingivalis, and the and gamma-butyrolactone (GBL) pathways comprising at following genes expressed on pZE13: 1. none (control); 2. least one exogenous nucleic acid encoding a 14-BDO path 0002; 3,0003: 4,0003n; 5, 0011; 6, 0013; 7, 0023; 8, 0025; way enzyme and at least one exogenous nucleic acid encod 9,0008n; 10, 0035. Gene numbers are defined in Table 56. ing a GBL pathway enzyme each expressed in a Sufficient For each position, the bars refer to aerobic, microaerobic, amount to produce 14-BDO and GBL. The invention addi and anaerobic conditions, respectively. Microaerobic condi tionally provides methods of using Such microbial organ tions were created by sealing the culture tubes but not isms to produce 14-BDO and GBL, which in some embodi evacuating them. US 2016/03193 13 A1 Nov. 3, 2016 0012 FIG. 5 is a schematic process flow diagram of bioprocesses. Separate strain design strategies were identi bioprocesses for the production of Y-butyrolactone. Panel (a) fied with incorporation of different non-native or heterolo illustrates fed-batch fermentation with batch separation and gous reaction capabilities into E. coli or other host organ panel (b) illustrates fed-batch fermentation with continuous isms leading to 14-BDO and GBL producing metabolic separation. pathways from either Succinate. Succinyl-CoA or alpha 0013 FIG. 6 shows the mass spectrum of 4-HB and BDO ketoglutarate. In silico metabolic designs were identified produced by MG1655 lacI pZE13-0004-0035-0002 that resulted in the biosynthesis of 14-BDO and GBL in pZA33-0034-0036 grown in M9 minimal medium supple microorganisms from each of these metabolic intermediates. mented with 4 g/L unlabeled glucose (a, c, e, and g) Embodiments of the invention include the controlled pro uniformly labeled 'C-glucose (b, d, f, and h).
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