SG11201907008RA - Methods and microorganisms for making 2,3-butanediol and derivatives thereof from c1 carbons - Google Patents

Methods and microorganisms for making 2,3-butanediol and derivatives thereof from c1 carbons

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Publication number
SG11201907008RA
SG11201907008RA SG11201907008RA SG11201907008RA SG11201907008RA SG 11201907008R A SG11201907008R A SG 11201907008RA SG 11201907008R A SG11201907008R A SG 11201907008RA SG 11201907008R A SG11201907008R A SG 11201907008RA SG 11201907008R A SG11201907008R A SG 11201907008RA
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Singapore
Prior art keywords
california
international
rule
methods
microorganisms
Prior art date
Application number
SG11201907008RA
Inventor
Xinhua Zhao
Mark Held
Tina Huynh
Lily Chao
Na Trinh
Matthias Schamlisch
Bryan Yeh
James Kealey
Kevin Dietzel
Original Assignee
Intrexon Corp
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Publication date
Application filed by Intrexon Corp filed Critical Intrexon Corp
Publication of SG11201907008RA publication Critical patent/SG11201907008RA/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/52—Genes encoding for enzymes or proenzymes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07C—ACYCLIC OR CARBOCYCLIC COMPOUNDS
    • C07C11/00—Aliphatic unsaturated hydrocarbons
    • C07C11/12—Alkadienes
    • C07C11/16—Alkadienes with four carbon atoms
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/74—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0006—Oxidoreductases (1.) acting on CH-OH groups as donors (1.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1022—Transferases (2.) transferring aldehyde or ketonic groups (2.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/88—Lyases (4.)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P5/00—Preparation of hydrocarbons or halogenated hydrocarbons
    • C12P5/02—Preparation of hydrocarbons or halogenated hydrocarbons acyclic
    • C12P5/023—Methane
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic
    • C12P7/16—Butanols
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic
    • C12P7/18—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic polyhydric
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y101/00—Oxidoreductases acting on the CH-OH group of donors (1.1)
    • C12Y101/01—Oxidoreductases acting on the CH-OH group of donors (1.1) with NAD+ or NADP+ as acceptor (1.1.1)
    • C12Y101/01076—(S,S)-Butanediol dehydrogenase (1.1.1.76)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y101/00—Oxidoreductases acting on the CH-OH group of donors (1.1)
    • C12Y101/01—Oxidoreductases acting on the CH-OH group of donors (1.1) with NAD+ or NADP+ as acceptor (1.1.1)
    • C12Y101/01304—Diacetyl reductase, (S)-acetoin forming (1.1.1.304)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y202/00—Transferases transferring aldehyde or ketonic groups (2.2)
    • C12Y202/01—Transketolases and transaldolases (2.2.1)
    • C12Y202/01006—Acetolactate synthase (2.2.1.6)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y401/00—Carbon-carbon lyases (4.1)
    • C12Y401/01—Carboxy-lyases (4.1.1)
    • C12Y401/01004—Acetoacetate decarboxylase (4.1.1.4)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y101/00—Oxidoreductases acting on the CH-OH group of donors (1.1)
    • C12Y101/01—Oxidoreductases acting on the CH-OH group of donors (1.1) with NAD+ or NADP+ as acceptor (1.1.1)
    • C12Y101/01004—R,R-butanediol dehydrogenase (1.1.1.4)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y401/00—Carbon-carbon lyases (4.1)
    • C12Y401/01—Carboxy-lyases (4.1.1)
    • C12Y401/01005—Acetolactate decarboxylase (4.1.1.5)
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02E—REDUCTION OF GREENHOUSE GAS [GHG] EMISSIONS, RELATED TO ENERGY GENERATION, TRANSMISSION OR DISTRIBUTION
    • Y02E50/00—Technologies for the production of fuel of non-fossil origin
    • Y02E50/10—Biofuels, e.g. bio-diesel
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02E—REDUCTION OF GREENHOUSE GAS [GHG] EMISSIONS, RELATED TO ENERGY GENERATION, TRANSMISSION OR DISTRIBUTION
    • Y02E50/00—Technologies for the production of fuel of non-fossil origin
    • Y02E50/30—Fuel from waste, e.g. synthetic alcohol or diesel

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Biotechnology (AREA)
  • Biomedical Technology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Medicinal Chemistry (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Virology (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)

Abstract

AisSOH OH -acetolactate co o pyruvate OH 0 CO 2 OH BudA rt. tr% OH OH Acetoin NAD(P)H NAD(P) 2,3 BDO ButA CO 2 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 02 August 2018 (02.08.2018) WIPO I PCT ill Hu °ninon olo olo Ho 11°111°1°1110 iflo oimIE (10) International Publication Number WO 2018/140928 Al (51) International Patent Classification: C12N 1/00 (2006.01) Cl 2N 15/52 (2006.01) C12N 1/21 (2006.01) Cl 2N 15/63 (2006.01) C12N 9/00 (2006.01) Cl 2P 7/16 (2006.01) C12N 9/04 (2006.01) (21) International Application Number: PCT/US2018/015909 (22) International Filing Date: 30 January 2018 (30.01.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/451,819 30 January 2017 (30.01.2017) US 62/504,626 11 May 2017 (11.05.2017) US 62/512,312 30 May 2017 (30.05.2017) US 62/588,985 21 November 2017 (21.11.2017) US (71) Applicant: INTREXON CORPORATION [US/US]; 1750 Kraft Drive, Suite 1400, Blacksburg, Virginia 24060 (US). (72) Inventors: ZHAO, Xinhua; 2771 Alliston Loop, Dublin, California 94568 (US). HELD, Mark, Anton; 1030 45th Street, REAR, Emeryville, California 94608 (US). HUYNH, Tina; 3301 High Street, Oakland, California 94619 (US). CHAO, Lily, Yuin; 72 Langton Street, Unit 3, San Francisco, California 94103 (US). TRINH, Na; 1839 Ygnacio Valley Road #181, Walnut Creek, Califor- nia 94598 (US). SCHAMLISCH, Matthias, Helmut; 340 Holly Avenue, South San Francisco, California 94080 (US). YEH, Bryan; 156 Arlene Drive, Walnut Creek, Califor- nia 94595 (US). KEALEY, James; 945 Midpine Way, Se- bastopol, California 95472 (US). DIETZEL, Kevin, Lee; 963 Fassler Avenue, Pacifica, California 94044 (US). (74) Agent: KELLY, David, A. et al.; Hunton & Williams LLP, Intellectual Property Department, 2200 Pennsylvania Ave., NW, Washington, District of Columbia 20037 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Declarations under Rule 4.17: as to the identity of the inventor (Rule 4.17(i)) as to applicant's entitlement to apply for and be granted a patent (Rule 4.17(ii)) as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(iii)) — (54) Title: METHODS AND MICROORGANISMS FOR MAKING 2,3-BUTANEDIOL AND DERIVATIVES THEREOF FROM Cl CARBONS Methane FIG.1 1-1 00 (57) : Genetically modified microorganisms that have the ability to convert carbon substrates into chemical products such as O 2,3-BDO are disclosed. For example, genetically modified methanotrophs that are capable of generating 2,3-BDO at high titers from \" a methane source are disclosed. Methods of making these genetically modified microorganisms and methods of using them are also C disclosed. [Continued on next page] WO 2018/140928 Al MIDEDIMOMMIDIREEMOMMEENHOIEHMEEN Published: — with international search report (Art. 21(3)) with sequence listing part of description (Rule 5.2(a))
SG11201907008RA 2017-01-30 2018-01-30 Methods and microorganisms for making 2,3-butanediol and derivatives thereof from c1 carbons SG11201907008RA (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201762451819P 2017-01-30 2017-01-30
US201762504626P 2017-05-11 2017-05-11
US201762512312P 2017-05-30 2017-05-30
US201762588985P 2017-11-21 2017-11-21
PCT/US2018/015909 WO2018140928A1 (en) 2017-01-30 2018-01-30 Methods and microorganisms for making 2,3-butanediol and derivatives thereof from c1 carbons

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US (4) US11198877B2 (en)
EP (2) EP3574092A4 (en)
KR (2) KR20230142696A (en)
CN (1) CN110475850B (en)
AU (2) AU2018213387B2 (en)
BR (1) BR112019015754A2 (en)
CA (2) CA3052046A1 (en)
IL (2) IL268337B1 (en)
MA (1) MA47381A (en)
MX (1) MX2019009032A (en)
PH (2) PH12019501768A1 (en)
SG (3) SG10202107750TA (en)
WO (2) WO2018140936A1 (en)
ZA (3) ZA201905095B (en)

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EP3615676A4 (en) * 2017-04-28 2021-07-07 Intrexon Corporation Methods and microorganisms for the fermentation of methane to multi-carbon compounds
CN112154207B (en) * 2018-08-24 2022-03-22 江苏省农业科学院 Rape anti-pyrimidine salicylic acid herbicide gene and application thereof
KR102481504B1 (en) * 2019-04-16 2022-12-27 경희대학교 산학협력단 Engineered methanotrophs for producing 2,3-BOD
KR20210045752A (en) 2019-10-17 2021-04-27 경희대학교 산학협력단 Transformed methanotrophs for producing 1,3-butanediol and uses thereof
CN114731793A (en) * 2022-04-07 2022-07-12 中山大学 Method for reducing methane emission of rice field soil
CN115058374B (en) * 2022-05-24 2023-08-01 天津大学前沿技术研究院有限公司 Recombinant zymomonas mobilis for synthesizing acetoin by utilizing pyruvic acid as well as construction method and application thereof

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PH12019501768A1 (en) 2020-03-16
EP3574092A4 (en) 2021-01-13
IL268337B1 (en) 2024-05-01
CN110475850B (en) 2023-11-07
MA47381A (en) 2021-04-14
BR112019015754A2 (en) 2020-06-09
IL268337A (en) 2019-09-26
KR20190112044A (en) 2019-10-02
AU2018213387B2 (en) 2024-06-13
US20200040344A1 (en) 2020-02-06
WO2018140928A1 (en) 2018-08-02
US11111496B2 (en) 2021-09-07
CA3052046A1 (en) 2018-08-02
KR102525517B1 (en) 2023-04-25
EP3574092A1 (en) 2019-12-04
CN110475850A (en) 2019-11-19
ZA201905094B (en) 2022-01-26
IL268339A (en) 2019-09-26
US11939584B2 (en) 2024-03-26
EP3574081A4 (en) 2021-04-14
ZA202105423B (en) 2023-12-20
MX2019009032A (en) 2019-09-10
RU2019124480A (en) 2021-03-01
AU2018213395A1 (en) 2019-08-15
AU2018213387A1 (en) 2019-08-15
US20200115713A1 (en) 2020-04-16
US20220049259A1 (en) 2022-02-17
ZA201905095B (en) 2022-12-21
US20220112506A1 (en) 2022-04-14
US11198877B2 (en) 2021-12-14
SG11201907012VA (en) 2019-08-27
WO2018140936A1 (en) 2018-08-02
EP3574081A1 (en) 2019-12-04
KR20230142696A (en) 2023-10-11
RU2019124480A3 (en) 2021-12-15
CA3052072A1 (en) 2018-08-02
SG10202107750TA (en) 2021-09-29

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