WO2012109534A2 - Cells and methods for producing isobutyric acid - Google Patents

Cells and methods for producing isobutyric acid Download PDF

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Publication number
WO2012109534A2
WO2012109534A2 PCT/US2012/024640 US2012024640W WO2012109534A2 WO 2012109534 A2 WO2012109534 A2 WO 2012109534A2 US 2012024640 W US2012024640 W US 2012024640W WO 2012109534 A2 WO2012109534 A2 WO 2012109534A2
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WO
WIPO (PCT)
Prior art keywords
cell
polypeptide
genetically modified
isobutyrate
recombinant cell
Prior art date
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Ceased
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PCT/US2012/024640
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English (en)
French (fr)
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WO2012109534A3 (en
Inventor
Kechun Zhang
Mingyong XIONG
Adam P. WOODRUFF
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University of Minnesota Twin Cities
University of Minnesota System
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University of Minnesota Twin Cities
University of Minnesota System
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Publication date
Application filed by University of Minnesota Twin Cities, University of Minnesota System filed Critical University of Minnesota Twin Cities
Priority to CN201280017985.8A priority Critical patent/CN103562375A/zh
Priority to EP12705215.7A priority patent/EP2673355A2/en
Priority to US13/984,502 priority patent/US20140065697A1/en
Priority to JP2013553588A priority patent/JP2014506466A/ja
Priority to KR1020137023666A priority patent/KR20140061303A/ko
Priority to AU2012214255A priority patent/AU2012214255A1/en
Priority to SG2013060769A priority patent/SG192706A1/en
Publication of WO2012109534A2 publication Critical patent/WO2012109534A2/en
Publication of WO2012109534A3 publication Critical patent/WO2012109534A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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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
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/70—Vectors or expression systems specially adapted for E. coli
    • 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; 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
    • C12N1/14—Fungi; 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
    • C12N1/00—Microorganisms; 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
    • C12N15/11—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
    • 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.)
    • C12N9/0008—Oxidoreductases (1.) acting on the aldehyde or oxo group of donors (1.2)
    • 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
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • 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
    • C12P7/40—Preparation of oxygen-containing organic compounds containing a carboxyl group including Peroxycarboxylic acids
    • C12P7/52—Propionic acid; Butyric acids

Definitions

  • the genetically modified polypeptide comprises a pyruvate formate lyase I such as, for example, a polypeptide encoded by a genetically modified pflB.
  • the genetically modified polypeptide comprises a pyruvate oxidase such as, for example, a polypeptide encoded by a genetically modified poxB.
  • FIG. 6 Isobutyrate synthetic pathway in E. coli.
  • glucose is metabolized to pyruvate (Compound 6) through glycolysis. Pyruvate is then converted into 2-ketovaline (Compound 9) by valine biosynthetic enzymes AlsS, IlvC, and IlvD. (Atsumi et al., 2008 Nature 451:86- 89).
  • 2-Ketovaline can be decarboxylated into isobutyraldehyde by Ehrlich pathway enzyme 2- ketoacid decarboxylase (KIVD) from Lactococcus lactis. (de la Plaza et al, 2004 FEMS Microbiol. Lett. 238:367-74).
  • KIVD 2- ketoacid decarboxylase
  • the dissolved oxygen (DO) level was maintained at 10% to burn excess NADH. Higher DO levels were avoided in order to prevent excessive oxidation of substrate into C0 2 through the TCA cycle.
  • isobutyrate can be produced from engineered microbes with a high accumulation and high yield. Since the production of isobutyrate described in this work is amenable to microbial fermentation, the modified microbial strains and the methods described herein can provide a new platform for commercial production of isobutyrate.
  • isobutyratedsobutanol ratio of at least 1:1 such as, for example, at least 2:1, at least 3:1, at least 4:1, at least 5:1, at least 6:1, at least 7:1, at least 8:1, at least 9:1, at least 10:1, at least 11:1, at least 12:1, at least 13:1, at least 14:1, at least 15:1, at least 20:1, at least 25:1, at least 30:1, at least 50:1, at least 60:1, at least 70:1, at least 80:1, at least 90:1, or at least 100:1.
  • the recombinant cell may be, or be derived from, a eukaryotic microbe such as, for example, a fungal cell.
  • the fungal cell may be, or be derived from, a member of the Saccharomycetaceae family such as, for example, Saccharomyces cerevisiae, a member of the genus Candida such as, for example, Candida albicans, a member of the genus Kluyvermyces, or a member of the genus Pichia such as, for example, Pichia pastoris.
  • the fungal cell may be a member of the family Dipodascaceae such as, for example, Yarrowia lipolytica.
  • the heterologous DNA molecule encodes a polypeptide having at least 80% amino acid sequence identitity to the amino acid sequence of any one of SEQ ID NO:l through SEQ ID NO: 106.
  • exemplary heterologous DNA molecules include those that encode a polypeptide having, for example, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%), at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the reference amino acid sequence.
  • polypeptide of this type can include, for example, a genetically modified version of an alcohol dehydrogenase such as, for example, a polypeptide encoded by a genetically modified adhE; or a genetically modified version of a phosphate acetyltransferase such as, for example, a polypeptide encoded by a genetically modified pta.
  • an alcohol dehydrogenase such as, for example, a polypeptide encoded by a genetically modified adhE
  • phosphate acetyltransferase such as, for example, a polypeptide encoded by a genetically modified pta.
  • Lactococcus lactis (ATCC) using the primers kivd_accfwd and kivd_xbarev.
  • the PCR product was digested with Acc65I and Xbal, and ligated into pZElac to yield plasmids pIBA2. Kivd was also amplified with kivd_accfwd and kivd_sphrev, and the PCR product was digested with Acc65I and SphI.
  • YdcWv as amplified from the E. coli genomic DNA with primers ydcw_sphfwd and ydcw_xbarev, which was then digested with SphI and Xbal.
  • Substrate isobutyraldehyde was purchased from Fisher Scientific International, Inc. (Hampton, NH), and NAD + was from New England Biolabs, Inc., (Ipswich, MA).
  • the reaction mixture contained 0.5 mM NAD + and 0.2-4 mM isobutyraldehyde in assay buffer (50 mM NaH 2 P04, pH 8.0, lmM DTT) with a total volume of 80 ⁇ .
  • the reactions were started by adding 2 ⁇ KTVD (final enzyme concentration 25 nM), and the generation of NADH was monitored at 340 nm (extinction coefficient, 6.22 mM "1 cm “1 ).
  • Kinetic parameters (k cat and K m ) were determined by fitting initial velocity data to the Michaelis-Menten equation using Origin software.

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Molecular Biology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Virology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Botany (AREA)
  • Mycology (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
PCT/US2012/024640 2011-02-11 2012-02-10 Cells and methods for producing isobutyric acid Ceased WO2012109534A2 (en)

Priority Applications (7)

Application Number Priority Date Filing Date Title
CN201280017985.8A CN103562375A (zh) 2011-02-11 2012-02-10 用于产生异丁酸的细胞和方法
EP12705215.7A EP2673355A2 (en) 2011-02-11 2012-02-10 Cells and methods for producing isobutyric acid
US13/984,502 US20140065697A1 (en) 2011-02-11 2012-02-10 Cells and methods for producing isobutyric acid
JP2013553588A JP2014506466A (ja) 2011-02-11 2012-02-10 イソ酪酸を製造するための細胞及び方法
KR1020137023666A KR20140061303A (ko) 2011-02-11 2012-02-10 이소부티르산을 생산하기 위한 세포 및 방법
AU2012214255A AU2012214255A1 (en) 2011-02-11 2012-02-10 Cells and methods for producing isobutyric acid
SG2013060769A SG192706A1 (en) 2011-02-11 2012-02-10 Cells and methods for producing isobutyric acid

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201161441939P 2011-02-11 2011-02-11
US61/441,939 2011-02-11

Publications (2)

Publication Number Publication Date
WO2012109534A2 true WO2012109534A2 (en) 2012-08-16
WO2012109534A3 WO2012109534A3 (en) 2012-10-04

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PCT/US2012/024640 Ceased WO2012109534A2 (en) 2011-02-11 2012-02-10 Cells and methods for producing isobutyric acid

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US (1) US20140065697A1 (https=)
EP (1) EP2673355A2 (https=)
JP (1) JP2014506466A (https=)
KR (1) KR20140061303A (https=)
CN (1) CN103562375A (https=)
AU (1) AU2012214255A1 (https=)
SG (1) SG192706A1 (https=)
WO (1) WO2012109534A2 (https=)

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013055667A3 (en) * 2011-10-10 2013-06-20 Regents Of The University Of Minnesota Biocatalysis cells and methods
WO2013180810A1 (en) * 2012-05-29 2013-12-05 Regents Of The University Of Minnesota Biosynthetic pathways, recombinant cells, and methods
WO2014028642A1 (en) * 2012-08-17 2014-02-20 Easel Biotechnologies, Llc Two stage production of higher alcohols
CN105705650A (zh) * 2013-08-28 2016-06-22 英威达技术有限责任公司 用于生物合成异丁烯酸盐的方法
WO2017194696A1 (en) 2016-05-12 2017-11-16 Danmarks Tekniske Universitet Bacterial cells with improved tolerance to isobutyric acid
US10704063B2 (en) 2015-05-19 2020-07-07 Lucite International Uk Limited Process for the biological production of methacrylic acid and derivatives thereof

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WO2013192237A1 (en) * 2012-06-18 2013-12-27 The Regents Of The University Of California Escherichia coli engineered for isobutyraldehyde production
JP2017131111A (ja) 2014-06-03 2017-08-03 味の素株式会社 Ｌ−アミノ酸の製造法
WO2015191611A1 (en) * 2014-06-09 2015-12-17 The Regents Of The University Of California Bacteria engineered for conversion of ethylene to n-butanol
CN105296410A (zh) * 2015-10-27 2016-02-03 中国科学院青岛生物能源与过程研究所 一种利用缬氨酸途径合成丙烷的大肠杆菌及其构建方法
US20200308610A1 (en) 2016-03-11 2020-10-01 Aemitis, Inc. Alpha-ketoisocaproic acid and & alpha-keto-3-methylvaleric acid decarboxylases and uses thereof
US10849938B2 (en) 2017-09-13 2020-12-01 ZBiotics Company Gene expression system for probiotic microorganisms
US11680280B2 (en) 2018-01-09 2023-06-20 Lygos, Inc. Recombinant host cells and methods for the production of isobutyric acid

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US4754074A (en) 1986-12-22 1988-06-28 Amoco Corporation Preparation of dialkyl ketones from aliphatic carboxylic acids

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KR100780324B1 (ko) * 2006-07-28 2007-11-29 한국과학기술원 신규 순수 숙신산 생성 변이 미생물 및 이를 이용한 숙신산제조방법
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US4754074A (en) 1986-12-22 1988-06-28 Amoco Corporation Preparation of dialkyl ketones from aliphatic carboxylic acids

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Cited By (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013055667A3 (en) * 2011-10-10 2013-06-20 Regents Of The University Of Minnesota Biocatalysis cells and methods
WO2013180810A1 (en) * 2012-05-29 2013-12-05 Regents Of The University Of Minnesota Biosynthetic pathways, recombinant cells, and methods
US10006064B2 (en) 2012-05-29 2018-06-26 Regents Of The University Of Minnesota Biosynthetic pathways, recombinant cells, and methods
US10233467B2 (en) 2012-08-17 2019-03-19 Easel Biotechnologies, Llc Two-stage production of higher alcohols
WO2014028642A1 (en) * 2012-08-17 2014-02-20 Easel Biotechnologies, Llc Two stage production of higher alcohols
US10676762B2 (en) 2012-08-17 2020-06-09 Easel Biotechnologies Llc Two-stage production of higher alcohols
CN105705650A (zh) * 2013-08-28 2016-06-22 英威达技术有限责任公司 用于生物合成异丁烯酸盐的方法
US10704063B2 (en) 2015-05-19 2020-07-07 Lucite International Uk Limited Process for the biological production of methacrylic acid and derivatives thereof
US10724058B2 (en) 2015-05-19 2020-07-28 Lucite International Uk Limited Process for the biological production of methacrylic acid and derivatives thereof
US11248243B2 (en) 2015-05-19 2022-02-15 Mitsubishi Chemical UK Limited Process for the biological production of methacrylic acid and derivatives thereof
US11753660B2 (en) 2015-05-19 2023-09-12 Mitsubishi Chemical UK Limited Process for the biological production of methacrylic acid and derivatives thereof
US11753661B2 (en) 2015-05-19 2023-09-12 Mitsubishi Chemical UK Limited Process for the biological production of methacrylic acid and derivatives thereof
WO2017194696A1 (en) 2016-05-12 2017-11-16 Danmarks Tekniske Universitet Bacterial cells with improved tolerance to isobutyric acid

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WO2012109534A3 (en) 2012-10-04
EP2673355A2 (en) 2013-12-18
SG192706A1 (en) 2013-09-30
KR20140061303A (ko) 2014-05-21
AU2012214255A1 (en) 2013-09-12
US20140065697A1 (en) 2014-03-06
CN103562375A (zh) 2014-02-05
JP2014506466A (ja) 2014-03-17

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