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WO2002029032A3 - Manipulation de cellule entiere par mutagenese d'une partie substantielle d'un genome de depart, par combinaison de mutations et eventuellement par repetition - Google Patents

Manipulation de cellule entiere par mutagenese d'une partie substantielle d'un genome de depart, par combinaison de mutations et eventuellement par repetition Download PDF

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Publication number
WO2002029032A3
WO2002029032A3 PCT/US2001/031004 US0131004W WO0229032A3 WO 2002029032 A3 WO2002029032 A3 WO 2002029032A3 US 0131004 W US0131004 W US 0131004W WO 0229032 A3 WO0229032 A3 WO 0229032A3
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WIPO (PCT)
Prior art keywords
provides
novel
methods
gene
mutagenizing
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Ceased
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PCT/US2001/031004
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English (en)
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WO2002029032A2 (fr
Inventor
Jay M Short
Pengcheng Fu
Martin Latterich
Jing Wei
Michael Levin
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BASF Enzymes LLC
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Diversa Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US09/677,584 external-priority patent/US7033781B1/en
Priority claimed from PCT/US2001/019367 external-priority patent/WO2001096551A2/fr
Priority to IL15515401A priority Critical patent/IL155154A0/xx
Priority to AU2002211402A priority patent/AU2002211402A1/en
Priority to JP2002532602A priority patent/JP2004536553A/ja
Priority to DE01979431T priority patent/DE01979431T1/de
Application filed by Diversa Corp filed Critical Diversa Corp
Priority to US10/398,271 priority patent/US20050124010A1/en
Priority to EP01979431A priority patent/EP1415160A2/fr
Priority to CA002424178A priority patent/CA2424178A1/fr
Publication of WO2002029032A2 publication Critical patent/WO2002029032A2/fr
Anticipated expiration legal-status Critical
Publication of WO2002029032A3 publication Critical patent/WO2002029032A3/fr
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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
    • 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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • 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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • C12N15/1027—Mutagenizing nucleic acids by DNA shuffling, e.g. RSR, STEP, RPR
    • 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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1058—Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
    • 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
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/531—Production of immunochemical test materials
    • G01N33/532—Production of labelled immunochemicals
    • G01N33/534—Production of labelled immunochemicals with radioactive label
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6848—Methods of protein analysis involving mass spectrometry
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

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  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
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  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • General Engineering & Computer Science (AREA)
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  • Wood Science & Technology (AREA)
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  • Physics & Mathematics (AREA)
  • Immunology (AREA)
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  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Cell Biology (AREA)
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  • General Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Food Science & Technology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Ecology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention concerne des procédés de transformation cellulaire, d'évolution dirigée et de criblage utiles pour produire de nouveaux organismes transgéniques possédant des propriétés voulues. Dans une forme de réalisation, l'invention concerne un procédé de production d'organisme transgénique, tel qu'un microbe ou une plante, comportant une pluralité de caractéristiques activables de manière différenciée. L'invention concerne aussi un procédé de remaniement de gènes et de voies géniques par l'introduction de séquences régulatrices, tels des promoteurs, qui peuvent être activées chez un hôte voulu et sont ainsi capables de conférer une capacité d'activation à une nouvelle voie génique après introduction de celle-ci dans un hôte voulu; par exemple, une nouvelle voie génique artificielle, produite sur la base de modèles de progéniteurs dérivés de microbes, qui peut être activée dans une cellule végétale. Cette invention concerne aussi un procédé de production de nouveaux organismes hôtes possédant une expression accrue de caractéristiques voulues, de gènes recombinés et de produits géniques; de nouveaux procédés servant à déterminer des profils de polypeptides et des variations d'expression de protéines, ces procédés pouvant être appliqués à tous les types d'échantillons décrits; des procédés permettant d'identifier et de quantifier simultanément des protéines individuelles dans des mélanges complexes de protéines. De plus, l'invention concerne des procédés de mise au point cellulaire et métabolique de nouveaux phénotypes modifiés utilisant une analyse de flux métabolique « en ligne » ou « en temps réel ».
PCT/US2001/031004 2000-09-30 2001-10-01 Manipulation de cellule entiere par mutagenese d'une partie substantielle d'un genome de depart, par combinaison de mutations et eventuellement par repetition Ceased WO2002029032A2 (fr)

Priority Applications (7)

Application Number Priority Date Filing Date Title
CA002424178A CA2424178A1 (fr) 2000-09-30 2001-10-01 Manipulation de cellule entiere par mutagenese d'une partie substantielle d'un genome de depart, par combinaison de mutations et eventuellement par repetition
EP01979431A EP1415160A2 (fr) 2000-09-30 2001-10-01 Manipulation de cellule entiere par mutagenese d'une partie substantielle d'un genome de depart, par combinaison de mutations et eventuellement par repetition
AU2002211402A AU2002211402A1 (en) 2000-09-30 2001-10-01 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating
JP2002532602A JP2004536553A (ja) 2000-09-30 2001-10-01 始原ゲノムの本質部分突然変異、突然変異の組合せおよび任意反復による全細胞工学
DE01979431T DE01979431T1 (de) 2000-09-30 2001-10-01 Konstruktion ganzer zellen durch mutagenese eines wesentlichen anteils eines ausgangsgenoms, kombination von mutationen und gegebenfalls wiederholung
IL15515401A IL155154A0 (en) 2000-09-30 2001-10-01 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating
US10/398,271 US20050124010A1 (en) 2000-09-30 2001-10-01 Whole cell engineering by mutagenizing a substantial portion of a starting genome combining mutations and optionally repeating

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US09/677,584 US7033781B1 (en) 1999-09-29 2000-09-30 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating
US09/677,584 2000-09-30
US27970201P 2001-03-28 2001-03-28
US60/279,702 2001-03-28
US11936701A 2001-06-14 2001-06-14
PCT/US2001/019367 WO2001096551A2 (fr) 2000-06-14 2001-06-14 Ingenierie cellulaire complete par mutagenese d'une partie substantielle d'un genome de depart, par combinaison de mutations et eventuellement repetition
USPCT/US01/19367 2001-06-14

Publications (2)

Publication Number Publication Date
WO2002029032A2 WO2002029032A2 (fr) 2002-04-11
WO2002029032A3 true WO2002029032A3 (fr) 2004-03-04

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PCT/US2001/031004 Ceased WO2002029032A2 (fr) 2000-09-30 2001-10-01 Manipulation de cellule entiere par mutagenese d'une partie substantielle d'un genome de depart, par combinaison de mutations et eventuellement par repetition

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WO (1) WO2002029032A2 (fr)

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6958213B2 (en) 2000-12-12 2005-10-25 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function
US7153655B2 (en) 1998-06-16 2006-12-26 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function involving the use of exonuclease enzyme and two populations of parent polynucleotide sequence
US7262012B2 (en) 2002-05-17 2007-08-28 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function using varied exonuclease digestion in two polynucleotide populations

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US20030044864A1 (en) * 2001-07-20 2003-03-06 Diversa Corporation Cellular engineering, protein expression profiling, differential labeling of peptides, and novel reagents therefor
CN103484486B (zh) 2003-07-02 2018-04-24 维莱尼姆公司 葡聚糖酶，编码它们的核酸以及制备和使用它们的方法
US7741089B2 (en) 2003-08-11 2010-06-22 Verenium Corporation Laccases, nucleic acids encoding them and methods for making and using them
US20080070291A1 (en) 2004-06-16 2008-03-20 David Lam Compositions and Methods for Enzymatic Decolorization of Chlorophyll
CN101432292B (zh) 2004-06-16 2013-03-13 维莱尼姆公司 对叶绿素进行酶促脱色的组合物和方法
WO2006099207A2 (fr) 2005-03-10 2006-09-21 Diversa Corporation Lyases, acides nucleiques codant pour celles-ci et methodes de fabrication et d'utilisation
DK1861506T3 (en) 2005-03-15 2015-07-20 Bp Corp North America Inc Cellulases, nucleic acids encoding them, and methods of making and using them
WO2007005053A1 (fr) * 2005-06-30 2007-01-11 Codon Devices, Inc. Procédés d'assemblage hiérarchique pour l'ingénierie des génomes
MY160770A (en) 2006-02-10 2017-03-15 Verenium Corp Cellulolytic enzymes, nucleic acids encoding them and methods for making and using them
USRE45660E1 (en) 2006-02-14 2015-09-01 Bp Corporation North America Inc. Xylanases, nucleic acids encoding them and methods for making and using them
EA019971B1 (ru) 2006-03-07 2014-07-30 Верениум Корпорейшн Альдолазы, кодирующие их нуклеиновые кислоты и способы их получения и применения
JP5441417B2 (ja) 2006-03-07 2014-03-12 カーギル・インコーポレイテッド アルドース、それをコードする核酸、ならびにそれを生成および使用する方法
AU2007237985A1 (en) * 2006-04-17 2007-10-25 Morphotek, Inc. Whole genome evolution technology applied to improve protein and antibody yields by cells
CA2669453C (fr) 2006-08-04 2018-11-13 Verenium Corporation Glucanases, acides nucleiques codant ceux-ci et procedes pour les fabriquer et les utiliser
US20100189706A1 (en) 2007-01-30 2010-07-29 Cathy Chang Enzymes for the treatment of lignocellulosics, nucleic acids encoding them and methods for making and using them
DK2205744T3 (en) 2007-10-03 2015-04-27 Bp Corp North America Inc Xylanases, nucleic acids encoding them, and methods of making and an-facing presence thereof
JP5563990B2 (ja) 2008-01-03 2014-07-30 ヴェレニウム コーポレイション トランスフェラーゼおよびオキシドレダクターゼ、それらをコードする核酸並びにそれらを製造および使用する方法
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WO2017100376A2 (fr) 2015-12-07 2017-06-15 Zymergen, Inc. Promoteurs de corynebacterium glutamicum
US11208649B2 (en) 2015-12-07 2021-12-28 Zymergen Inc. HTP genomic engineering platform
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EP3478845A4 (fr) 2016-06-30 2019-07-31 Zymergen, Inc. Procédés de production d'une banque de glucose perméase et utilisations associées
WO2018005655A2 (fr) 2016-06-30 2018-01-04 Zymergen Inc. Procédés de génération d'une bibliothèque d'hémoglobines bactériennes et utilisations associées
KR20200015916A (ko) * 2017-06-06 2020-02-13 지머젠 인코포레이티드 표현형 최적화의 처리량을 증가시키기 위한 유전자 변형의 우선순위 결정
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Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7153655B2 (en) 1998-06-16 2006-12-26 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function involving the use of exonuclease enzyme and two populations of parent polynucleotide sequence
US6958213B2 (en) 2000-12-12 2005-10-25 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function
US7282334B2 (en) 2000-12-12 2007-10-16 Alligator Bioscience, Ab Method for in vitro molecular evolution of protein function
US7563578B2 (en) 2000-12-12 2009-07-21 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function
US7262012B2 (en) 2002-05-17 2007-08-28 Alligator Bioscience Ab Method for in vitro molecular evolution of protein function using varied exonuclease digestion in two polynucleotide populations

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