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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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provides
novel
methods
gene
mutagenizing
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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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Diversa Corp
Jay M Short
Pengcheng Fu
Martin Latterich
Jing Wei
Michael Levin
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
Application filed by Diversa Corp, Jay M Short, Pengcheng Fu, Martin Latterich, Jing Wei, Michael Levin filed Critical Diversa Corp
Priority to AU2002211402A priority Critical patent/AU2002211402A1/en
Priority to IL15515401A priority patent/IL155154A0/xx
Priority to CA002424178A priority patent/CA2424178A1/fr
Priority to US10/398,271 priority patent/US20050124010A1/en
Priority to JP2002532602A priority patent/JP2004536553A/ja
Priority to DE01979431T priority patent/DE01979431T1/de
Priority to EP01979431A priority patent/EP1415160A2/fr
Publication of WO2002029032A2 publication Critical patent/WO2002029032A2/fr
Publication of WO2002029032A3 publication Critical patent/WO2002029032A3/fr

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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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  • 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 WO2002029032A2 (fr)

Priority Applications (7)

Application Number Priority Date Filing Date Title
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
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
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
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
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
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

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 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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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
EP1641910B1 (fr) 2003-07-02 2013-02-20 Verenium Corporation Glucanases, acides nucleiques les codant et procedes de fabrication et d'utilisation associes
CA2891101A1 (fr) 2003-08-11 2005-03-10 Basf Enzymes Llc Laccases, acides nucleiques codant pour ces enzymes et procedes permettant de les produire et de les utiliser
WO2006009676A2 (fr) 2004-06-16 2006-01-26 Diversa Corporation Compositions et procedes pour la decoloration enzymatique de la chlorophylle
US20080070291A1 (en) 2004-06-16 2008-03-20 David Lam Compositions and Methods for Enzymatic Decolorization of Chlorophyll
EP2886658A1 (fr) 2005-03-10 2015-06-24 BASF Enzymes LLC Enzymes de lyase, acides nucléiques les codant et leurs procédés de fabrication et d'utilisation
NZ594810A (en) 2005-03-15 2012-12-21 Verenium Corp Cellulases, nucleic acids encoding them and methods for making and using them
US20070004041A1 (en) * 2005-06-30 2007-01-04 Codon Devices, Inc. Heirarchical assembly methods for genome engineering
DK2415864T3 (da) 2006-02-10 2014-05-05 Bp Corp North America Inc Oligomerase-2-enzymer (eller beta-xylosidaseenzymer), nucleinsyrer, som koder for dem, og fremgangsmåder til at fremstille og anvende dem
EP2548955A1 (fr) 2006-02-14 2013-01-23 Verenium Corporation Xylanases, acides nucléiques les codant et leurs procédés de fabrication et dýutilisation
EP1999256B1 (fr) 2006-03-07 2012-03-07 Verenium Corporation Aldolases, acides nucleiques les codant et procedes de fabrication et d'utilisation de celles-ci
WO2007103389A2 (fr) 2006-03-07 2007-09-13 Cargill, Incorporated Aldolases, acides nucléiques les codant et procédés de fabrication et d'utilisation de celles-ci
CA2649698A1 (fr) * 2006-04-17 2007-10-25 Morphotek, Inc. Technologie d'evolution du genome entier appliquee a l'amelioration des rendements de proteine et d'anticorps par les cellules
CN103397043A (zh) 2006-08-04 2013-11-20 维莱尼姆公司 葡聚糖酶、编码它们的核酸及制备和使用它们的方法
EP2074136A4 (fr) 2007-01-30 2012-11-07 Verenium Corp Enzymes pour le traitement de matières lignocellulosiques, des acides nucléiques les codant et procédés pour leur fabrication et leur utilisation
NZ601191A (en) 2007-10-03 2014-01-31 Verenium Corp Xylanases, nucleic acids encoding them and methods for making and using them
WO2009088949A1 (fr) 2008-01-03 2009-07-16 Verenium Corporation Transférases et oxydoréductases, acides nucléiques codant pour celles-ci, et leurs procédés de fabrication et d'utilisation
GB201314695D0 (en) * 2013-08-16 2013-10-02 Oxford Nanopore Tech Ltd Method
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US9988624B2 (en) 2015-12-07 2018-06-05 Zymergen Inc. Microbial strain improvement by a HTP genomic engineering platform
US11208649B2 (en) 2015-12-07 2021-12-28 Zymergen Inc. HTP genomic engineering platform
CN109997192A (zh) * 2016-06-15 2019-07-09 哈佛学院董事及会员团体 用于基于规则的基因组设计的方法
US10544390B2 (en) 2016-06-30 2020-01-28 Zymergen Inc. Methods for generating a bacterial hemoglobin library and uses thereof
JP2019519241A (ja) 2016-06-30 2019-07-11 ザイマージェン インコーポレイテッド グルコース透過酵素ライブラリーを生成するための方法およびその使用
CA3064053A1 (fr) * 2017-06-06 2018-12-13 Zymergen Inc. Hierarchisation de modifications genetiques pour augmenter le rendement de l'optimisation phenotypique
ES2875579T3 (es) * 2017-06-06 2021-11-10 Zymergen Inc Plataforma de ingeniería genómica de HTP para mejorar Escherichia coli
KR102741381B1 (ko) * 2017-06-06 2024-12-11 지머젠 인코포레이티드 사카로폴리스포라 스피노사를 개량하기 위한 고 처리량(htp) 게놈 공학 플랫폼
US20200102554A1 (en) * 2017-06-06 2020-04-02 Zymergen Inc. High throughput transposon mutagenesis
CA3111472A1 (fr) * 2018-09-04 2020-03-12 Encodia, Inc. Analyse d'interaction de proximite
EP3696278A1 (fr) * 2019-02-13 2020-08-19 Nipd Genetics Public Company Limited Procédé de détermination de l'origine d'acides nucléiques dans un échantillon mixte
WO2020184080A1 (fr) * 2019-03-13 2020-09-17 パナソニックＩｐマネジメント株式会社 Procédé de fourniture d'informations, programme de fourniture d'informations, dispositif de fourniture d'informations, dispositif de diffusion de parfum, et dispositif de gestion d'informations
CN114774398B (zh) * 2022-06-20 2022-10-04 北京惠之衡生物科技有限公司 一种重组ek酶工程菌的高密度发酵方法
WO2025010715A1 (fr) * 2023-07-13 2025-01-16 深圳华大生命科学研究院 Système et procédé de confinement biologique modifié

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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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