WO2001096551A3 - Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating - Google Patents

Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating Download PDF

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Publication number
WO2001096551A3
WO2001096551A3 PCT/US2001/019367 US0119367W WO0196551A3 WO 2001096551 A3 WO2001096551 A3 WO 2001096551A3 US 0119367 W US0119367 W US 0119367W WO 0196551 A3 WO0196551 A3 WO 0196551A3
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Prior art keywords
novel
mutagenizing
substantial portion
gene
whole cell
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/US2001/019367
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French (fr)
Other versions
WO2001096551A2 (en
Inventor
Jay M Short
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
BASF Enzymes LLC
Original Assignee
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 US09/594,459 external-priority patent/US6605449B1/en
Priority claimed from US09/677,584 external-priority patent/US7033781B1/en
Application filed by Diversa Corp filed Critical Diversa Corp
Priority to AU2001266978A priority Critical patent/AU2001266978A1/en
Priority to CA002413022A priority patent/CA2413022A1/en
Priority to EP01944583A priority patent/EP1294869A2/en
Priority to EP01979431A priority patent/EP1415160A2/en
Priority to AU2002211402A priority patent/AU2002211402A1/en
Priority to JP2002532602A priority patent/JP2004536553A/en
Priority to DE01979431T priority patent/DE01979431T1/en
Priority to IL15515401A priority patent/IL155154A0/en
Priority to CA002424178A priority patent/CA2424178A1/en
Priority to PCT/US2001/031004 priority patent/WO2002029032A2/en
Publication of WO2001096551A2 publication Critical patent/WO2001096551A2/en
Publication of WO2001096551A3 publication Critical patent/WO2001096551A3/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
    • C12N15/10—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
    • C12N15/10—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
    • C12N15/63—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
    • G01N33/6818—Sequencing of polypeptides

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Cell Biology (AREA)
  • Pathology (AREA)
  • General Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Food Science & Technology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Ecology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

An invention comprising cellular transformation, directed evolution, and screening methods for creating novel transgenic organisms having desirable properties. Thus in one aspect, this invention relates to a method of generating a transgenic organism, such as a microbe or a plant, having a plurality of traits that are differentially activatable. Also, a method of retooling genes and gene pathways by the introduction of regulatory sequences, such as promoters, that are operable in an intended host, thus conferring operability to a novel gene pathway when it is introduced into an intended host. For example a novel man-made gene pathway, generated based on microbially-derived progenitor templates, that is operable in a plant cell. Furthermore, a method of generating novel host organisms having increased expression of desirable traits, recombinant genes, and gene products.
PCT/US2001/019367 2000-06-14 2001-06-14 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating Ceased WO2001096551A2 (en)

Priority Applications (10)

Application Number Priority Date Filing Date Title
AU2001266978A AU2001266978A1 (en) 2000-06-14 2001-06-14 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating
CA002413022A CA2413022A1 (en) 2000-06-14 2001-06-14 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating
EP01944583A EP1294869A2 (en) 2000-06-14 2001-06-14 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating
PCT/US2001/031004 WO2002029032A2 (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 (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 (en) 2000-09-30 2001-10-01 Whole-cell engineering by essentially partial mutation of the primordial genome, combination of mutations, and arbitrary 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
EP01979431A EP1415160A2 (en) 2000-09-30 2001-10-01 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating
DE01979431T DE01979431T1 (en) 2000-09-30 2001-10-01 CONSTRUCTION OF WHOLE CELLS THROUGH MUTAGENESE OF A SIGNIFICANT PART OF AN INITIAL GENE, COMBINATION OF MUTATIONS AND, IF REQUIRED, REPEAT
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

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US09/594,459 US6605449B1 (en) 1999-06-14 2000-06-14 Synthetic ligation reassembly in directed evolution
US09/594,459 2000-06-14
US09/677,584 2000-09-30
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

Publications (2)

Publication Number Publication Date
WO2001096551A2 WO2001096551A2 (en) 2001-12-20
WO2001096551A3 true WO2001096551A3 (en) 2002-05-23

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/019367 Ceased WO2001096551A2 (en) 2000-06-14 2001-06-14 Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating

Country Status (4)

Country Link
EP (1) EP1294869A2 (en)
AU (1) AU2001266978A1 (en)
CA (1) CA2413022A1 (en)
WO (1) WO2001096551A2 (en)

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

Families Citing this family (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6991922B2 (en) 1998-08-12 2006-01-31 Proteus S.A. Process for in vitro creation of recombinant polynucleotide sequences by oriented ligation
US6951719B1 (en) 1999-08-11 2005-10-04 Proteus S.A. Process for obtaining recombined nucleotide sequences in vitro, libraries of sequences and sequences thus obtained
CN103484486B (en) 2003-07-02 2018-04-24 维莱尼姆公司 Dextranase, encode they nucleic acid and preparation and use their method
EP1668113B1 (en) 2003-08-11 2013-06-19 Verenium Corporation Laccases, nucleic acids encoding them and methods for making and using them
CN101432292B (en) 2004-06-16 2013-03-13 维莱尼姆公司 Compositions and methods for enzymatic decolorization of chlorophyll
US20080070291A1 (en) 2004-06-16 2008-03-20 David Lam Compositions and Methods for Enzymatic Decolorization of Chlorophyll
EP2886658A1 (en) 2005-03-10 2015-06-24 BASF Enzymes LLC Lyase enzymes, nucleic acids encoding them and methods for making and using them
MX300732B (en) 2005-03-15 2012-06-28 Verenium Corp Cellulases, nucleic acids encoding them and methods for making and using them.
WO2007094852A2 (en) 2006-02-10 2007-08-23 Verenium Corporation Cellulolytic enzymes, nucleic acids encoding them and methods for making and using them
EP2548955A1 (en) 2006-02-14 2013-01-23 Verenium Corporation Xylanases, nucleic acids encoding them and methods for making and using them
MX2008011477A (en) 2006-03-07 2008-09-23 Cargill Inc Aldolases, nucleic acids encoding them and methods for making and using them.
BRPI0708614A2 (en) 2006-03-07 2011-06-07 Verenium Corp aldolases, nucleic acids encoding the same and methods for producing and using the same
BRPI0714876B1 (en) 2006-08-04 2022-04-19 Verenium Corporation Isolated, synthetic or recombinant nucleic acid, expression cassette, cloning vector or vehicle, transformed bacterial, fungal or yeast cell, isolated, synthetic or recombinant polypeptide, composition, as well as production methods and uses thereof
NZ578309A (en) 2007-01-30 2012-06-29 Verenium Corp Enzymes for the treatment of lignocellulosics, nucleic acids encoding them and methods for making and using them
WO2009045627A2 (en) 2007-10-03 2009-04-09 Verenium Corporation Xylanases, nucleic acids encoding them and methods for making and using them
CA2710683A1 (en) 2008-01-03 2009-07-16 Verenium Corporation Transferases and oxidoreductases, nucleic acids encoding them and methods for making and using them
CN111154798B (en) * 2020-02-18 2021-07-20 杭州师范大学 Application and application method of potato X virus in inducing fetal germination of tomato seeds
CN113041190B (en) * 2021-03-19 2023-03-17 河南董欣生物科技有限公司 Antioxidant composition, preparation method and application
CN118028194B (en) * 2023-12-26 2024-09-06 浙江大学 Pseudomonas putida strains with streamlined genomes
CN117467751B (en) * 2023-12-27 2024-03-29 北京百力格生物科技有限公司 Targeting target gene FISH fluorescent probe and self-assembled amplification probe system thereof
CN121587297A (en) * 2026-01-30 2026-03-03 浙江大学 Application of RALF small peptide in improving hardness of strawberry fruits

Citations (7)

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Publication number Priority date Publication date Assignee Title
WO1997026334A1 (en) * 1996-01-19 1997-07-24 Board Of Regents, The University Of Texas System Recombinant expression of proteins from secretory cell lines
WO1998031837A1 (en) * 1997-01-17 1998-07-23 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
FR2761576A1 (en) * 1997-04-04 1998-10-09 Inst Nat Sante Rech Med NON-HUMAN TRANSGENIC ANIMAL IN WHICH EXPRESSION OF THE GENE CODING FOR INSULIN IS SUPPRESSED
WO2000004190A1 (en) * 1998-07-15 2000-01-27 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
WO2000018906A2 (en) * 1998-09-29 2000-04-06 Maxygen, Inc. Shuffling of codon altered genes
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WO2001002555A1 (en) * 1999-07-06 2001-01-11 Institut Pasteur Method of making and identifying attenuated microorganisms, compositions utilizing the sequences responsible for attenuation, and preparations containing attenuated microorganisms

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AU772879B2 (en) * 1998-08-12 2004-05-13 Napro Biotherapeutics, Inc. Domain specific gene evolution
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WO1998031837A1 (en) * 1997-01-17 1998-07-23 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
FR2761576A1 (en) * 1997-04-04 1998-10-09 Inst Nat Sante Rech Med NON-HUMAN TRANSGENIC ANIMAL IN WHICH EXPRESSION OF THE GENE CODING FOR INSULIN IS SUPPRESSED
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WO2000018906A2 (en) * 1998-09-29 2000-04-06 Maxygen, Inc. Shuffling of codon altered genes
WO2000055346A2 (en) * 1999-03-17 2000-09-21 Paradigm Genetics, Inc. Methods and materials for the rapid and high volume production of a gene knock-out library in an organism
WO2001002555A1 (en) * 1999-07-06 2001-01-11 Institut Pasteur Method of making and identifying attenuated microorganisms, compositions utilizing the sequences responsible for attenuation, and preparations containing attenuated microorganisms

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HENSEL M ET AL: "SIMULTANEOUS IDENTIFICATION OF BACTERIAL VIRULENCE GENES BY NEGATIVE SELECTION", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE,, US, vol. 269, 21 July 1995 (1995-07-21), pages 400 - 403, XP000645478, ISSN: 0036-8075 *
HUTCHISON C A ET AL: "GLOBAL TRANSPOSON MUTAGENESIS AND A MINIMAL MYCOPLASMA GENOME", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE,, US, vol. 286, no. 5447, 10 December 1999 (1999-12-10), pages 2165 - 2169, XP000865808, ISSN: 0036-8075 *
See also references of EP1294869A2 *

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

Also Published As

Publication number Publication date
EP1294869A2 (en) 2003-03-26
CA2413022A1 (en) 2001-12-20
AU2001266978A1 (en) 2001-12-24
WO2001096551A2 (en) 2001-12-20

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