CA2352451A1 - High throughput method for discovery of gene clusters - Google Patents

High throughput method for discovery of gene clusters Download PDF

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Publication number
CA2352451A1
CA2352451A1 CA002352451A CA2352451A CA2352451A1 CA 2352451 A1 CA2352451 A1 CA 2352451A1 CA 002352451 A CA002352451 A CA 002352451A CA 2352451 A CA2352451 A CA 2352451A CA 2352451 A1 CA2352451 A1 CA 2352451A1
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Canada
Prior art keywords
fragments
biosynthesis
involved
gene
library
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Granted
Application number
CA002352451A
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French (fr)
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CA2352451C (en
Inventor
Chris M. Farnet
Emmanuel Zazopoulos
Alfredo Staffa
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Thallion Pharmaceuticals Inc
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Ecopia Biosciences Inc
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Priority to CA002352451A priority Critical patent/CA2352451C/en
Publication of CA2352451A1 publication Critical patent/CA2352451A1/en
Application granted granted Critical
Publication of CA2352451C publication Critical patent/CA2352451C/en
Anticipated expiration legal-status Critical
Expired - Fee Related 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
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Genetics & Genomics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Theoretical Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Biomedical Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Microbiology (AREA)
  • Plant Pathology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

A method for identifying gene cluster is disclosed. The method may be used for identifying gene dusters involved in the biosynthesis of natural products. A
small insert library of DNA fragments of genomic DNA and a large insert library of DNA
fragments of genomic DNA are prepared. Fragments in the small insert: library are sequenced and compared by homology comparison under computer control to a database containing genes, gene fragments or proteins known to be involved in the biosynthesis of microbial natural products. Fragments having similar structure to genes, gene fragments or proteins known to be involved in the biosynthesis of naturally occurring metabolites are used as probes to screen the large insert library of genomic DNA to detect gene clusters involved in the biosynthesis of microbial natural products.
CA002352451A 2001-07-24 2001-07-24 High throughput method for discovery of gene clusters Expired - Fee Related CA2352451C (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
CA002352451A CA2352451C (en) 2001-07-24 2001-07-24 High throughput method for discovery of gene clusters

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
CA002352451A CA2352451C (en) 2001-07-24 2001-07-24 High throughput method for discovery of gene clusters

Publications (2)

Publication Number Publication Date
CA2352451A1 true CA2352451A1 (en) 2001-10-28
CA2352451C CA2352451C (en) 2003-04-08

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Family Applications (1)

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CA002352451A Expired - Fee Related CA2352451C (en) 2001-07-24 2001-07-24 High throughput method for discovery of gene clusters

Country Status (1)

Country Link
CA (1) CA2352451C (en)

Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002079505A2 (en) * 2001-03-28 2002-10-10 Ecopia Biosciences Inc. Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci
WO2002101051A2 (en) * 2001-06-11 2002-12-19 Ecopia Biosciences Inc. Genes and proteins for the biosynthesis of anthramycin
WO2003060127A2 (en) * 2001-12-26 2003-07-24 Ecopia Biosciences Inc. Genes and proteins involved in the biosynthesis of lipopeptides
WO2003062458A2 (en) * 2002-01-24 2003-07-31 Ecopia Biosciences Inc. Method, system and knowledge repository for identifying a secondary metabolite from a microorganism
WO2003080828A2 (en) * 2002-03-21 2003-10-02 Gbf - Gesellschaft Für Biotechnologischeforschung M.B.H. Nucleic acid molecules involved in the synthesis of melithiazols
WO2004065401A1 (en) * 2003-01-21 2004-08-05 Ecopia Biosciences Inc. Polyene polyketides, processes for their production and their use as a pharmaceutical
EP1585814A1 (en) * 2003-01-21 2005-10-19 Ecopia Biosciences Inc. Farnesyl dibenzodiazepinones, processes for their production and their use as pharmaceuticals
US7235651B2 (en) 2001-12-26 2007-06-26 Cubist Pharmaceuticals, Inc. Genes and proteins involved in the biosynthesis of lipopeptides
US7257562B2 (en) 2000-10-13 2007-08-14 Thallion Pharmaceuticals Inc. High throughput method for discovery of gene clusters
US7300921B2 (en) 2003-09-11 2007-11-27 Ecopia Biosciences, Inc. Polyene polyketides and methods of production
CN111133135A (en) * 2017-07-17 2020-05-08 希昆斯生物科学公司 Rapid library construction for high throughput sequencing

Cited By (22)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7257562B2 (en) 2000-10-13 2007-08-14 Thallion Pharmaceuticals Inc. High throughput method for discovery of gene clusters
WO2002079505A3 (en) * 2001-03-28 2003-10-09 Ecopia Biosciences Inc Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci
WO2002079505A2 (en) * 2001-03-28 2002-10-10 Ecopia Biosciences Inc. Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci
WO2002101051A2 (en) * 2001-06-11 2002-12-19 Ecopia Biosciences Inc. Genes and proteins for the biosynthesis of anthramycin
WO2002101051A3 (en) * 2001-06-11 2003-04-10 Ecopia Biosciences Inc Genes and proteins for the biosynthesis of anthramycin
WO2003060127A3 (en) * 2001-12-26 2004-04-29 Ecopia Biosciences Inc Genes and proteins involved in the biosynthesis of lipopeptides
US7235651B2 (en) 2001-12-26 2007-06-26 Cubist Pharmaceuticals, Inc. Genes and proteins involved in the biosynthesis of lipopeptides
WO2003060127A2 (en) * 2001-12-26 2003-07-24 Ecopia Biosciences Inc. Genes and proteins involved in the biosynthesis of lipopeptides
WO2003060128A3 (en) * 2001-12-26 2004-06-10 Ecopia Biosciences Inc Compositions, methods and systems for discovery of lipopeptides
WO2003060128A2 (en) * 2001-12-26 2003-07-24 Ecopia Biosciences Inc. Compositions, methods and systems for discovery of lipopeptides
WO2003062458A3 (en) * 2002-01-24 2003-11-20 Chris M Farnet Method, system and knowledge repository for identifying a secondary metabolite from a microorganism
WO2003062458A2 (en) * 2002-01-24 2003-07-31 Ecopia Biosciences Inc. Method, system and knowledge repository for identifying a secondary metabolite from a microorganism
WO2003080828A3 (en) * 2002-03-21 2003-11-27 Biotechnolog Forschung Gmbh Nucleic acid molecules involved in the synthesis of melithiazols
WO2003080828A2 (en) * 2002-03-21 2003-10-02 Gbf - Gesellschaft Für Biotechnologischeforschung M.B.H. Nucleic acid molecules involved in the synthesis of melithiazols
WO2004065401A1 (en) * 2003-01-21 2004-08-05 Ecopia Biosciences Inc. Polyene polyketides, processes for their production and their use as a pharmaceutical
EP1585814A1 (en) * 2003-01-21 2005-10-19 Ecopia Biosciences Inc. Farnesyl dibenzodiazepinones, processes for their production and their use as pharmaceuticals
US7375088B2 (en) 2003-01-21 2008-05-20 Thallion Pharmaceuticals Inc. Polyene polyketides, processes for their production and their use as a pharmaceutical
US7416868B2 (en) 2003-01-21 2008-08-26 Thallion Pharmaceuticals, Inc. Polyene polyketides, processes for their production and their use as a pharmaceutical
EP1585814B1 (en) * 2003-01-21 2014-05-07 Thallion Pharmaceuticals Inc. Farnesyl dibenzodiazepinones, processes for their production and their use as pharmaceuticals
US7300921B2 (en) 2003-09-11 2007-11-27 Ecopia Biosciences, Inc. Polyene polyketides and methods of production
CN111133135A (en) * 2017-07-17 2020-05-08 希昆斯生物科学公司 Rapid library construction for high throughput sequencing
CN111133135B (en) * 2017-07-17 2024-04-16 希昆斯生物科学公司 Rapid library construction for high throughput sequencing

Also Published As

Publication number Publication date
CA2352451C (en) 2003-04-08

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