WO2002079505A3 - Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci - Google Patents

Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci Download PDF

Info

Publication number
WO2002079505A3
WO2002079505A3 PCT/CA2002/000432 CA0200432W WO02079505A3 WO 2002079505 A3 WO2002079505 A3 WO 2002079505A3 CA 0200432 W CA0200432 W CA 0200432W WO 02079505 A3 WO02079505 A3 WO 02079505A3
Authority
WO
WIPO (PCT)
Prior art keywords
orthosomycin
compositions
type
orthosomycins
methods
Prior art date
Application number
PCT/CA2002/000432
Other languages
French (fr)
Other versions
WO2002079505A2 (en
Inventor
Chris M Farnet
Emmanuel Zazopoulos
Alfredo Staffa
Original Assignee
Ecopia Biosciences Inc
Chris M Farnet
Emmanuel Zazopoulos
Alfredo Staffa
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
Application filed by Ecopia Biosciences Inc, Chris M Farnet, Emmanuel Zazopoulos, Alfredo Staffa filed Critical Ecopia Biosciences Inc
Priority to EP02713968A priority Critical patent/EP1373309A2/en
Priority to JP2002577914A priority patent/JP2004532021A/en
Priority to AU2002245973A priority patent/AU2002245973A1/en
Publication of WO2002079505A2 publication Critical patent/WO2002079505A2/en
Publication of WO2002079505A3 publication Critical patent/WO2002079505A3/en

Links

Classifications

    • 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
    • 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
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/44—Preparation of O-glycosides, e.g. glucosides
    • 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
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/44—Preparation of O-glycosides, e.g. glucosides
    • C12P19/445—The saccharide radical is condensed with a heterocyclic radical, e.g. everninomycin, papulacandin

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (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)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Plant Pathology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention provides compositions and methods useful to identify orthosomycin biosynthetic gene clusters. The invention also provides compositions and methods useful to distinguish everninomicin-type orthosomycin gene clusters and avilamycin-type orthosomycin gene clusters. An orthosomycin gene cluster may be identified using compositions of the invention such as hybridization probes, PCR primers derived from specific protein families responsible for the unique structural features that distinguish orthosomycins, everninomycin-type orthosomycins and avilamycin-type orthosomycins. An orthosomycin gene cluster may be identified using compositions of the invention such as the sequence code for the reference sequences stored on computer readable medium.
PCT/CA2002/000432 2001-03-28 2002-03-28 Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci WO2002079505A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP02713968A EP1373309A2 (en) 2001-03-28 2002-03-28 Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci
JP2002577914A JP2004532021A (en) 2001-03-28 2002-03-28 Compositions for identification and identification of orthosomycin biosynthetic loci and methods of identification and identification
AU2002245973A AU2002245973A1 (en) 2001-03-28 2002-03-28 Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US27909501P 2001-03-28 2001-03-28
US60/279,095 2001-03-28
US27970901P 2001-03-30 2001-03-30
US60/279,709 2001-03-30
US28521401P 2001-04-20 2001-04-20
US60/285,214 2001-04-20

Publications (2)

Publication Number Publication Date
WO2002079505A2 WO2002079505A2 (en) 2002-10-10
WO2002079505A3 true WO2002079505A3 (en) 2003-10-09

Family

ID=27403041

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/CA2002/000432 WO2002079505A2 (en) 2001-03-28 2002-03-28 Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci

Country Status (5)

Country Link
EP (1) EP1373309A2 (en)
JP (1) JP2004532021A (en)
AU (1) AU2002245973A1 (en)
CA (1) CA2375097A1 (en)
WO (1) WO2002079505A2 (en)

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001051639A2 (en) * 2000-01-12 2001-07-19 Schering Corporation Everninomicin biosynthetic genes
WO2001055180A2 (en) * 2000-01-27 2001-08-02 Ecopia Biosciences Inc. Gene cluster for everninomicin biosynthesis
CA2352451A1 (en) * 2001-07-24 2001-10-28 Ecopia Biosciences Inc. High throughput method for discovery of gene clusters
WO2002068436A1 (en) * 2001-02-25 2002-09-06 Combinature Biopharm Ag Avilamycin derivatives

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001051639A2 (en) * 2000-01-12 2001-07-19 Schering Corporation Everninomicin biosynthetic genes
WO2001055180A2 (en) * 2000-01-27 2001-08-02 Ecopia Biosciences Inc. Gene cluster for everninomicin biosynthesis
WO2002068436A1 (en) * 2001-02-25 2002-09-06 Combinature Biopharm Ag Avilamycin derivatives
CA2352451A1 (en) * 2001-07-24 2001-10-28 Ecopia Biosciences Inc. High throughput method for discovery of gene clusters

Non-Patent Citations (12)

* Cited by examiner, † Cited by third party
Title
BECHTHOLD A ET AL: "Oligosaccharide antibiotics: perspective for combinatorial biosynthesis", BIOORGANIC CHEMISTRY, ACADEMIC PRESS INC., NEW YORK, NY, US, 1999, pages 313 - 321, XP002173417, ISSN: 0045-2068 *
DATABASE EMBL [online] 2 August 2001 (2001-08-02), DECKER H., ET AL.,: "Streptomyces viridochromogenes Avilamycin A biosynthetic gene cluster, complete sequence", XP002244111, Database accession no. AF333038 *
DATABASE SWALL [online] 1 March 2001 (2001-03-01), WEITNAUER G. ET AL.: "Putative ATP binding protein.", XP002248663, Database accession no. Q9F5K4 *
DATABASE SWALL [online] 1 March 2001 (2001-03-01), WEITNAUER G. ET AL.: "Putative transmembrane protein.", XP002248664, Database accession no. Q9F5K3 *
DECKER H ET AL: "A GENERAL APPROACH FOR CLONING AND CHARACTERIZING DNDP-GLUCOSE DEHYDRATASE GENES FROM ACTINOMYCETES", FEMS MICROBIOLOGY LETTERS, AMSTERDAM, NL, vol. 141, no. 2/3, 1996, pages 195 - 201, XP001010562, ISSN: 0378-1097 *
FOSTER D R ET AL: "PHARMACOLOGIC AND BACTERIOLOGIC PROPERTIES OF SCH-27899 (ZIRACIN), AN INVESTIGATIONAL ANTIBIOTIC FROM THE EVERNINOMICIN FAMILY", PHARMACOTHERAPY, BOSTON, US, vol. 19, no. 10, 1999, pages 1111 - 1117, XP001010659, ISSN: 0277-0008 *
GAISSER S ET AL: "Cloning of an avilamycin biosynthetic gene cluster from Streptomyces viridochromogenes Tu57", JOURNAL OF BACTERIOLOGY, WASHINGTON, DC, US, vol. 179, no. 20, 1997, pages 6271 - 6278, XP002173414, ISSN: 0021-9193 *
HOSTED T J ET AL: "Characterization of the biosynthetic gene cluster for the oligosaccharide antibiotic, evernimicin, in Micromonospora carbonacea var. africana ATCC39149.", JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, vol. 27, no. 6, December 2001 (2001-12-01), December, 2001, pages 386 - 392, XP002244110, ISSN: 1367-5435 *
LOMBO F ET AL: "Characterization of Streptomyces argillaceus genes encoding a polyketide synthase involved in the biosynthesis of the antitumor mithramycin", GENE, ELSEVIER BIOMEDICAL PRESS. AMSTERDAM, NL, vol. 172, no. 1, 12 June 1996 (1996-06-12), pages 87 - 91, XP004042714, ISSN: 0378-1119 *
MALPARTIDA F ET AL: "Homology between Streptomyces genes coding for synthesis of different polyketides used to clone antibiotic biosynthetic genes", NATURE, MACMILLAN MAGAZINES, US, vol. 325, 1987, pages 818 - 821, XP002075972, ISSN: 0028-0836 *
WEITNAUER G ET AL: "AN ATP-BINDING CASSETTE TRANSPORTER AND TWO RRNA METHYLTRANSFERASESARE INVOLVED IN RESISTANCE TO AVILAMYCIN IN THE PRODUCER ORGANISM STREPTOMYCES VIRIDOCHROMOGENES TU57", ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON, DC, US, vol. 45, no. 3, March 2001 (2001-03-01), pages 690 - 695, XP001010575, ISSN: 0066-4804 *
WEITNAUER G., ET AL.: "BIOSYNTHESIS OF THE ORTHOSOMYCIN ANTIBIOTIC AVILAMYCIN A: DEDUCTIONS FROM THE MOLECULAR ANALYSIS OF THE AVI BIOSYNTHETIC GENECLUSTER OF STREPTOMYCES VIRIDOCHOMOGENES TUE57 AND PRODUCTION OF NEW ANTIBIOTICS", CHEMISTRY & BIOLOGY, vol. 8, no. 6, June 2001 (2001-06-01), pages 569 - 581, XP001026843 *

Also Published As

Publication number Publication date
CA2375097A1 (en) 2002-06-08
EP1373309A2 (en) 2004-01-02
WO2002079505A2 (en) 2002-10-10
AU2002245973A1 (en) 2002-10-15
JP2004532021A (en) 2004-10-21

Similar Documents

Publication Publication Date Title
WO2001096612A3 (en) Method of identifying and quantifying specific fungi and bacteria
WO1999014375A3 (en) Dna typing by mass spectrometry with polymorphic dna repeat markers
EP1256630A3 (en) Selective polymerase chain reaction of DNA of which base sequence is completely unknown
WO2004023092A3 (en) Genetic analysis and authentication
WO2003010328A3 (en) Complexity management of genomic dna
WO2001013086A3 (en) Detection of nucleic acids
WO2004013346A3 (en) Methods and compositions for genotyping
WO2005014850A3 (en) Systems and methods for analyzing nucleic acid sequences
DE60112746D1 (en) COLD-SENSITIVE DNA POLYMERIC MUTANTS
WO2003062454A3 (en) Compositions and methods for polynucleotide sequence determination
WO2002022890A3 (en) Compositions, methods and kits for determining the presence of cryptosporidium organisms in a test sample
WO2004010101A3 (en) Detection of chemical ligation using fluorescence quenching leaving groups
WO2000029623A3 (en) Nucleic acids containing single nucleotide polymorphisms and methods of use thereof
WO2003087763A3 (en) Association of polymorphisms in the sost gene region with bone mineral density
WO2004048397A3 (en) Detectable labeled nucleoside analogs and methods of use thereof
WO2002063049A3 (en) Methods for determining a nucleotide at a specific location within a nucleic acid molecule
WO2003048309A3 (en) Thermus thermophilus nucleic acid polymerases
WO2003072828A3 (en) Fcgammariib polymorphisms detection in system lupus erythematosus
AU2003211947A1 (en) PRIMERS FOR NUCLEIC ACID AMPLIFICATION IN DETECTING HOUSEKEEPING GENE mRNA AND TEST METHOD USING THESE PRIMERS
WO2002057481A3 (en) Repeat-free probes for molecular cytogenetics
WO2001029262A3 (en) Genotyping reagents, kits and methods of use thereof
WO2000031299A3 (en) Method for determining nucleotide sequences using arbitrary primers and low stringency
WO2003020887A3 (en) Gene identification
WO2002079505A3 (en) Compositions and methods for identifying and distinguishing orthosomycin biosynthetic loci
WO2004097003A3 (en) Multiply-primed amplification of nucleic acid sequences

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ OM PH PL PT RO RU SD SE SG SI SK SL TJ TM TN TR TT TZ UA UG US UZ VN YU ZA ZM ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZM ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
WWE Wipo information: entry into national phase

Ref document number: 2002577914

Country of ref document: JP

WWE Wipo information: entry into national phase

Ref document number: 2002713968

Country of ref document: EP

WWP Wipo information: published in national office

Ref document number: 2002713968

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWW Wipo information: withdrawn in national office

Ref document number: 2002713968

Country of ref document: EP