메뉴 건너뛰기




Volumn 48, Issue 2, 2010, Pages 234-242

From DNA sequences to chemical structures - methods for mining microbial genomic and metagenomic data sets for new natural products

Author keywords

Actinobacteria; Homologous recombination; Non ribosomal peptides; Polyketides

Indexed keywords

ACTINOBACTERIA; BIOSYNTHETIC GENE CLUSTER; COMPUTER AIDED DRUG DESIGN; EUKARYOTIC MICROORGANISMS; GRAPHICAL PRESENTATIONS; HIERARCHICAL STRUCTURING; HOMOLOGOUS RECOMBINATION; POLYKETIDES;

EID: 77955073433     PISSN: 13309862     EISSN: 13342606     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (9)

References (54)
  • 1
    • 9244234513 scopus 로고    scopus 로고
    • Biosynthesis of non-ribosomal peptides
    • R. Finking, M.A. Marahiel, Biosynthesis of non-ribosomal peptides, Ann. Rev. Microbiol. 58 (2004) 453-488.
    • (2004) Ann. Rev. Microbiol. , vol.58 , pp. 453-488
    • Finking, R.1    Marahiel, M.A.2
  • 2
    • 21244462769 scopus 로고    scopus 로고
    • Plasticity of the Streptomyces genome - Evolution and engineering of new antibiotics
    • D. Hranueli, J. Cullum, B. Basrak, P. Goldstein, P.F. Long, Plasticity of the Streptomyces genome - Evolution and engineering of new antibiotics, Curr. Med. Chem. 12 (2005) 1697- 1704.
    • (2005) Curr. Med. Chem. , vol.12 , pp. 1697-1704
    • Hranueli, D.1    Cullum, J.2    Basrak, B.3    Goldstein, P.4    Long, P.F.5
  • 3
    • 48249137414 scopus 로고    scopus 로고
    • Total biosynthesis: In vitro reconstitution of polyketide and nonribosomal peptide pathways
    • E.S. Sattely, M.A. Fischbach, C.T. Walsh, Total biosynthesis: In vitro reconstitution of polyketide and nonribosomal peptide pathways, Nat. Prod. Rep. 25 (2008) 757-793.
    • (2008) Nat. Prod. Rep. , vol.25 , pp. 757-793
    • Sattely, E.S.1    Fischbach, M.A.2    Walsh, C.T.3
  • 4
    • 30544434619 scopus 로고    scopus 로고
    • Combinatorial biosynthesis of reduced polyketides
    • K.J. Weissman, P.F. Leadlay, Combinatorial biosynthesis of reduced polyketides, Nat. Rev. Microbiol. 3 (2005) 925-936.
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 925-936
    • Weissman, K.J.1    Leadlay, P.F.2
  • 5
    • 70349231218 scopus 로고    scopus 로고
    • Bioinformatic perspectives on NRPS/PKS megasynthases: Advances and challenges
    • H. Jenke-Kodama, E. Dittmann, Bioinformatic perspectives on NRPS/PKS megasynthases: Advances and challenges, Nat. Prod. Rep. 26 (2009) 874-883.
    • (2009) Nat. Prod. Rep. , vol.26 , pp. 874-883
    • Jenke-Kodama, H.1    Dittmann, E.2
  • 6
    • 0000378637 scopus 로고
    • On the antibacterial action of cultures of a Penicillium, with special reference to their use in the isolation of B. influenzae
    • A. Fleming, On the antibacterial action of cultures of a Penicillium, with special reference to their use in the isolation of B. influenzae, Brit. J. Exp. Pathol. 10 (1929) 226-236.
    • (1929) Brit. J. Exp. Pathol. , vol.10 , pp. 226-236
    • Fleming, A.1
  • 7
    • 70350448473 scopus 로고    scopus 로고
    • Antibiotics: Natural products essential to human health
    • A.L. Demain, Antibiotics: Natural products essential to human health, Med. Res. Rev. 29 (2009) 821-842.
    • (2009) Med. Res. Rev. , vol.29 , pp. 821-842
    • Demain, A.L.1
  • 8
    • 84876644233 scopus 로고    scopus 로고
    • Prokaryotic Projects, National Center for Biotechnology Information, Bethesda, MD, USA
    • Prokaryotic Projects, National Center for Biotechnology Information, Bethesda, MD, USA (http://www.ncbi.nlm.nih.gov/).
  • 9
    • 34848911303 scopus 로고    scopus 로고
    • Polyketide synthases and nonribosomal peptide synthetases: The emerging view from bacterial genomics
    • S. Donadio, P. Monciardini, M. Sosio, Polyketide synthases and nonribosomal peptide synthetases: The emerging view from bacterial genomics, Nat. Prod. Rep. 24 (2007) 1073- 1109.
    • (2007) Nat. Prod. Rep. , vol.24 , pp. 1073-1109
    • Donadio, S.1    Monciardini, P.2    Sosio, M.3
  • 10
    • 70350722394 scopus 로고    scopus 로고
    • Genomic basis for natural product biosynthetic diversity in the actinomycetes
    • M. Nett, H. Ikeda, B.S. Moore, Genomic basis for natural product biosynthetic diversity in the actinomycetes, Nat. Prod. Rep. 26 (2009) 1362-1384.
    • (2009) Nat. Prod. Rep. , vol.26 , pp. 1362-1384
    • Nett, M.1    Ikeda, H.2    Moore, B.S.3
  • 11
    • 37749031255 scopus 로고    scopus 로고
    • Next-generation sequencing transforms today's biology
    • S.C. Schuster, Next-generation sequencing transforms today's biology, Nat. Methods, 5 (2008) 16-18.
    • (2008) Nat. Methods , vol.5 , pp. 16-18
    • Schuster, S.C.1
  • 14
    • 84876610757 scopus 로고    scopus 로고
    • Bioserv server, Faculty of Food Technology and Biotechnology
    • Bioserv server, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia (http://bioserv.pbf.hr/).
    • University of Zagreb, Zagreb, Croatia
  • 16
    • 3442896886 scopus 로고    scopus 로고
    • NRPS-PKS: A knowledge-based resource for analysis of NRPS/PKS megasynthases
    • M.Z. Ansari, G. Yadav, R.S. Gokhale, D. Mohanty, NRPS-PKS: A knowledge-based resource for analysis of NRPS/PKS megasynthases, Nucleic Acids Res. 32 (2004) W405- W413.
    • (2004) Nucleic Acids Res. , vol.32
    • Ansari, M.Z.1    Yadav, G.2    Gokhale, R.S.3    Mohanty, D.4
  • 17
    • 35248844459 scopus 로고    scopus 로고
    • ASMPKS: An analysis system for modular polyketide synthases
    • H. Tae, E.B. Kong, K. Park, ASMPKS: An analysis system for modular polyketide synthases, BMC Bioinformatics, 8 (2007) 327.
    • (2007) BMC Bioinformatics , vol.8 , pp. 327
    • Tae, H.1    Kong, E.B.2    Park, K.3
  • 19
    • 57149112966 scopus 로고    scopus 로고
    • ClustScan: An integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures
    • A. Starcevic, J. Zucko, J. Simunkovic, P.F. Long, J. Cullum, D. Hranueli, ClustScan: An integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures, Nucleic Acids Res. 36 (2008) 6882-6892.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6882-6892
    • Starcevic, A.1    Zucko, J.2    Simunkovic, J.3    Long, P.F.4    Cullum, J.5    Hranueli, D.6
  • 20
  • 21
    • 23144452801 scopus 로고    scopus 로고
    • GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses
    • J. Besemer, M. Borodovsky, GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses, Nucleic Acids Res. 33 (2005) W451-454.
    • (2005) Nucleic Acids Res. , vol.33
    • Besemer, J.1    Borodovsky, M.2
  • 22
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • P. Rice, I. Longden, A. Bleasby, EMBOSS: The European Molecular Biology Open Software Suite, Trends Genet. 16 (2000) 276-277.
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 23
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • S.R. Eddy, Profile hidden Markov models, Bioinformatics, 14 (1998) 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 25
    • 84876647548 scopus 로고    scopus 로고
    • TMSS web portal, Thiotemplate Modular Systems Studies
    • TMSS web portal, Thiotemplate Modular Systems Studies (http://bioserv.pbf.hr/cms/).
  • 27
    • 84876660255 scopus 로고    scopus 로고
    • BioSQL schema, Open Bioinformatics Foundation, USA
    • BioSQL schema, Open Bioinformatics Foundation, USA (http://obda.open-bio.org/).
  • 28
    • 84876640858 scopus 로고    scopus 로고
    • Perl programming language, Perl Foundation, Gran Ledge, MI, USA
    • Perl programming language, Perl Foundation, Gran Ledge, MI, USA (http://www.perl.org/).
  • 29
    • 84876624173 scopus 로고    scopus 로고
    • The Source for Java Developers, Oracle and Sun, Redwood Shores, CA, USA
    • The Source for Java Developers, Oracle and Sun, Redwood Shores, CA, USA (http://java.sun.com/).
  • 30
    • 84876598233 scopus 로고    scopus 로고
    • The JavaScript Source, Jupitermedia Corp., Darien, CT, USA
    • The JavaScript Source, Jupitermedia Corp., Darien, CT, USA (http://javascript.internet.com/).
  • 31
    • 0023965741 scopus 로고
    • SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
    • D. Weininger, SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules, J. Chem. Inf. Comput. Sci. 28 (1988) 31-36.
    • (1988) J. Chem. Inf. Comput. Sci. , vol.28 , pp. 31-36
    • Weininger, D.1
  • 32
    • 84876637839 scopus 로고    scopus 로고
    • Jmol: An open-source Java viewer for chemical structures in 3D
    • Jmol: An open-source Java viewer for chemical structures in 3D (http://www.jmol.org/).
  • 33
    • 0001611357 scopus 로고    scopus 로고
    • Java applets and modules supporting chemical database handling from web browsers
    • F. Csizmadia, J Chem: Java applets and modules supporting chemical database handling from web browsers, J. Chem. Inf. Comput. Sci. 40 (2000) 323-324.
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 323-324
    • Csizmadia, F.1    Chem, J.2
  • 34
    • 84876608523 scopus 로고    scopus 로고
    • WWW READSEQ Sequence Conversion, National Institutes of Health, Bethesda, MA, USA
    • WWW READSEQ Sequence Conversion, National Institutes of Health, Bethesda, MA, USA (http://www-bimas.cit.nih.gov/molbio/readseq/).
  • 35
    • 84876647006 scopus 로고    scopus 로고
    • Google Web Toolkit. Chapter 10 Database Editor on Google App Engine Java, USA
    • Google Web Toolkit. Chapter 10 Database Editor on Google App Engine Java, USA (http://www.gwtapps.com/).
  • 37
    • 84876624636 scopus 로고    scopus 로고
    • The genome of Streptomyces scabies strain 87.22, Wellcome Trust Sanger Institute, Hinxton, UK
    • The genome of Streptomyces scabies strain 87.22, Wellcome Trust Sanger Institute, Hinxton, UK (http://www.sanger.ac.uk/Projects/S_scabies/).
  • 39
    • 40649111872 scopus 로고    scopus 로고
    • Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins
    • A. Starcevic, S. Akthar, W.C. Dunlap, J.M. Shick, D. Hranueli, J. Cullum, P.F. Long, Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins, Proc. Natl. Acad. Sci. USA, 105 (2008) 2533-2537.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 2533-2537
    • Starcevic, A.1    Akthar, S.2    Dunlap, W.C.3    Shick, J.M.4    Hranueli, D.5    Cullum, J.6    Long, P.F.7
  • 40
    • 0345735309 scopus 로고    scopus 로고
    • Shape signatures: A new approach to computer-aided ligandand receptor-based drug design
    • R.J, Zauhar, G. Moyna, L. Tian, Z. Li, W.J. Welsh, Shape signatures: A new approach to computer-aided ligandand receptor-based drug design, J. Med. Chem. 46 (2003) 5674-5690.
    • (2003) J. Med. Chem. , vol.46 , pp. 5674-5690
    • Zauhar, R.J.1    Moyna, G.2    Tian, L.3    Li, Z.4    Welsh, W.J.5
  • 41
    • 0022689021 scopus 로고
    • Homologous recombination in Escherichia coli: Dependence on substrate length and homology
    • P. Shen, H.V. Huang, Homologous recombination in Escherichia coli: Dependence on substrate length and homology, Genetics, 112 (1986) 441-457.
    • (1986) Genetics , vol.112 , pp. 441-457
    • Shen, P.1    Huang, H.V.2
  • 43
    • 0024469392 scopus 로고
    • The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants
    • C. Rayssiguier, D.S. Thaler, M. Radman, The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants, Nature, 342 (1989) 396-401.
    • (1989) Nature , vol.342 , pp. 396-401
    • Rayssiguier, C.1    Thaler, D.S.2    Radman, M.3
  • 46
    • 0026739997 scopus 로고
    • Intramolecular homologous recombination in Bacillus subtilis 168
    • J.C. Alonso, G. Lüder, T.A. Trautner, Intramolecular homologous recombination in Bacillus subtilis 168, Mol. Gen. Genet. 236 (1992) 60-64.
    • (1992) Mol. Gen. Genet. , vol.236 , pp. 60-64
    • Alonso, J.C.1    Lüder, G.2    Trautner, T.A.3
  • 48
    • 0041620248 scopus 로고    scopus 로고
    • SEARCHPKS: A program for detection and analysis of polyketide synthase domains
    • G. Yadav, R.S. Gokhale, D. Mohanty, SEARCHPKS: A program for detection and analysis of polyketide synthase domains, Nucleic Acids Res. 31 (2003) 3654-3658.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3654-3658
    • Yadav, G.1    Gokhale, R.S.2    Mohanty, D.3
  • 50
    • 33645405075 scopus 로고    scopus 로고
    • Rational design of macrolides by virtual screening of combinatorial libraries generated through in silico manipulation of polyketide synthases
    • S.B. Zotchev, A.V. Stepanchikova, A.P. Sergeyko, B.N. Sobolev, D.A. Filimonov, V.V. Poroikov, Rational design of macrolides by virtual screening of combinatorial libraries generated through in silico manipulation of polyketide synthases, J. Med. Chem. 49 (2006) 2077-2087.
    • (2006) J. Med. Chem. , vol.49 , pp. 2077-2087
    • Zotchev, S.B.1    Stepanchikova, A.V.2    Sergeyko, A.P.3    Sobolev, B.N.4    Filimonov, D.A.5    Poroikov, V.V.6
  • 51
    • 26944502019 scopus 로고    scopus 로고
    • Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)
    • C. Rausch, T. Weber, O. Kohlbacher, W. Wohlleben, D.H. Huson, Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs), Nucleic Acids Res. 33 (2005) 5799-5808.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 5799-5808
    • Rausch, C.1    Weber, T.2    Kohlbacher, O.3    Wohlleben, W.4    Huson, D.H.5
  • 52
    • 70350708768 scopus 로고    scopus 로고
    • Evolution of metabolic diversity: Insights from microbial polyketide synthases
    • H. Jenke-Kodama, E. Dittmann, Evolution of metabolic diversity: Insights from microbial polyketide synthases, Phytochemistry, 70 (2009) 1858-1866.
    • (2009) Phytochemistry , vol.70 , pp. 1858-1866
    • Jenke-Kodama, H.1    Dittmann, E.2
  • 53
    • 61649111711 scopus 로고    scopus 로고
    • CLUSEAN: A computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters
    • T. Weber, C. Rausch, P. Lopez, I. Hoof, V. Gaykova, D.H. Huson, W. Wohlleben, CLUSEAN: A computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters, J. Bacteriol. 140 (2009) 13-17.
    • (2009) J. Bacteriol. , vol.140 , pp. 13-17
    • Weber, T.1    Rausch, C.2    Lopez, P.3    Hoof, I.4    Gaykova, V.5    Huson, D.H.6    Wohlleben, W.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.