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Volumn 67, Issue 1, 2014, Pages 89-97

Computational identification and analysis of orphan assembly-line polyketide synthases

Author keywords

Assembly line; Orphan antibiotics; Polyketide synthase

Indexed keywords

ALBOCYCLINE; ANTIBIOTIC AGENT; NONRIBOSOMAL PEPTIDE SYNTHETASE; POLYKETIDE; POLYKETIDE SYNTHASE;

EID: 84893117737     PISSN: 00218820     EISSN: 18811469     Source Type: Journal    
DOI: 10.1038/ja.2013.125     Document Type: Article
Times cited : (51)

References (55)
  • 1
    • 69249202590 scopus 로고    scopus 로고
    • The biosynthetic logic of polyketide diversity
    • Hertweck, C. The biosynthetic logic of polyketide diversity. Angew. Chem. Int. Ed. 48, 4688-4716 (2009
    • (2009) Angew. Chem. Int , vol.48 , pp. 4688-4716
    • Hertweck, C.1
  • 2
    • 0001747786 scopus 로고    scopus 로고
    • Genetic contributions to understanding polyketide synthases
    • Hopwood, D. A. Genetic contributions to understanding polyketide synthases. Chem. Rev. 97, 2465-2497 (1997
    • (1997) Chem. Rev , vol.97 , pp. 2465-2497
    • Hopwood, D.A.1
  • 3
    • 0001436716 scopus 로고    scopus 로고
    • Manipulation of modular polyketide synthases
    • Katz, L. Manipulation of modular polyketide synthases. Chem. Rev. 97, 2557-2575 (1997
    • (1997) Chem. Rev , vol.97 , pp. 2557-2575
    • Katz, L.1
  • 4
  • 5
    • 0026415106 scopus 로고
    • Modular organization of genes required for complex polyketide biosynthesis
    • Donadio, S., Staver, M. J., McAlpine, J. B., Swanson, S. J. & Katz, L. Modular organization of genes required for complex polyketide biosynthesis. Science 252, 675-679 (1991
    • (1991) Science , vol.252 , pp. 675-679
    • Donadio, S.1    Staver, M.J.2    McAlpine, J.B.3    Swanson, S.J.4    Katz, L.5
  • 6
    • 0025081416 scopus 로고
    • An unusually large multifunctional polypeptide in the erythromycin-producing polyketide synthase of Saccharopolyspora erythraea
    • Cortes, J., Haydock, S. F., Roberts, G. A., Bevitt, D. J. & Leadlay, P. F. An unusually large multifunctional polypeptide in the erythromycin- producing polyketide synthase of Saccharopolyspora erythraea. Nature 348, 176-178 (1990
    • (1990) Nature , vol.348 , pp. 176-178
    • Cortes, J.1    Haydock, S.F.2    Roberts, G.A.3    Bevitt, D.J.4    Leadlay, P.F.5
  • 7
    • 34249907531 scopus 로고    scopus 로고
    • Strategies to unravel the function of orphan biosynthesis pathways: Recent examples and future prospects
    • Gross, H. Strategies to unravel the function of orphan biosynthesis pathways: Recent examples and future prospects. Appl. Microbiol. Biotechnol. 75, 267-277 (2007
    • (2007) Appl. Microbiol. Biotechnol , vol.75 , pp. 267-277
    • Gross, H.1
  • 8
    • 84862907959 scopus 로고    scopus 로고
    • A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria J
    • Chen,Y.et al. A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria. J. Proteome Res. 11, 85-94 (2012
    • (2012) Proteome Res , vol.11 , pp. 85-94
    • Chen, Y.1
  • 9
    • 79851515868 scopus 로고    scopus 로고
    • Recent advances in awakening silent biosynthetic gene clusters and linking orphan clusters to natural products in microorganisms
    • Chiang, Y-M., Chang, S-L., Oakley, B. R. & Wang, C. C. C. Recent advances in awakening silent biosynthetic gene clusters and linking orphan clusters to natural products in microorganisms. Curr. Opin. Chem. Biol. 15, 137-143 (2011
    • (2011) Curr. Opin. Chem. Biol , vol.15 , pp. 137-143
    • Chiang, Y.-M.1    Chang, S.-L.2    Oakley, B.R.3    Wang, C.C.C.4
  • 10
    • 77954265333 scopus 로고    scopus 로고
    • SBSPKS: Structure based sequence analysis of polyketide synthases
    • Anand, S. et al. SBSPKS: Structure based sequence analysis of polyketide synthases. Nucleic Acids Res. 38, W487-W496 (2010
    • (2010) Nucleic Acids Res , vol.38
    • Anand, S.1
  • 11
    • 69249223048 scopus 로고    scopus 로고
    • An integrated web database for type i polyketide synthases
    • Tae, H., Sohng, J. K. & Park, K. MapsiDB: An integrated web database for type I polyketide synthases. Bioprocess Biosyst. Eng. 32, 723-727 (2009
    • (2009) Bioprocess Biosyst. Eng , vol.32 , pp. 723-727
    • Tae, H.1    Sohng, J.K.2    Park, K.3    Mapsi, D.B.4
  • 12
    • 84876566794 scopus 로고    scopus 로고
    • ClusterMine360: A database of microbial PKS/NRPS biosynthesis
    • Conway, K. R. & Boddy, C. N. ClusterMine360: A database of microbial PKS/NRPS biosynthesis. Nucl. Acids Res. 41, D402-D407 (2013
    • (2013) Nucl. Acids Res , vol.41
    • Conway, K.R.1    Boddy, C.N.2
  • 13
    • 84876517188 scopus 로고    scopus 로고
    • DoBISCUIT: A database of secondary metabolite biosynthetic gene clusters
    • Ichikawa, N. et al. DoBISCUIT: A database of secondary metabolite biosynthetic gene clusters. Nucl. Acids Res. 41, D408-D414 (2013
    • (2013) Nucl. Acids Res , vol.41
    • Ichikawa, N.1
  • 14
    • 27144509740 scopus 로고    scopus 로고
    • Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes
    • Menzella, H. G. et al. Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes. Nat. Biotechnol. 23, 1171-1176 (2005
    • (2005) Nat. Biotechnol , vol.23 , pp. 1171-1176
    • Menzella, H.G.1
  • 16
    • 84883353135 scopus 로고    scopus 로고
    • AntiSMASH 2.0- A versatile platform for genome mining of secondary metabolite producers
    • Blin, K. et al. antiSMASH 2.0- A versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 41, W204-W212 (2013
    • (2013) Nucleic Acids Res , vol.41
    • Blin, K.1
  • 18
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamove, A. A. & Solovyev, V. V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516-522 (2000
    • (2000) Genome Res , vol.10 , pp. 516-522
    • Salamove, A.A.1    Solovyev, V.V.2
  • 19
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • Lukashin, A. V. & Borodovsky, M. GeneMark.hmm: New solutions for gene finding. Nucl. Acids Res. 26, 1107-1115 (1998
    • (1998) Nucl. Acids Res , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 20
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • Korf, I. Gene finding in novel genomes. BMC Bioinformatics 5, 59 (2004
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 23
    • 79959920872 scopus 로고    scopus 로고
    • Antismash: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
    • Medema, M. H. et al. antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39, W339-W346 (2011
    • (2011) Nucleic Acids Res , vol.39
    • Medema, M.H.1
  • 25
    • 61649111711 scopus 로고    scopus 로고
    • CLUSEAN: A computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters
    • Weber, T. et al. CLUSEAN: A computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J. Biotechnol. 140, 13-17 (2009
    • (2009) J. Biotechnol , vol.140 , pp. 13-17
    • Weber, T.1
  • 26
    • 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
    • Starcevic, S. et al. 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, 6882-6892 (2008
    • (2008) Nucleic Acids Res , vol.36 , pp. 6882-6892
    • Starcevic, S.1
  • 27
    • 34247279292 scopus 로고    scopus 로고
    • Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes
    • Minowa, Y., Araki, M. & Kanehisa, M. Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J. Mol. Biol. 368, 1500-1517 (2007
    • (2007) J. Mol. Biol , vol.368 , pp. 1500-1517
    • Minowa, Y.1    Araki, M.2    Kanehisa, M.3
  • 28
    • 79959936207 scopus 로고    scopus 로고
    • NRPSpredictor2- A web server for predicting NRPS adenylation domain specificity
    • Rottig, M. et al. NRPSpredictor2- A web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res. 39, W362-W367 (2011
    • (2011) Nucleic Acids Res , vol.39
    • Rottig, M.1
  • 29
    • 0141519279 scopus 로고    scopus 로고
    • Orthomcl: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C. J. Jr & Roos, D. S. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003
    • (2003) Genome Res , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert Jr., C.J.2    Roos, D.S.3
  • 30
    • 33750428183 scopus 로고    scopus 로고
    • Natural biocombinatorics in the polyketide synthase genes of the actinobacterium Streptomyces avermitilis
    • Jenke-Kodama, H., B ö: rner, T. & Dittmann, E. Natural biocombinatorics in the polyketide synthase genes of the actinobacterium Streptomyces avermitilis. PLoS Comput. Biol. 2, e132 (2006
    • (2006) PLoS Comput Biol , vol.2
    • Jenke-Kodama, H.1    Börner, T.2    Dittmann, E.3
  • 31
    • 0001179368 scopus 로고
    • Similarity analysis by reciprocal pairs for discrete and continuous data
    • McQuitty, L. L. Similarity analysis by reciprocal pairs for discrete and continuous data. Educ. Psychol. Meas. 26, 825-831 (1966
    • (1966) Educ. Psychol. Meas , vol.26 , pp. 825-831
    • McQuitty, L.L.1
  • 32
    • 0037466331 scopus 로고    scopus 로고
    • Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases
    • Yadav, G., Gokhale, R. S. & Mohanty, D. Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J. Mol. Biol. 328, 335-363 (2003
    • (2003) J. Mol. Biol , vol.328 , pp. 335-363
    • Yadav, G.1    Gokhale, R.S.2    Mohanty, D.3
  • 33
    • 38949203821 scopus 로고    scopus 로고
    • Exploiting the mosaic structure of trans-Acyltransferase polyketide synthases for natural product discovery and pathway dissection
    • Nguyen, T. et al. Exploiting the mosaic structure of trans- Acyltransferase polyketide synthases for natural product discovery and pathway dissection. Nat. Biotechnol 26, 225-233 (2008
    • (2008) Nat. Biotechnol , vol.26 , pp. 225-233
    • Nguyen, T.1
  • 35
    • 47649104484 scopus 로고    scopus 로고
    • Horizontal gene transfer in eukaryotic evolution
    • Keeling, P. J. & Palmer, J. D. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9, 605-618 (2008
    • (2008) Nat. Rev. Genet , vol.9 , pp. 605-618
    • Keeling, P.J.1    Palmer, J.D.2
  • 36
    • 24744433982 scopus 로고    scopus 로고
    • Evolutionary implications of bacterial polyketide synthases
    • Jenke-Kodama, H., Sandmann, A., Muller, R. & Dittmann, E. Evolutionary implications of bacterial polyketide synthases. Mol. Biol. Evol. 22, 2027-2039 (2005
    • (2005) Mol. Biol. Evol , vol.22 , pp. 2027-2039
    • Jenke-Kodama, H.1    Sandmann, A.2    Muller, R.3    Dittmann, E.4
  • 37
    • 84878590232 scopus 로고    scopus 로고
    • New structural scaffold 14-membered macrocyclic lactone ring for selective inhibitors of cell wall peptidoglycan biosynthesis in Staphylococcus aureus
    • Koyama, N., Yotsumoto, M., Onaka, H. & Tomoda, H. New structural scaffold 14-membered macrocyclic lactone ring for selective inhibitors of cell wall peptidoglycan biosynthesis in Staphylococcus aureus. J. Antibiot. 66, 303-304 (2013
    • (2013) J. Antibiot , vol.66 , pp. 303-304
    • Koyama, N.1    Yotsumoto, M.2    Onaka, H.3    Tomoda, H.4
  • 38
    • 0014133190 scopus 로고
    • Studies on a new antibiotic, albocycline i isolation, purification and properties
    • Nagahama, N., Suzuki, M., Awataguchi, S. & Okuda, T. Studies on a new antibiotic, albocycline. I. isolation, purification and properties. J. Antibiot. 20, 261-266 (1967
    • (1967) J. Antibiot , vol.20 , pp. 261-266
    • Nagahama, N.1    Suzuki, M.2    Awataguchi, S.3    Okuda, T.4
  • 39
    • 0037138356 scopus 로고    scopus 로고
    • Characterization of the biosynthetic gene cluster for the antifungal polyketide soraphen a from sorangium cellulosum so ce26
    • Ligon, J et al. Characterization of the biosynthetic gene cluster for the antifungal polyketide soraphen A from Sorangium cellulosum So ce26. Gene 285, 257-267 (2002
    • (2002) Gene , vol.285 , pp. 257-267
    • Ligon, J.1
  • 40
    • 0029098323 scopus 로고
    • The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin
    • Schwecke, T. et al. The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin. Proc. Natl Acad. Sci. USA 92, 7839-7843 (1995
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 7839-7843
    • Schwecke, T.1
  • 41
    • 0034723333 scopus 로고    scopus 로고
    • Cloning and heterologous exoression of the epothilone gene cluster
    • Tang, L. et al. Cloning and heterologous exoression of the epothilone gene cluster. Science 287, 640-642 (2000
    • (2000) Science , vol.287 , pp. 640-642
    • Tang, L.1
  • 42
    • 77957930925 scopus 로고    scopus 로고
    • Molecular insights into Burkholderia pseudomallei and Burkholderia mallei pathogenesis
    • Galyov, E. E., Brett, P. J. & DeShazer, D. Molecular insights into Burkholderia pseudomallei and Burkholderia mallei pathogenesis. Annu. Rev. Microbiol. 64, 495-517 (2010
    • (2010) Annu. Rev. Microbiol , vol.64 , pp. 495-517
    • Galyov, E.E.1    Brett, P.J.2    Deshazer, D.3
  • 43
    • 84868515764 scopus 로고    scopus 로고
    • Genomics-driven discovery of burkholderic acid, a noncanonical cryptic polyketide from human pathogenic Burkholderia species
    • Franke, J., Ishida, K. & Hertweck, C. Genomics-driven discovery of burkholderic acid, a noncanonical cryptic polyketide from human pathogenic Burkholderia species. Angew. Chem. Int. Ed. 51, 11611-11615 (2012
    • (2012) Angew. Chem. Int. Ed. , vol.51 , pp. 11611-11615
    • Franke, J.1    Ishida, K.2    Hertweck, C.3
  • 44
    • 84865138150 scopus 로고    scopus 로고
    • Malleilactone a polyketide synthase-derived virulence factor encoded by the cryptic secondary metabolome of Burkholderia pseudomallei group pathogens
    • Biggins, J. B., Ternei, M. A. & Brady, S. F. Malleilactone, a polyketide synthase-derived virulence factor encoded by the cryptic secondary metabolome of Burkholderia pseudomallei group pathogens. J. Am. Chem. Soc. 134, 13192-13195 (2012
    • (2012) J. Am. Chem. Soc , vol.134 , pp. 13192-13195
    • Biggins, J.B.1    Ternei, M.A.2    Brady, S.F.3
  • 45
    • 0037195174 scopus 로고    scopus 로고
    • A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles
    • Piel, J. A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proc. Natl Acad. Sci. USA 99, 14002-14007 (2002
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 14002-14007
    • Piel, J.1
  • 46
    • 84867785420 scopus 로고    scopus 로고
    • Molecular insights into the biosynthesis of guadinomine: A type III secretion system inhibitor
    • 177797-17806
    • Holmes, T. C. et al. Molecular insights into the biosynthesis of guadinomine: A type III secretion system inhibitor. J. Am. Chem. Soc. 134, 177797-17806 (2012
    • (2012) J. Am. Chem. Soc , vol.134
    • Holmes, T.C.1
  • 47
    • 70349567537 scopus 로고    scopus 로고
    • A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in Planktothrix rubescens strain
    • Rounge, T. B., Rohrlack, T., Nederbragt, A. J., Kristensen, T. & Jakobsen, K. S. A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in Planktothrix rubescens strain. BMC Genomics 10, 396 (2009
    • (2009) BMC Genomics , vol.10 , pp. 396
    • Rounge, T.B.1    Rohrlack, T.2    Nederbragt, A.J.3    Kristensen, T.4    Jakobsen, K.S.5
  • 48
    • 77950547477 scopus 로고    scopus 로고
    • A flavin-dependent halogenase catalyzes the chlorination step in the biosynthesis of Dictyostelium differentiation-inducing factor 1
    • Neumann, C. S., Walsh, C. T. & Kay, R. R. A flavin-dependent halogenase catalyzes the chlorination step in the biosynthesis of Dictyostelium differentiation-inducing factor 1. Proc. Natl Acad. Sci. USA 107, 5798-5803 (2010
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 5798-5803
    • Neumann, C.S.1    Walsh, C.T.2    Kay, R.R.3
  • 49
    • 33747598945 scopus 로고    scopus 로고
    • Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type i fatty acid-type III polyketide synthase
    • Austin, M. B. et al. Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type I fatty acid-type III polyketide synthase. Nat. Chem. Biol. 2, 494-502 (2006
    • (2006) Nat. Chem. Biol , vol.2 , pp. 494-502
    • Austin, M.B.1
  • 50
    • 36849010759 scopus 로고    scopus 로고
    • Novel insights into evolution of protistan polyketide synthases through phylogenomic analysis
    • John, U. et al. Novel insights into evolution of protistan polyketide synthases through phylogenomic analysis. Protist 159, 21-30 (2007
    • (2007) Protist , vol.159 , pp. 21-30
    • John, U.1
  • 51
    • 0037130946 scopus 로고    scopus 로고
    • Cryptosporidium parvum: The first protest known to encode a putative polyketide synthase
    • Zhu, G. et al. Cryptosporidium parvum: The first protest known to encode a putative polyketide synthase. Gene 298, 79-89 (2002
    • (2002) Gene , vol.298 , pp. 79-89
    • Zhu, G.1
  • 52
    • 84861207340 scopus 로고    scopus 로고
    • WormBase 2012: More genomes, more data, new website
    • Yook, K. et al. WormBase 2012: More genomes, more data, new website. Nucl. Acids Res. 40, D735-D741 (2012
    • (2012) Nucl. Acids Res , vol.40
    • Yook, K.1
  • 53
    • 78650410139 scopus 로고    scopus 로고
    • Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    • Gerstein, M. B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775-1787 (2010
    • (2010) Science , vol.330 , pp. 1775-1787
    • Gerstein, M.B.1
  • 54
    • 84860729900 scopus 로고    scopus 로고
    • Ascaroside signaling is widely conserved among nematodes
    • Choe, A. et al. Ascaroside signaling is widely conserved among nematodes. Curr. Biol. 22, 772-780 (2012
    • (2012) Curr. Biol , vol.22 , pp. 772-780
    • Choe, A.1
  • 55
    • 84856262927 scopus 로고    scopus 로고
    • Comparative metabolomics reveals biogenesis of ascarosides, a modular library of small-molecule signals in C
    • von Reuss, S. H. et al. Comparative metabolomics reveals biogenesis of ascarosides, a modular library of small-molecule signals in C. elegans. J. Am. Chem. Soc. 134, 1817-1824 (2012
    • (2012) Elegans. J. Am. Chem. Soc , vol.134 , pp. 1817-1824
    • Von Reuss, S.H.1


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