A roadmap for natural product discovery based on large-scale genomics and metabolomics (original) (raw)

• Bérdy, J. Bioactive microbial metabolites. J. Antibiot. (Tokyo) 58, 1–26 (2005).
  Article Google Scholar
• Bérdy, J. Thoughts and facts about antibiotics: where we are now and where we are heading. J. Antibiot. (Tokyo) 65, 385–395 (2012).
  Article Google Scholar
• Bentley, S.D. et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141–147 (2002).
  Article PubMed Google Scholar
• Lautru, S., Deeth, R.J., Bailey, L.M. & Challis, G.L. Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat. Chem. Biol. 1, 265–269 (2005).
  Article CAS PubMed Google Scholar
• Kersten, R.D. et al. A mass spectrometry–guided genome mining approach for natural product peptidogenomics. Nat. Chem. Biol. 7, 794–802 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Ziemert, N. et al. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS ONE 7, e34064 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• 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).
  Article CAS PubMed PubMed Central Google Scholar
• Conway, K.R. & Boddy, C.N. ClusterMine360: a database of microbial PKS/NRPS biosynthesis. Nucleic Acids Res. 41, D402–D407 (2013).
  Article CAS PubMed Google Scholar
• Diminic, J. et al. Databases of the thiotemplate modular systems (CSDB) and their in silico recombinants (r-CSDB). J. Ind. Microbiol. Biotechnol. 40, 653–659 (2013).
  Article CAS PubMed Google Scholar
• Yadav, G., Gokhale, R.S. & Mohanty, D. SEARCHPKS: a program for detection and analysis of polyketide synthase domains. Nucleic Acids Res. 31, 3654–3658 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Tae, H., Kong, E.-B. & Park, K. ASMPKS: an analysis system for modular polyketide synthases. BMC Bioinformatics 8, 327 (2007).
  Article PubMed PubMed Central Google Scholar
• Ichikawa, N. et al. DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters. Nucleic Acids Res. 41, D408–D414 (2013).
  Article CAS PubMed Google Scholar
• Caboche, S. et al. NORINE: a database of nonribosomal peptides. Nucleic Acids Res. 36, D326–D331 (2008).
  Article CAS PubMed Google Scholar
• Kim, J. & Yi, G.-S. PKMiner: a database for exploring type II polyketide synthases. BMC Microbiol. 12, 169 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Fischbach, M.A. & Walsh, C. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem. Rev. 106, 3468–3496 (2006).
  Article CAS PubMed Google Scholar
• Raghupathy, N. & Durand, D. Gene cluster statistics with gene families. Mol. Biol. Evol. 26, 957–968 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, X. et al. Identification and characterization of the actinomycin G gene cluster of Streptomyces iakyrus. Mol. Biosyst. 9, 1286–1289 (2013).
  Article CAS PubMed Google Scholar
• Colwell, R.K. et al. Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages. J. Plant Ecol. 5, 3–21 (2012).
  Article Google Scholar
• Doroghazi, J.R. & Metcalf, W.W. Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes. BMC Genomics 14, 611 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Jensen, P.R., Williams, P.G., Oh, D.C., Zeigler, L. & Fenical, W. Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl. Environ. Microbiol. 73, 1146–1152 (2007).
  Article CAS PubMed Google Scholar
• Dunbar, K.L., Melby, J.O. & Mitchell, D.A. YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations. Nat. Chem. Biol. 8, 569–575 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Charlop-Powers, Z., Owen, J.G., Reddy, B.V.B., Ternei, M.A. & Brady, S.F. Chemical-biogeographic survey of secondary metabolism in soil. Proc. Natl. Acad. Sci. USA 111, 3757–3762 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Bunge, J., Willis, A. & Walsh, F. Estimating the number of species in microbial diversity studies. Annual Review of Statistics and Its Application 1, 427–445 (2014).
  Article Google Scholar
• Nguyen, D.D. et al. MS/MS networking guided analysis of molecule and gene cluster families. Proc. Natl. Acad. Sci. USA 110, E2611–E2620 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Cote, R. in ATCC Bacteria and Bacteriophages 19th edn (eds. Pienta, P., Tang, J. & Cote, R.) 484 (American Type Culture Collection, 1996).
• Zerbino, D.R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Chaisson, M.J., Brinza, D. & Pevzner, P.A. De novo fragment assembly with short mate-paired reads: does the read length matter? Genome Res. 19, 336–346 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005); erratum Nature 4, 120 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D. & Pirovano, W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578–579 (2011).
  Article CAS PubMed Google Scholar
• Peng, Y., Leung, H.C., Yiu, S.-M. & Chin, F.Y. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420–1428 (2012).
  Article CAS PubMed Google Scholar
• Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
  Article PubMed PubMed Central Google Scholar
• Li, L., Stoeckert, C.J. & Roos, D.S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
  Article PubMed PubMed Central Google Scholar
• Edgar, R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
  Article CAS PubMed Google Scholar
• Ester, M., Kriegel, H.-P., Sander, J. & Xu, X. A density-based algorithm for discovering clusters in large spatial databases with noise. in Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96) (eds. Simoudis, E., Han, J. & Fayyad, U.) 226–231 (AAAI Press, 1996).
• Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
  CAS PubMed PubMed Central Google Scholar
• Price, M.N., Dehal, P.S. & Arkin, A.P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
  Article PubMed PubMed Central Google Scholar
• Zhang, Q., Yu, Y., Vélasquez, J.E. & van der Donk, W.A. Evolution of lanthipeptide synthetases. Proc. Natl. Acad. Sci. USA 109, 18361–18366 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Yutin, N., Puigbò, P., Koonin, E.V. & Wolf, Y.I. Phylogenomics of prokaryotic ribosomal proteins. PLoS ONE 7, e36972 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Larkin, M.A. et al. Clustal W and clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).
  Article CAS PubMed Google Scholar
• Huerta-Cepas, J., Dopazo, J. & Gabaldón, T. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 11, 24 (2010).
  Article PubMed PubMed Central Google Scholar
• Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• El-Nakeeb, M.A. & Lechevalier, H.A. Selective isolation of aerobic actinomycetes. Appl. Microbiol. 11, 75–77 (1963).
  CAS PubMed PubMed Central Google Scholar
• Smith, S.E. et al. Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PLoS ONE 7, e50070 (2012).
  Article CAS PubMed PubMed Central Google Scholar