Natural products discovery from micro-organisms in the post-genome eraFootnote^†

† This work is a translation of an original work in Japanese in the Japan Society for Bioscience, Biotechnology, and Agrochemistry http://doi.10.1271/kagakutoseibutsu.54.17

References

• Ōmura S, Ikeda H, Ishikawa J, et al. Genome sequence of an industrial microorganism Streptomyces avermitilis: Deducing the ability of producing secondary metabolites. Proc Natl Acad Sci USA. 2001;98:12215–12220.10.1073/pnas.211433198
   PubMed Web of Science ®Google Scholar
• Bentley SD, Chater KF, Cerdeño-Tárraga A-M, et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 2002;417:141–147.10.1038/417141a
   PubMed Web of Science ®Google Scholar
• Ikeda H, Ishikawa J, Hanamoto A, et al. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol. 2003;21:526–531.10.1038/nbt820
   PubMed Web of Science ®Google Scholar
• McLeod MP, Warren RL, Hsiao WW, et al. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci USA. 2006;103:15582–15587.10.1073/pnas.0607048103
   PubMed Web of Science ®Google Scholar
• Ichikawa N, Oguchi A, Ikeda H, et al. Genome sequence of Kitasatospora setae NBRC 14216T: An evolutionary snapshot of the family Streptomycetaceae. DNA Res. 2010;17:393–406.10.1093/dnares/dsq026
   PubMed Web of Science ®Google Scholar
• Oliynyk M, Samborskyy M, Lester JB, et al. Complete genome sequence of the erythromycin-producing bacterium Saccharopolysporaerythraea NRRL23338. Nat Biotechnol. 2007;25:447–453.10.1038/nbt1297
   PubMed Web of Science ®Google Scholar
• Tang B, Wang Q, Yang M, et al. ContigScape: a Cytoscape plugin facilitating microbial genome gap closing. BMC Genomics. 2013;14:289.10.1186/1471-2164-14-289
   PubMed Web of Science ®Google Scholar
• Stover CK, Pham XQ, Erwin AL, et al. Complete genome sequence of Pseudomonasaeruginosa PAO1, an opportunistic pathogen. Nature. 2000;406:959–964.
   PubMed Web of Science ®Google Scholar
• Weber T, Blin K, Duddela S, et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43:W237–243.10.1093/nar/gkv437
   PubMed Web of Science ®Google Scholar
• Ikeda H, Kotaki H, Omura S. Genetic studies of avermectin biosynthesis in Streptomyces avermitilis. J Bacteriol. 1987;169:5615–5621.
   PubMed Web of Science ®Google Scholar
• Ikeda H, Nonomiya T, Usami M, et al. Organization of the biosynthetic gene cluster for the polyketide anthelmintic macrolide avermectin in Streptomycesavermitilis. Proc Natl Acad Sci USA. 1999;96:9509–9514.10.1073/pnas.96.17.9509
   PubMed Web of Science ®Google Scholar
• Ikeda H, Nonomiya T, Omura S. Organization of biosynthetic gene cluster for avermectin in Streptomyces avermitilis: Analysis of enzymatic domains in four polyketide synthases. J Ind Microbiol Biotechnol. 2001;27:170–176.10.1038/sj.jim.7000092
   PubMed Web of Science ®Google Scholar
• Nett M, Ikeda H, Moore BS. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep. 2009;26:1362–1384.10.1039/b817069j
   PubMed Web of Science ®Google Scholar
• Ikeda H, Takada Y, Pang CH. Transposon mutagenesis by Tn4560 and applications with avermectin-producing Streptomyces avermitilis. J Bacteriol. 1993;175:2077–2082.
   PubMed Web of Science ®Google Scholar
• Tetzlaff CN, You Z, Cane DE, et al. A gene cluster for biosynthesis of the sesquiterpenoid antibiotic pentalenolactone in Streptomyces avermitilis. Biochemistry. 2006;45:6179–6186.10.1021/bi060419n
   PubMed Web of Science ®Google Scholar
• Komatsu M, Uchiyama T, Omura S, et al. Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci USA. 2010;107:2646–2651.10.1073/pnas.0914833107
   PubMed Web of Science ®Google Scholar
• Komatsu M, Komatsu K, Koiwai H, et al. Engineered Streptomyces avermitilis host for heterologous expression of biosynthetic gene cluster for secondary metabolites. ACS Synth Biol. 2013;2:384–396.10.1021/sb3001003
   PubMed Web of Science ®Google Scholar
• Ikeda H, Shin-ya K, Omura S. Genome mining of the Streptomyces avermitilis genome and development of genome-minimized hosts for heterologous expression of biosynthetic gene clusters. J Ind Microbiol Biotechnol. 2014;41:233–250.10.1007/s10295-013-1327-x
   PubMed Web of Science ®Google Scholar
• Komatsu M, Tsuda M, Omura S, et al. Identification and functional analysis of genes controlling biosynthesis of 2-methylisoborneol. Proc Natl Acad Sci USA. 2008;105:7422–7427.10.1073/pnas.0802312105
   PubMed Web of Science ®Google Scholar
• Yamada Y, Kuzuyama T, Komatsu M, et al. Terpene synthases are widely distributed in bacteria. Proc Natl Acad Sci USA. 2015;112:857–862.10.1073/pnas.1422108112
   PubMed Web of Science ®Google Scholar
• Yamada Y, Arima S, Nagamitsu T, et al. Novel terpenes generated by heterologous expression of bacterial terpene synthase genes in an engineered Streptomyces host. J Antibiot (Tokyo). 2015;68:385–394.10.1038/ja.2014.171
   PubMed Web of Science ®Google Scholar
• Hopwood DA, Malpartida F, Kieser HM, et al. Production of ‘hybrid’ antibiotics by genetic engineering. Nature. 1985;314:642–644.10.1038/314642a0
   PubMed Web of Science ®Google Scholar