PRISM 3: Expanded prediction of natural product chemical structures from microbial genomes

Nucleic Acids Research

Volumn 45, Issue W1, 2017, Pages W49-W54

  Skinnider, Michael A ^a   Merwin, Nishanth J ^a   Johnston, Chad W ^a   Magarvey, Nathan A ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOCOUMARIN DERIVATIVE; ANTIMETABOLITE; BISINDOLE DERIVATIVE; INDOLE DERIVATIVE; NATURAL PRODUCT; PHOSPHONIC ACID DERIVATIVE; UNCLASSIFIED DRUG; BIOLOGICAL PRODUCT;

ARTICLE; CHEMICAL STRUCTURE; GENE CLUSTER; GENE IDENTIFICATION; GENETIC ALGORITHM; METABOLOME; MICROBIAL GENOME; NONHUMAN; OPEN READING FRAME; PREDICTION; PRIORITY JOURNAL; PROTEIN PROCESSING; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; ALGORITHM; BIOSYNTHESIS; CHEMISTRY; GENETICS; INTERNET; SECONDARY METABOLISM; SOFTWARE;

ALGORITHMS; BIOLOGICAL PRODUCTS; BIOSYNTHETIC PATHWAYS; GENOME, MICROBIAL; INTERNET; METABOLOME; SECONDARY METABOLISM; SOFTWARE;

EID: 85023161576     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx320     Document Type: Article

References (20)

1. Newman, D.J., and Cragg, G.M. (2016) Natural products as sources of new drugs from 1981 to 2014. J. Nat. Prod., 79, 629-661.
2. Nett, M., Ikeda, H., and Moore, B.S. (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat. Prod. Rep., 26, 1362-1384.
3. Doroghazi, J.R., Albright, J.C., Goering, A.W., Ju, K.S., Haines, R.R., Tchalukov, K.A., Labeda, D.P., Kelleher, N.L., and Metcalf, W.W. (2014) A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat. Chem. Biol., 10, 963-968.
4. Starcevic, A., Zucko, J., Simunkovic, J., Long, P.F., Cullum, J., and Hranueli, D. (2008) 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.
5. Bachmann, B.O., and Ravel, J. (2009) Chapter 8. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods Enzymol., 458, 181-217.
6. Li, M.H., Ung, P.M., Zajkowski, J., Garneau-Tsodikova, S., and Sherman, D.H. (2009) Automated genome mining for natural products. BMC Bioinformatics, 10, 185.
7. Kim, J., and Yi, G.S. (2012) PKMiner: a database for exploring type II polyketide synthases. BMC Microbiol., 12, 169.
8. Ziemert, N., Podell, S., Penn, K., Badger, J.H., Allen, E., and Jensen, P.R. (2012) The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One, 7, e34064.
9. van Heel, A.J., de Jong, A., Montalban-Lopez, M., Kok, J., and Kuipers, O.P. (2013) BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res., 41, W448-W453.
10. Cimermancic, P., Medema, M.H., Claesen, J., Kurita, K., Wieland Brown, L.C., Mavrommatis, K., Pati, A., Godfrey, P.A., Koehrsen, M., Clardy, J., et al. (2014) Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell, 158, 412-421.
11. Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H.U., Bruccoleri, R., Lee, S.Y., Fischbach, M.A., Muller, R., Wohlleben, W., et al. (2015) antiSMASH 3.0-A comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res., 43, W237-W243.
12. Skinnider, M.A., Dejong, C.A., Rees, P.N., Johnston, C.W., Li, H., Webster, A.L., Wyatt, M.A., and Magarvey, N.A. (2015) Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic Acids Res., 43, 9645-9662.
13. Skinnider, M.A., Johnston, C.W., Edgar, R.E., Dejong, C.A., Merwin, N.J., Rees, P.N., and Magarvey, N.A. (2016) Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining. Proc. Natl. Acad. Sci. U.S.A., 113, E6343-E6351.
14. Johnston, C.W., Skinnider, M.A., Dejong, C.A., Rees, P.N., Chen, G.M., Walker, C.G., French, S., Brown, E.D., Berdy, J., Liu, D.Y. et al. (2016) Assembly and clustering of natural antibiotics guides target identification. Nat. Chem. Biol., 12, 233-239.
15. Dejong, C.A., Chen, G.M., Li, H., Edwards, M.R., Rees, P.N., Skinnider, M.A., Webster, A.L.H., and Magarvey, N.A. (2016) Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching. Nat. Chem. Biol., 12, 1007-1014.
16. Walsh, C.T., Chen, H., Keating, T.A., Hubbard, B.K., Losey, H.C., Luo, L., Marshall, C.G., Miller, D.A., and Patel, H.M. (2001) Tailoring enzymes that modify nonribosomal peptides during and after chain elongation on NRPS assembly lines. Curr. Opin. Chem. Biol., 5, 525-534.
17. Rogers, D., and Hahn, M. (2010) Extended-connectivity fingerprints. J. Chem. Inf. Model., 50, 742-754.
18. Markowitz, V.M., Chen, I.M.A., Palaniappan, K., Chu, K., Szeto, E., Pillay, M., Ratner, A., Huang, J., Woyke, T., Huntemann, M., et al. (2013) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res., 42, D560-D567.
19. Prlic, A., Yates, A., Bliven, S.E., Rose, P.W., Jacobsen, J., Troshin, P.V., Chapman, M., Gao, J., Koh, C.H., Foisy, S., et al. (2012) BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 28, 2693-2695.
20. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.