ClusterMine360: A database of microbial PKS/NRPS biosynthesis

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Conway, Kyle R ^a   Boddy, Christopher N ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

NONRIBOSOMAL PEPTIDE SYNTHETASE; POLYKETIDE SYNTHASE;

ARTICLE; AUTOMATION; BIOINFORMATICS; CLUSTERMINE360 DATABASE; COMPUTER PROGRAM; CROWDSOURCING; ENZYME SYNTHESIS; FILE TRANSFER PROTOCOL; FREDERICAMYCIN GENE; GENE; GENE CLUSTER; GENETIC DATABASE; MICROBIAL GENETICS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

DATABASES, GENETIC; GENES, BACTERIAL; INTERNET; MULTIGENE FAMILY; PEPTIDE BIOSYNTHESIS, NUCLEIC ACID-INDEPENDENT; PEPTIDE SYNTHASES; PHYLOGENY; POLYKETIDE SYNTHASES; POLYKETIDES; SOFTWARE;

EID: 84876566794     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks993     Document Type: Article

References (29)

1. Benson, D.A., Karsch-Mizrachi, I., Clark, K., Lipman, D.J., Ostell, J. and Sayers, E.W. (2012) GenBank. Nucleic Acids Res., 40, D48-D53.
2. Pruitt, K.D., Tatusova, T., Brown, G.R. and Maglott, D.R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
3. Garcia, I., Vior, N.M., Braña, A.F., González-Sabin, J., Rohr, J., Moris, F., Méndez, C. and Salas, J.A. (2012) Elucidating the biosynthetic pathway for the polyketide-nonribosomal peptide collismycin A: mechanism for formation of the 2, 2'-bipyridyl ring. Chem. Biol., 19, 399-413.
4. Goldman, B.S., Nierman, W.C., Kaiser, D., Slater, S.C., Durkin, A.S., Eisen, J.A., Eisen, J., Ronning, C.M., Barbazuk, W.B., Blanchard, M. et al. (2006) Evolution of sensory complexity recorded in a myxobacterial genome. Proc. Natl Acad. Sci. USA, 103, 15200-15205.
5. Jenke-Kodama, H. and Dittmann, E. (2009) Bioinformatic perspectives on NRPS/PKS megasynthases: advances and challenges. Nat. Prod. Rep., 26, 874-883.
6. Ansari, M.Z., Yadav, G., Gokhale, R.S. and Mohanty, D. (2004) NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic Acids Res., 32, W405-W413.
7. Tae, H., Sohng, J.K. and Park, K. (2009) MapsiDB: an integrated web database for type I polyketide synthases. Bioprocess Biosyst. Eng., 32, 723-727.
8. Caboche, S., Pupin, M., Leclère, V., Fontaine, A., Jacques, P. and Kucherov, G. (2008) NORINE: a database of nonribosomal peptides. Nucleic Acids Res., 36, D326-D331.
9. Yi, G.-S. and Kim, J. (2012) PKMiner: a database for exploring type II polyketide synthases. BMC Microbiol., 12, 169.
10. Challis, G.L. (2008) Mining microbial genomes for new natural products and biosynthetic pathways. Microbiology, 154, 1555-1569.
11. Brikun, I.A., Reeves, A.R., Cernota, W.H., Luu, M.B. and Weber, J.M. (2004) The erythromycin biosynthetic gene cluster of Aeromicrobium erythreum. J. Indust. Microbiol. Biotechnol., 31, 335-344.
12. Mootz, H.D. and Marahiel, M.A. (1997) The tyrocidine biosynthesis operon of Bacillus brevis: complete nucleotide sequence and biochemical characterization of functional internal adenylation domains. J. Bacteriol., 179, 6843-6850.
13. Bucheler, T. and Sieg, J.H. (2011) Understanding science 2.0: crowdsourcing and open innovation in the scientific method. Procedia. Comput. Sci., 7, 327-329.
14. Meyer, P., Hoeng, J., Rice, J.J., Norel, R., Sprengel, J., Stolle, K., Bonk, T., Corthesy, S., Royyuru, A., Peitsch, M.C. et al. (2012) Industrial methodology for process verification in research (IMPROVER): toward systems biology verification. Bioinformatics, 28, 1193-1201.
15. Medema, M.H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M.A., Weber, T., Takano, E. and Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res., 39, W339-W346.
16. Shen, B., Wendt-Pienkowski, E., Huang, Y., Zhang, J., Li, B., Jiang, H., Kwon, H. and Hutchinson, C.R. (2005) Cloning, sequencing, analysis, and heterologous expression of the fredericamycin biosynthetic gene cluster from Streptomyces griseus. J. Am. Chem. Soc., 127, 16442-16452.
17. Gerth, K., Bedorf, N., Höfle, G., Irschik, H. and Reichenbach, H. (1996) Epothilons A and B: antifungal and cytotoxic compounds from Sorangium cellulosum (Myxobacteria). Production, physicochemical and biological properties. J. Antibiot., 49, 560-563.
18. Hardt, I., Steinmetz, H. and Gerth, K. (2001) New natural epothilones from sorangium c ellulosum, strains so ce90/B2 and So ce90/D13: isolation, structure elucidation, and SAR studies. J. Nat. Prod., 64, 847-856.
19. Willett, P. (2000) Chemoinformatics - similarity and diversity in chemical libraries. Curr. Opin. Biotechnol., 11, 85-88.
20. Molnár, I., Schupp, T., Ono, M., Zirkle, R., Milnamow, M., Nowak-Thompson, B., Engel, N., Toupet, C., Stratmann, A., Cyr, D.D. et al. (2000) The biosynthetic gene cluster for the microtubule-stabilizing agents epothilones A and B from Sorangium cellulosum So ce90. Chem. Biol., 7, 97-109.
21. Tang, L., Shah, S., Chung, L., Carney, J. and Katz, L. (2000) Cloning and heterologous expression of the epothilone gene cluster. Science, 287, 640-642.
22. Oliynyk, M., Samborskyy, M., Lester, J.B., Mironenko, T., Scott, N., Dickens, S., Haydock, S.F. and Leadlay, P.F. (2007) Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338. Nat. Biotechnol., 25, 447-453.
23. Bolton, E., Wang, Y., Thiessen, P. and Bryant, S. (2008) PubChem: integrated platform of small molecules and biological activities. Annu. Rep. Comput. Chem., 4, 217-241.
24. Wang, Y., Xiao, J., Suzek, T.O., Zhang, J., Wang, J. and Bryant, S.H. (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res., 37, W623-W633.
25. Chen, H., O'Connor, S., Cane, D.E. and Walsh, C.T. (2001) Epothilone biosynthesis: assembly of the methylthiazolylcarboxy starter unit on the EpoB subunit. Chem. Biol., 8, 899-912.
26. Kelly, W.L., Hillson, N.J. and Walsh, C.T. (2005) Excision of the epothilone synthetase B cyclization domain and demonstration of in trans condensation/cyclodehydration activity. Biochemistry, 44, 13385-13393.
27. Duerfahrt, T., Eppelmann, K., Müller, R. and Marahiel, M.A. (2004) Rational design of a bimodular model system for the investigation of heterocyclization in nonribosomal peptide biosynthesis. Chem. Biol., 11, 261-271.
28. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
29. Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.