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Development of an Analysis Program of Type I Polyketide Synthase Gene Clusters Using Homology Search and Profile Hidden Markov Model  

Tae, Hong-Seok (Information Technology Institute, SmallSoft Co., Ltd.)
Sohng, Jae-Kyung (Department of Pharmaceutical Engineering, Sunmoon University)
Park, Kie-Jung (Information Technology Institute, SmallSoft Co., Ltd.)
Publication Information
Journal of Microbiology and Biotechnology / v.19, no.2, 2009 , pp. 140-146 More about this Journal
Abstract
MAPSI(Management and Analysis for Polyketide Synthase Type I) has been developed to offer computational analysis methods to detect type I PKS(polyketide synthase) gene clusters in genome sequences. MAPSI provides a genome analysis component, which detects PKS gene clusters by identifying domains in proteins of a genome. MAPSI also contains databases on polyketides and genome annotation data, as well as analytic components such as new PKS assembly and domain analysis. The polyketide data and analysis component are accessible through Web interfaces and are displayed with diverse information. MAPSI, which was developed to aid researchers studying type I polyketides, provides diverse components to access and analyze polyketide information and should become a very powerful computational tool for polyketide research. The system can be extended through further studies of factors related to the biological activities of polyketides.
Keywords
ASMPKS; MAPSI; modular; PKS; polyketide;
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1 Broadhurst, R. W., D. Nietlispach, M. P. Wheatcroft, P. F. Leadlay, and K. J. Weissman. 2003. The structure of docking domains in modular polyketide synthases. Chem. Biol. 10: 723-731   DOI   ScienceOn
2 Long, P. F., C. J. Wilkinson, C. P. Bisang, J. Cortes, N. Dunster, M. Oliynyk, et al. 2002. Engineering specificity of starter unit selection by the erythromycin-producing polyketide synthase. Mol. Microbiol. 43: 1215-1225   DOI   ScienceOn
3 Moore, B. S. and C. Hertweck. 2002. Biosynthesis and attachmentof novel bacterial polyketide synthase starter units. Nat. Prod.Rep. 19: 70-99   DOI   ScienceOn
4 Rawlings, B. J. 2001. Type I polyketide biosynthesis in bacteria(Part A - erythromycin biosynthesis). Nat. Prod. Rep. 18: 190-227   DOI   PUBMED   ScienceOn
5 Rawlings, B. J. 2001. Type I polyketide biosynthesis in bacteria(Part B). Nat. Prod. Rep. 18: 231-281   DOI   PUBMED   ScienceOn
6 Shen, B. and C. R. Hutchinson. 1996. Deciphering the mechanism for the assembly of aromatic polyketides by a bacterial polyketide synthase. Proc. Natl. Acad. Sci. U.S.A. 93: 6600-6604   DOI   ScienceOn
7 Witkowski, A., V. S. Rangan, Z. I. Randhawa, C. M. Amy, and S. Smith. 1991. Structural organization of the multifunctional animal fatty-acid synthase. Eur. J. Biochem. 198: 571-579   DOI   ScienceOn
8 Yadav, G., R. S. Gokhale, and D. Mohanty. 2003. SEARCHPKS: A program for detection and analysis of polyketide synthase domains. Nucleic Acids Res. 31: 3654-3658   DOI   ScienceOn
9 Wiesmann, K. E., J. Cortes, M. J. Brown, A. L. Cutter, J. Staunton, and P. F. Leadlay. 1995. Polyketide synthesis in vitro on a modular polyketide synthase. Chem. Biol. 2: 583-589   DOI   ScienceOn
10 McDaniel, R., A. Thamchaipenet, C. Gustafsson, H. Fu, M. Betlach, and G. Ashley. 1999. Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel 'unnatural' natural products. Proc. Natl. Acad. Sci. U.S.A. 96: 1846-1851   DOI   ScienceOn
11 O'Hagan, D. 1993. Biosynthesis of fatty acid and polyketide metabolites. Nat. Prod. Rep. 10: 593-624   DOI   ScienceOn
12 Salzberg, S. L., A. L. Delcher, S. Kasif, and O. White. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26: 544-548   DOI   ScienceOn
13 Watanabe, K., C. C. Wang, C. N. Boddy, D. E. Cane, and C. Khosla. 2003. Understanding substrate specificity of polyketide synthase modules by generating hybrid multimodular synthases. J. Biol. Chem. 278: 42020-42026   DOI   ScienceOn
14 Cheng, Y. Q., G. L. Tang, and B. Shen. 2003. Type I polyketide synthase requiring a discrete acyltransferase for polyketide biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 100: 3149-3154   DOI   ScienceOn
15 Kim, B. S., D. H. Sherman, and K. A. Reynolds. 2004. An efficient method for creation and functional analysis of libraries of hybrid type I polyketide synthases. Protein Eng. Des. Sel. 17: 277-284   DOI   ScienceOn
16 Omura, S., H. Ikeda, J. Ishikawa, A. Hanamoto, C. Takahashi, M. Shinose, et al. 2001. Genome sequence of an industrial microorganism Streptomyces avermitilis: Deducing the ability of producing secondary metabolites. Proc. Nat. Acad. Sci. U.S.A. 98: 12215-12220   DOI   ScienceOn
17 Wu, K., L. Chung, W. P. Revill, L. Katz, and C. D. Reeves. 2000. The FK520 gene cluster of Streptomycetes hygroscopicus var. ascomyceticus (ATCC 14891) contains genes for biosynthesis of unusual polyketide extender units. Gene 251: 81-90   DOI   ScienceOn
18 Marchler-Bauer, A., A. R. Panchenko, B. A. Shoemaker, P. A. Thiessen, L. Y. Geer, and S. H. Bryant. 2002. CDD: A database of conserved domain alignments with links to domain threedimensional structure. Nucleic Acids Res. 30: 281-283   DOI   ScienceOn
19 Pfeifer, B. A. and C. Khosla. 2001. Biosynthesis of polyketides in heterologous hosts. Microbiol. Mol. Biol. Rev. 65: 106-118   DOI   ScienceOn
20 Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410   PUBMED   ScienceOn
21 Tae, H., E. B. Kong, and K. Park. 2007. ASMPKS: An analysis system for modular polyketide synthases. BMC Bioinformatics 8: 327   DOI   PUBMED
22 Jain, A. K., M. N. Murty, and P. J. Flynn. 1999. Data clustering: A review. ACM Computing Surveys 31: 264-323   DOI   ScienceOn
23 McDaniel, R., C. M. Kao, S. J. Hwang, and C. Khosla. 1997. Engineered intermodular and intramodular polyketide synthase fusions. Chem. Biol. 4: 667-674   DOI   ScienceOn
24 Gaitatzis, N., B. Silakowski, B. Kunze, G. Nordsiek, H. Blöcker, G. Höfle, and R. Müller. 2002. The biosynthesis of the aromatic myxobacterial electron transport inhibitor stigmatellin is directed by a novel type of modular polyketide synthase. J. Biol. Chem. 277: 13082-13090   DOI   ScienceOn
25 Floss, H. G. and T. W. Yu. 1999. Lessons from the rifamycin biosynthetic gene cluster. Curr. Opin. Chem. Biol. 3: 592- 597   DOI   ScienceOn
26 Aparicio, J. F., P. Caffrey, A. F. A. Marsden, J. Staunton, and P. F. Leadlay. 1994. Limited proteolysis and active-site studies of the first multienzyme component of the erythromycin-producing polyketide synthase. J. Biol. Chem. 269: 8524-8528   PUBMED   ScienceOn
27 Eddy, S. R. 1999. Profile hidden Markov models. Bioinformatics 14: 755-763   DOI   PUBMED   ScienceOn
28 Zdobnov, E. M. and R. Apweiler. 2001. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848   DOI   ScienceOn
29 Ikeda, H., T. Nonomiya, M. Usami, T. Ohta, and S. Omura. 1999. Organization of the biosynthetic gene cluster for the polyketide antihelmintic macrolide avermectin in Streptomyces avermitilis. Proc. Natl. Acad. Sci. U.S.A. 96: 9509-9514   DOI   ScienceOn