Phylogenetic analysis of type I and type II polyketide synthase from tropical forest soil

Biotechnology

Volumn 7, Issue 4, 2008, Pages 660-668

  Pang, Mei Fong ^a   Tan, Geok Yuan Annie ^a   Abdullah, Noorlidah ^a   Lee, Choon Weng ^a   Ng, ChiNg Ching ^a  

^a UNIVERSITY OF MALAYA   (Malaysia)

Author keywords

Culture independent; Ketosynthase (KS); Phylogenetic analysis; Polyketide synthase (PKS); Tropical soil

Indexed keywords

CULTURE-INDEPENDENT; KETOSYNTHASE (KS); PHYLOGENETIC ANALYSIS; POLYKETIDE SYNTHASE (PKS); TROPICAL SOIL;

AMINES; AMINO ACIDS; BACTERIOLOGY; GENES; NUCLEIC ACIDS; ORGANIC ACIDS; SOILS; TROPICS;

ENZYMES;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); CHLOROFLEXI; CHLOROFLEXI (CLASS); CYANOBACTERIA; MYXOCOCCALES; PROTEOBACTERIA; UNCULTURED BACTERIUM;

EID: 67651015405     PISSN: 1682296X     EISSN: 16822978     Source Type: Journal    
DOI: 10.3923/biotech.2008.660.668     Document Type: Article

References (34)

1. Bhuyan, B. K. and F. Reusser, 1970. Comparative biological activity of nogalamycin and its analogs. Cancer Res., 30:984-989.
2. Gerth, K., S. Pradella, O. Perlova, S. Beyer and R. Muller, 2003. Myxobacteria: Proficient producers of novel natural products with various biological activities-past and future biotechnological aspects with the focus on the genus Sorangium. J. Biotechnol., 106:233-253.
3. Gillespie, D. E., S. F. Brady, A. D. Bettermann, N. P. Cianciotto and M. R. Liles et al., 2002. Isolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA. Applied Environ. Microbiol., 68:4301-4306.
4. Ginolhac, A., C. Jarrin, B. Gillet, P. Robe and P. Pujic et al., 2004. Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Applied Environ. Microbiol., 70:5522-5527.
5. Ginolhac, A., C. Jarrin, P. Robe, G. Perriere, T. M. Vogel, P. Simonet and R. Nalin, 2005. Type 1 polyketide synthases may have evolved through horizontal gene transfer. J. Mol. Evol., 60:716-725.
6. Gokhale, R. S., S. Y. Tsuji, D. E. Cane and C. Khosla, 1999. Dissecting and exploiting intermodular communication in polyketide synthases. Science, 284:482-485.
7. Hertweck, C, A. Luzhetskyy, Y. Rebets and A. Bechthold, 2007. Type 2 polyketide synthases: Gaining a deeper insight into enzymatic teamwork. Nat. Prod. Rep., 24:162-190.
8. Hopwood, D. A. and D. H. Sherman, 1990. Molecular genetics of polyketides and its comparison to fatty acid biosynthesis. Annu. Rev. Genet, 24:37-66.
9. Hugenholtz, P. and N. R. Pace, 1996. Identifying microbial diversity in the natural environment: A molecular phylogenetic approach. Trends Biotechnol., 14:190-197.
10. Hutchinson, C. R., 1998. Combinatorial biosynthesis for new drug discovery. Curr. Opin. Microbiol., 1:319-329.
11. Ichinose, K., M. Ozawa, K. Itou, K. Kunieda and Y. Ebizuka, 2003. Cloning, sequencing and heterologous expression of the medermycin biosynthetic gene cluster of Streptomyces sp. AM-7161: Towards comparative analysis of the benzoisochromanequinone gene clusters. Microbiology, 149:1633-1645.
12. Janssen, P. H., 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Applied Environ. Microbiol., 72:1719-1728.
13. Jenke-Kodama, H., A. Sandmann, R. Muller and E. Dittmann, 2005. Evolutionary implications of bacterial polyketide synthases. Mol. Biol. Evol., 22:2027-2039.
14. Kittendorf, J. D. and D. H. Sherman, 2006. Developing tools for engineering hybrid polyketide synthetic pathways. Curr. Opin. Biotechnol., 17:597-605.
15. Li, Z. F., J. Y. Zhao, Z. J. Xia, J. Shi and H. Liu et al., 2007. Evolutionary diversity of ketoacyl synthases in cellulolytic myxobacterium Sorangium. Syst. Applied Microbiol., 30:189-196.
16. Lorenz, M. G. and W. Wackernagel, 1994. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev., 58:563-602.
17. 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. USA., 96:1846-1851.
18. Metsa-Ketela, M., V. Salo, L. Halo, A. Hautala and J. Hakala et al., 1999. An efficient approach for screening minimal PKS genes from Streptomyces. FEMS Microbiol. Lett, 180:1-6.
19. Moffitt, M. C. and B. A. Neilan, 2003. Evolutionary affiliations within the superfamily of ketosynthases reflect complex pathway associations. J. Mol. Evol., 56:446-457.
20. Nett, M., O. Erol, S. Kehraus, M. Kock and A. Krick et al., 2006. Siphonazole, an unusual metabolite from Herpetosiphon sp. Angew Chem. Int. Ed. Engl., 45:3863-3867.
21. Pettit, R. K., 2004. Soil DNA libraries for anticancer drug discovery. Cancer Chemother. Pharmacol., 54:1-6.
22. Sarma, H. K., B. K. Sharma and S. C. Tiwari, 2003. A novel calcimycin antibiotic from Gram-positive actinomycete Frankia microsymbiont. Curr. Sci., 85:1401-1403.
23. Schupp, T., C. Toupet, B. Cluzel, S. Neff, S. Hill, J. J. Beck and J. M. Ligon, 1995. A Sorangium cellulosum (Myxobacterium) gene cluster for the biosynthesis of the macrolide antibiotic soraphen A: Cloning, characterization and homology to polyketide synthase genes from actinomycetes. J. Bacteriol., 177:3673-3679.
24. Shen, B., 2003. Polyketide biosynthesis beyond the type 1, 2 and 3 polyketide synthase paradigms. Curr. Opin. Chem. Biol., 7:285-295.
25. Staunton, J. and K. J. Weissman, 2001. Polyketide biosynthesis: A millennium review. Nat. Prod. Rep., 18:380-416.
26. Tamura, K., J. Dudley, M. Nei and S. Kumar, 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24:1596-1599.
27. Torsvik, V., J. Goksoyr and F. L. Daae, 1990. High diversity in DNA of soil bacteria. Applied Environ. Microbiol., 56:782-787.
28. Varon, M., N. Fuchs, M. Monosov, S. Tolchinsky and E. Rosenberg, 1992. Mutation and mapping of genes involved in production of the antibiotic TA in Myxococcus xanthus. Antimicrob. Agents Chemother., 36:2316-2321.
29. Wawrik, B., L. Kerkhof, G. J. Zylstra and J. J. Kukor, 2005. Identification of unique type 2 polyketide synthase genes in soil. Applied Environ. Microbiol., 71:2232-2238.
30. Weimg, S., H. J. Hecht, T. Mahmud and R. Muller, 2003. Melithiazol biosynthesis: Further insights into myxobacterial PKS/NRPS systems and evidence for a new subclass of methyl transferases. Chem. Biol., 10:939-952.
31. Weissman, K. J. and P. F. Leadlay, 2005. Combinatorial biosynthesis of reduced polyketides. Nat. Rev. Microbiol., 3:925-936.
32. Whitman, W. B., D. C. Coleman and W. J. Wiebe, 1998. Prokaryotes: The unseen majority. Proc. Nat. Acad Sci. USA., 95:6578-6583.
33. Xue, Y., L. Zhao, H. W. Liu and D. H. Sherman, 1998. A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: Architecture of metabolic diversity. Proc. Natl. Acad Sci. USA., 95:12111-12116.
34. Yeates, C., M. R. Gillings, A. D. Davison, N. Altavilla and D. A. Veal, 1998. Methods for microbial DNA extraction from soil for PCR amplification. Biol. Proceed. Online, 1:40-47.