Evolution of secondary metabolite genes in three closely related marine actinomycete species

Applied and Environmental Microbiology

Volumn 77, Issue 20, 2011, Pages 7261-7270

  Freel, Kelle C ^a   Nam, Sang Jip ^a   Fenical, William ^a   Jensen, Paul R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL SPECIES; BIOSYNTHETIC GENE; COMPLEX PROCESSES; GEOGRAPHIC ISOLATION; KETOSYNTHASE; MARINE ACTINOMYCETE; PACIFICA; PHYLOGENETIC RELATIONSHIPS; RELATED COMPOUNDS; SECONDARY METABOLISM; SECONDARY METABOLITES; STAUROSPORINES;

BIOCHEMISTRY; BIOMOLECULES; BIOSYNTHESIS; GENES; METABOLISM; METABOLITES; PLANTS (BOTANY);

BACTERIA;

ALKALOID; BACTERIAL DNA; BACTERIAL PROTEIN; LACTONE; RIBOSOME DNA; RNA 16S; SEA WATER;

ALLELE; BACTERIUM; ENZYME ACTIVITY; GENE EXPRESSION; HERITABILITY; MARINE ENVIRONMENT; PHYLOGENETICS; PHYLOGENY; RECOMBINATION; SECONDARY METABOLITE;

ARTICLE; BACTERIAL GENE; BIOSYNTHESIS; CHEMISTRY; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MICROMONOSPORACEAE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ALKALOIDS; BACTERIAL PROTEINS; BIOSYNTHETIC PATHWAYS; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, BACTERIAL; LACTONES; MICROMONOSPORACEAE; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 82955206440     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.05943-11     Document Type: Article

References (36)

1. Berdy, J. 2005. Bioactive microbial metabolites. A personal view. J. Antibiot. 58:1-26.
2. Challis, G. L., and D. A. Hopwood. 2003. Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc. Natl. Acad. Sci. USA 100:14555-14561.
3. Davies, J. 2006. Are antibiotics naturally antibiotics? J. Ind. Microbiol. Biotechnol. 33:496-499.
4. Donadio, S., M. Staver, J. McAlpine, S. Swanson, and L. Katz. 1991. Modular organization of genes required for complex polyketide biosynthesis. Science 252:675-679.
5. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
6. Eustáquio, A. S., et al. 2009. Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-L-methionine. Proc. Natl. Acad. Sci. U.S.A. 106:12295-12300.
7. Eustáquio, A. S., et al. 2011. The discovery of salinosporamide K from the marine bacterium "Salinispora pacifica" by genome mining gives insight into pathway evolution. Chembiochem. 12:61-64.
8. Eustáquio, A. S., F. Pojer, J. P. Noe, and B. S. Moore. 2008. Discovery and characterization of a marine bacterial SAM-dependent chlorinase. Nat. Chem. Biol. 4:69-74.
9. Feling, R. H., et al. 2003. Salinosporamide A: a highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora. Angew. Chem. Int. Ed. Engl. 42:355-357.
10. Fenical, W., et al. 2009. Discovery and development of the anticancer agent salinosporamide A (NPI-0052). Bioorg. Med. Chem. 17:2175-2180.
11. Fischbach, M. A., and C. T. Walsh. 2006. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem. Rev. 106:3468-3496.
12. Fischbach, M. A., C. T. Walsh, and J. Clardy. 2008. The evolution of gene collectives: how natural selection drives chemical innovation. Proc. Natl. Acad. Sci. U.S.A. 105:4601-4608.
13. Furusaki, A., et al. 1978. X-ray crystal structure of staurosporine: a new alkaloid from a Streptomyces strain. J. Chem. Soc. Chem. Commun. 1978: 800-801.
14. Gontang, E., S. Gaudíncio, W. Fenical, and P. Jensen. 2010. Sequence-based analysis of secondary-metabolite biosynthesis in marine actinobacteria. Appl. Environ. Microbiol. 76:2487-2499.
15. Gontang, E. A., W. Fenical, and P. R. Jensen. 2007. Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl. Environ. Microbiol. 73:3272-3282.
16. Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
17. Jenke-Kodama, H., R. Muller, and E. Dittmann. 2008. Evolutionary mechanisms underlying secondary metabolite diversity. Prog. Drug Res. 65:119, 121-140.
18. Jenke-Kodama, H., A. Sandmann, R. Muller, and E. Dittmann. 2005. Evolutionary implications of bacterial polyketide synthases. Mol. Biol. Evol. 22:2027-2039.
19. Jensen, P. R., and C. Mafnas. 2006. Biogeography of the marine actinomycete Salinispora. Environ. Microbiol. 8:1881-1888.
20. Jensen, P. R., P. G. Williams, D. C. Oh, L. Zeigler, and W. Fenical. 2007. Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl. Environ. Microbiol. 73:1146-1152.
21. Kurosawa, K., et al. 2008. Rhodostreptomycins, antibiotics biosynthesized following horizontal gene transfer from Streptomyces padanus to Rhodococcus fascians. J. Am. Chem. Soc. 130:1126-1127.
22. Larsen, T. O., J. Smedsgaard, K. F. Nielsen, M. E. Hansen, and J. C. Frisvad. 2005. Phenotypic taxonomy and metabolite profiling in microbial drug discovery. Nat. Prod. Rep. 22:672-695.
23. Lopez, J. 2003. Naturally mosaic operons for secondary metabolite biosynthesis: variability and putative horizontal transfer of discrete catalytic domains of the epothilone polyketide synthase locus. Mol. Genet. Genomics 270:420-431.
24. Maldonado, L. A., et al. 2005. Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae. Int. J. Syst. Evol. Microbiol. 55:1759-1766.
25. Medema, M. H., et al. 2010. The sequence of a 1.8-Mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol. Evol. 2:212-224.
26. Metsa-Ketela, M., et al. 2002. Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various Streptomyces species. Appl. Environ. Microbiol. 68:4472-4479.
27. Mincer, T. J., W. Fenical, and P. R. Jensen. 2005. Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora. Appl. Environ. Microbiol. 71:7019-7028.
28. 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.
29. Onaka, H., S. Taniguchi, Y. Igarashi, and T. Furumai. 2002. Cloning of the staurosporine biosynthetic gene cluster from Streptomyces sp. TP-A0274 and its heterologous expression in Streptomyces lividans. J. Antibiot. 55:1063- 1071.
30. Penn, K., et al. 2009. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J. 3:1193-1203.
31. Rachid, S., et al. 2011. Mining the cinnabaramide biosynthetic pathway to generate novel proteasome inhibitors. Chembiochem. 12:922-931.
32. Stadler, M., et al. 2007. Cinnabaramides A-G: analogues of lactacystin and salinosporamide from a terrestrial streptomycete. J. Nat. Prod. 70:246-252.
33. Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods), 4.0b, 10th ed. Sinauer Associates, Sunderland, MA.
34. ++ dependent protein kinase. Biochem. Biophys. Res. Commun. 135:397- 402.
35. Udwary, D. W., et al. 2007. Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc. Natl. Acad. Sci. U. S. A. 104:10376-10381.
36. Williams, P. G., et al. 2005. New cytotoxic salinosporamides from the marine actinomycete Salinispora tropica. J. Org. Chem. 70:6196-6203.