Long-chain n-acyl amino acid synthases are linked to the putative PEP-CTERM/exosortase protein-sorting system in gram-negative bacteria

Journal of Bacteriology

Volumn 193, Issue 20, 2011, Pages 5707-5715

  Craig, Jeffrey W ^a   Cherry, Marisa A ^a   Brady, Sean F ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; LONG CHAIN N ACYL AMINO ACID SYNTHASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENOME; BACTERIUM CULTURE; CHEMICAL STRUCTURE; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; METAGENOMICS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PEP CTERM EXOSORTASE SYSTEM; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN TARGETING; PROTEOBACTERIA;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; AMINO ACIDS; AMINO ACYL-TRNA SYNTHETASES; AMINOACYLTRANSFERASES; BACTERIAL PROTEINS; GRAM-NEGATIVE BACTERIA; METAGENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN TRANSPORT; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA; PROTEOBACTERIA;

EID: 80053586701     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.05426-11     Document Type: Article

References (42)

1. Audit, B., and C. A. Ouzounis. 2003. From genes to genomes: universal scale-invariant properties of microbial chromosome organisation. J. Mol. Biol. 332:617-633.
2. Belas, R., D. Bartlett, and M. Silverman. 1988. Cloning and gene replacement mutagenesis of a Pseudomonas atlantica agarase gene Appl. Environ. Microbiol. 54:30-37.
3. Brady, S. F. 2007. Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat. Protoc. 2:1297-1305.
4. Brady, S. F., C. J. Chao, and J. Clardy. 2004. Long-chain N-acyltyrosine synthases from environmental DNA. Appl. Environ. Microbiol. 70:6865-6870.
5. Brady, S. F., C. J. Chao, and J. Clardy. 2002. New natural product families from an environmental DNA (eDNA) gene cluster. J. Am. Chem. Soc. 124:9968-9969.
6. Brady, S. F., and J. Clardy. 2000. Long-chain N-acyl amino acid antibiotics isolated from heterologously expressed environmental DNA. J. Am. Chem. Soc. 122:12903-12904.
7. Brady, S. F., and J. Clardy. 2005. N-acyl derivatives of arginine and tryptophan isolated from environmental DNA expressed in Escherichia coli. Org. Lett. 7:3613-3616.
8. Brady, S. F., L. Simmons, J. H. Kim, and E. W. Schmidt. 2009. Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat. Prod. Rep. 26:1488-1503.
9. Cao, J. G., and E. A. Meighen. 1989. Purification and structural identification of an autoinducer for the luminescence system of Vibrio harveyi. J. Biol. Chem. 264:21670-21676.
10. Case, R. J., M. Labbate, and S. Kjelleberg. 2008. AHL-driven quorumsensing circuits: their frequency and function among the Proteobacteria. ISME J. 2:345-349.
11. Cheung, J., and W. A. Hendrickson. 2010. Sensor domains of two-component regulatory systems. Curr. Opin. Microbiol. 13:116-123.
12. Clardy, J., and S. F. Brady. 2007. Cyclic AMP directly activates NasP, an N-acyl amino acid antibiotic biosynthetic enzyme cloned from an uncultured beta-proteobacterium. J. Bacteriol. 189:6487-6489.
13. Craig, J. W., F.-Y. Chang, J. H. Kim, S. C. Obiajulu, and S. F. Brady. 2010. Expanding small molecule functional metagenomics through parallel screening of broad host-range cosmid environmental DNA libraries in diverse Proteobacteria. Appl. Environ. Microbiol. 76:1633-1641.
14. Delcher, A. L., K. A. Bratke, E. C. Powers, and S. L. Salzberg. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679.
15. Fukuda, H., S. Iwade, and A. Kimura. 1982. A new enzyme: long acyl aminoacylase from Pseudomonas diminuta. J. Biochem. 91:1731-1738.
16. Gao, J. L., et al. 2004. Identification of a gene required for the formation of lyso-ornithine lipid, an intermediate in the biosynthesis of ornithine-containing lipids. Mol. Microbiol. 53:1757-1770.
17. Geiger, O., N. Gonzalez-Silva, I. M. Lopez-Lara, and C. Sohlenkamp. 2010. Amino acid-containing membrane lipids in bacteria. Prog. Lipid Res. 49:46-60.
18. Haft, D. H., I. T. Paulsen, N. Ward, and J. D. Selengut. 2006. Exopolysaccharide-associated protein sorting in environmental organisms: the PEPCTERM/ EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biol. 4:29.
19. Hunter, S., et al. 2009. InterPro: the integrative protein signature database. Nucleic Acids Res. 37:D211-D215.
20. Jung, K., T. Odenbach, and M. Timmen. 2007. The quorum-sensing hybrid histidine kinase LuxN of Vibrio harveyi contains a periplasmically located N terminus. J. Bacteriol. 189:2945-2948.
21. Matsumoto, J., and S. Nagai. 1972. Amidohydrolases for N-short and long chain fatty acyl-L-amino acids from mycobacteria. J. Biochem. 72:269-279.
22. McDowall, J., and S. Hunter. 2011. InterPro protein classification. Methods Mol. Biol. 694:37-47.
23. Michael, B., J. N. Smith, S. Swift, F. Heffron, and B. M. Ahmer. 2001. SdiA of Salmonella enterica is a LuxR homolog that detects mixed microbial communities. J. Bacteriol. 183:5733-5742.
24. Patankar, A. V., and J. E. Gonzalez. 2009. Orphan LuxR regulators of quorum sensing. FEMS Microbiol. Rev. 33:739-756.
25. Pellegrini, M., E. M. Marcotte, M. J. Thompson, D. Eisenberg, and T. O. Yeates. 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U. S. A. 96:4285-4288.
26. Peypoux, F., O. Laprevote, M. Pagadoy, and J. Wallach. 2004. N-Acyl derivatives of Asn, new bacterial N-acyl D-amino acids with surfactant activity. Amino Acids 26:209-214.
27. Quaiser, A., et al. 2003. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50:563-575.
28. Quevillon, E., et al. 2005. InterProScan: protein domains identifier. Nucleic Acids Res. 33:W116-W120.
29. Reynolds, S. M., L. Kall, M. E. Riffle, J. A. Bilmes, and W. S. Noble. 2008. Transmembrane topology and signal peptide prediction using dynamic Bayesian networks. PLoS Comput. Biol. 4:e1000213.
30. Rogozin, I. B., K. S. Makarova, Y. I. Wolf, and E. V. Koonin. 2004. Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Brief Bioinform. 5:131-149.
31. Shintani, Y., H. Fukuda, N. Okamoto, K. Murata, and A. Kimura. 1984. Isolation and characterization of N-long chain acyl aminoacylase from Pseudomonas diminuta. J. Biochem. 96:637-643.
32. Smith, D., et al. 2006. Variations on a theme: diverse N-acyl homoserine lactone-mediated quorum sensing mechanisms in Gram-negative bacteria. Sci. Prog. 89:167-211.
33. Spiteller, D., K. Dettner, and W. Bolan. 2000. Gut bacteria may be involved in interactions between plants, herbivores and their predators: microbial biosynthesis of N-acylglutamine surfactants as elicitors of plant volatiles. Biol. Chem. 381:755-762.
34. Swem, L. R., D. L. Swem, N. S. Wingreen, and B. L. Bassler. 2008. Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi. Cell 134:461-473.
35. Tatusov, R. L., et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.
36. Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637.
37. Van Wagoner, R. M., and J. Clardy. 2006. FeeM, an N-acyl amino acid synthase from an uncultured soil microbe: structure, mechanism, and acyl carrier protein binding. Structure 14:1425-1435.
38. Ward, N. L., et al. 2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl. Environ. Microbiol. 75:2046-2056.
39. Winson, M. K., et al. 1995. Multiple N-acyl-L-homoserine lactone signal molecules regulate production of virulence determinants and secondary metabolites in Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U. S. A. 92:9427-9431.
40. Wolf, Y. I., I. B. Rogozin, A. S. Kondrashov, and E. V. Koonin. 2001. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11:356-372.
41. Yagi, H., G. Corzo, and T. Nakahara. 1997. N-acyl amino acid biosynthesis in marine bacterium, Deleya marina. Biochim. Biophys. Acta 1336:28-32.
42. Zheng, Y., B. P. Anton, R. J. Roberts, and S. Kasif. 2005. Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics 6:243.