Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2

Nucleic Acids Research

Volumn 34, Issue 12, 2006, Pages 3484-3493

  Livny, Jonathan ^a   Brencic, Anja ^b   Lory, Stephen ^b   Waldor, Matthew K ^a  

^a TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; UNTRANSLATED RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BIOLOGY; COMPUTER PROGRAM; ESCHERICHIA COLI; EVALUATION; GENETICS; GENOMICS; METHODOLOGY; PATHOGENICITY; PSEUDOMONAS AERUGINOSA; VIBRIO CHOLERAE;

COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; PSEUDOMONAS AERUGINOSA; RNA, BACTERIAL; RNA, UNTRANSLATED; SOFTWARE; VIBRIO CHOLERAE;

EID: 33746533172     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl453     Document Type: Article

References (32)

1. Dennis,P.P. and Omer,A. (2005) Small non-coding RNAs in archaea. Curr. Opin. Microbiol., 8, 685-694. (Pubitemid 41643037)
2. Gottesman,S. (2005) Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet., 21, 399-404.
3. Zhang,A., Wassarman,K.M., Rosenow,C., Tjaden,B.C., Storz,G. and Gottesman,S. (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol., 50, 1111-1124. (Pubitemid 37475847)
4. Brown,L. and Elliott,T. (1996) Efficient translation of the RpoS sigma factor in Salmonella typhimurium requires host factor I, an RNA-binding protein encoded by the hfq gene. J. Bacteriol., 178, 3763-3770. (Pubitemid 26227190)
5. Ding,Y., Davis,B.M. and Waldor,M.K. (2004) Hfq is essential for Vibrio cholerae virulence and downregulates sigma expression. Mol. Microbiol., 53, 345-354. (Pubitemid 38901403)
6. Nakao,H., Watanabe,H., Nakayama,S. and Takeda,T. (1995) yst gene expression in Yersinia enterocolitica is positively regulated by a chromosomal region that is highly homologous to Escherichia coli host factor 1 gene (hfq). Mol. Microbiol., 18, 859-865.
7. Robertson,G.T. and Roop,R.M.J. (1999) The Brucella abortus host factor I (HF-I) protein contributes to stress resistance during stationary phase and is a major determinant of virulence in mice. Mol. Microbiol., 34, 690-700.
8. Sonnleitner,E., Hagens,S., Rosenau,F., Wilhelm,S., Habel,A., Jager,K.E. and Blasi,U. (2003) Reduced virulence of a hfq mutant of Pseudomonas aeruginosa O1. Microb. Pathog., 35, 217-228. (Pubitemid 37163722)
9. Lenz,D.H., Mok,K.C., Lilley,B.N., Kulkarni,R.V., Wingreen,N.S. and Bassler,B.L. (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell, 118, 69-82. (Pubitemid 38902815)
10. Hershberg,R., Altuvia,S. and Margalit,H. (2003) A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res., 31, 1813-1820. (Pubitemid 36432687)
11. Griffiths-Jones,S., Moxon,S., Marshall,M., Khanna,A., Eddy,S.R. and Bateman,A. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124. (Pubitemid 40207843)
12. Argaman,L., Hershberg,R., Vogel,J., Bejerano,G., Wagner,E.G., Margalit,H. and Altuvia,S. (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol., 11, 941-950. (Pubitemid 32589185)
13. Chen,S., Lesnik,E.A., Hall,T.A., Sampath,R., Griffey,R.H., Ecker,D.J. and Blyn,L.B. (2002) A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems, 65, 157-177. (Pubitemid 34586776)
14. Wassarman,K.M., Repoila,F., Rosenow,C., Storz,G. and Gottesman,S. (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev., 15, 1637-1651. (Pubitemid 32702586)
15. Livny,J., Fogel,M.A., Davis,B.M. and Waldor,M.K. (2005) sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res., 33, 4096-4105. (Pubitemid 41487270)
16. Pichon,C. and Felden,B. (2005) Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc. Natl Acad. Sci. USA, 102, 14249-14254. (Pubitemid 41429684)
17. Wilderman,P.J., Sowa,N.A., FitzGerald,D.J., FitzGerald,P.C., Gottesman,S., Ochsner,U.A. and Vasil,M.L. (2004) Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc. Natl Acad. Sci. USA, 101, 9792-9797. (Pubitemid 38869315)
18. Macke,T.J., Ecker,D.J., Gutell,R.R., Gautheret,D., Case,D.A. and Sampath,R. (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res., 29, 4724-4735. (Pubitemid 33095034)
19. Ermolaeva,M.D., Khalak,H.G., White,O., Smith,H.O. and Salzberg,S.L. (2000) Prediction of transcription terminators in bacterial genomes. J. Mol. Biol., 301, 27-33.
20. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)
21. Keseler,I.M., Collado-Vides,J., Gama-Castro,S., Ingraham,J., Paley,S., Paulsen,I.T., Peralta-Gil,M. and Karp,P.D. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res., 33, D334-D337. (Pubitemid 40207890)
22. Alifano,P., Rivellini,F., Limauro,D., Bruni,C.B. and Carlomagno,M.S. (1991) A consensus motif common to all Rho-dependent prokaryotic transcription terminators. Cell, 64, 553-563. (Pubitemid 121002971)
23. Heeb,S., Heurlier,K., Valverde,C., Cámara,M., Haas,D. and Williams,P. (2004) Post-transcriptional regulation in Pseudomonas spp. via the Gac/Rsm regulatory network. In Ramos,J.L. (ed.), The Pseudomonads. Kluwer Academic/Plenum Publishers, NY,Vol. 2, pp. 239-255.
24. Valverde,C., Heeb,S., Keel,C. and Haas,D. (2003) RsmY, a small regulatory RNA, is required in concert with RsmZ for GacA-dependent expression of biocontrol traits in Pseudomonas fluorescens CHA0. Mol. Microbiol., 50, 1361-1379. (Pubitemid 37475866)
25. Heurlier,K., Williams,F., Heeb,S., Dormond,C., Pessi,G., Singer,D., Camara,M., Williams,P. and Haas,D. (2004) Positive control of swarming, rhamnolipid synthesis, and lipase production by the posttranscriptional RsmA/RsmZ system in Pseudomonas aeruginosa PAO1. J. Bacteriol., 186, 2936-2945. (Pubitemid 38609736)
26. Vogel,J., Argaman,L., Wagner,E.G. and Altuvia,S. (2004) The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr. Biol., 14, 2271-2276. (Pubitemid 40033365)
27. Davis,B.M., Quinones,M., Pratt,J., Ding,Y. and Waldor,M.K. (2005) Characterization of the small untranslated RNA RyhB and its regulon in Vibrio cholerae. J. Bacteriol., 187, 4005-4014. (Pubitemid 40827784)
28. Gopalan,V., Vioque,A. and Altman,S. (2002) RNase P: variations and uses. J. Biol. Chem., 277, 6759-6762. (Pubitemid 34953054)
29. Rivas,E., Klein,R.J., Jones,T.A. and Eddy,S.R. (2001) Computational identification of noncoding RNAs in E.coli by comparative genomics. Curr. Biol., 11, 1369-1373. (Pubitemid 32835879)
30. Withey,J.H. and Friedman,D.I. (2003) A salvage pathway for protein structures: tmRNA and trans-translation. Annu. Rev. Microbiol., 57, 101-123. (Pubitemid 37392937)
31. Rivas,E. and Eddy,S.R. (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2, 8.
32. Rhodius,V.A., Suh,W.C., Nonaka,G., West,J. and Gross,C.A. (2005) Conserved and variable functions of the sigma(E) stress response in related genomes. PLoS Biol., 4, 757-774.