Livny J, Waldor MK: Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol. 2007, 10: 96-101.
Article
PubMed
Google Scholar
Wassarman KM, Zhang A, Storz G: Small RNAs in Escherichia coli. Trends Microbiol. 1999, 7: 37-45.
Article
PubMed
Google Scholar
Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S: Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol. 2001, 11: 941-950.
Article
PubMed
Google Scholar
Lenz DH, Miller MB, Zhu J, Kulkarni RV, Bassler BL: CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae. Mol Microbiol. 2005, 58: 1186-1202.
Article
PubMed
Google Scholar
Rivas E, Eddy SR: Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics. 2001, 2: 8-
Article
PubMed
PubMed Central
Google Scholar
Silvaggi JM, Perkins JB, Losick R: Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J Bacteriol. 2006, 188: 532-541.
Article
PubMed
PubMed Central
Google Scholar
Afonyushkin T, Vecerek B, Moll I, Bläsi U, Kaberdin VR: Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Res. 2005, 33: 1678-1689.
Article
PubMed
PubMed Central
Google Scholar
Babitzke P, Romeo T: CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr Opin Microbiol. 2007, 10: 156-163.
Article
PubMed
Google Scholar
Heeb S, Blumer C, Haas D: Regulatory RNA as mediator in GacA/RsmA-dependent global control of exoproduct formation in Pseudomonas fluorescens CHA0. J Bacteriol. 2002, 184: 1046-1056.
Article
PubMed
PubMed Central
Google Scholar
Kay E, Dubuis C, Haas D: Three small RNAs jointly ensure secondary metabolism and biocontrol in Pseudomonas fluorescens CHA0. Proc Natl Acad Sci USA. 2005, 102: 17136-17141.
Article
PubMed
PubMed Central
Google Scholar
Valverde C, Heeb S, Keel C, Haas D: RsmY, a small regulatory RNA, is required in concert with RsmZ for GacA-dependent expression of biocontrol traits in Pseudomonas fluorescens CHA0. Mol Microbiol. 2003, 50: 1361-1379.
Article
PubMed
Google Scholar
Aarons S, Abbas A, Adams C, Fenton A, O'Gara F: A regulatory RNA (PrrB RNA) modulates expression of secondary metabolite genes in Pseudomonas fluorescens F113. J Bacteriol. 2000, 182: 3913-3919.
Article
PubMed
PubMed Central
Google Scholar
Reimmann C, Valverde C, Kay E, Haas D: Posttranscriptional repression of GacS/GacA-controlled genes by the RNA-binding protein RsmE acting together with RsmA in the biocontrol strain Pseudomonas fluorescens CHA0. J Bacteriol. 2005, 187: 276-285.
Article
PubMed
PubMed Central
Google Scholar
Heeb S, Valverde C, Gigot-Bonnefoy C, Haas D: Role of the stress sigma factor RpoS in GacA/RsmA-controlled secondary metabolism and resistance to oxidative stress in Pseudomonas fluorescens CHA0. FEMS Microbiol Lett. 2005, 243: 251-258.
Article
PubMed
Google Scholar
Haas D, Défago G: Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol. 2005, 3: 307-319.
Article
PubMed
Google Scholar
Kay E, Humair B, Dénervaud V, Riedel K, Spahr S, Eberl L, Valverde C, Haas D: Two GacA-dependent small RNAs modulate the quorum-sensing response in Pseudomonas aeruginosa. J Bacteriol. 2006, 188: 6026-6033.
Article
PubMed
PubMed Central
Google Scholar
Reimmann C, Beyeler M, Latifi A, Winteler H, Foglino M, Lazdunski A, Haas D: The global activator GacA of Pseudomonas aeruginosa PAO positively controls the production of the autoinducer N-butyryl-homoserine lactone and the formation of the virulence factors pyocyanin, cyanide, and lipase. Mol Microbiol. 1997, 24: 309-319.
Article
PubMed
Google Scholar
Pessi G, Williams F, Hindle Z, Heurlier K, Holden MT, Cámara M, Haas D, Williams P: The global posttranscriptional regulator RsmA modulates production of virulence determinants and N -acylhomoserine lactones in Pseudomonas aeruginosa. J Bacteriol. 2001, 183: 6676-6683.
Article
PubMed
PubMed Central
Google Scholar
Wilderman PJ, Sowa NA, FitzGerald DJ, FitzGerald PC, Gottesman S, Ochsner UA, Vasil ML: Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc Natl Acad Sci USA. 2004, 101: 9792-9797.
Article
PubMed
PubMed Central
Google Scholar
Livny J, Brencic A, Lory S, Waldor MK: Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res. 2006, 34: 3484-3493.
Article
PubMed
PubMed Central
Google Scholar
Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S: Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 2001, 15: 1637-1651.
Article
PubMed
PubMed Central
Google Scholar
Gottesman S: The small RNA regulators of Escherichia coli : roles and mechanisms. Annu Rev Microbiol. 2004, 58: 303-328.
Article
PubMed
Google Scholar
Hershberg R, Altuvia S, Margalit H: A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 2003, 31: 1813-1820.
Article
PubMed
PubMed Central
Google Scholar
Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL: Prediction of transcription terminators in bacterial genomes. J Mol Biol. 2000, 301: 27-33.
Article
PubMed
Google Scholar
Toschka HY, Struck JC, Erdmann VA: The 4.5S RNA gene from Pseudomonas aeruginosa. Nucleic Acids Res. 1989, 17: 31-36.
Article
PubMed
PubMed Central
Google Scholar
Li Z, Pandit S, Deutscher MP: 3' exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc Natl Acad Sci USA. 1998, 95: 2856-2861.
Article
PubMed
PubMed Central
Google Scholar
Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, Wagner EG: RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res. 2003, 31: 6435-6443.
Article
PubMed
PubMed Central
Google Scholar
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS: Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 2002, 30: 3141-3151.
Article
PubMed
PubMed Central
Google Scholar
Winkler WC, Cohen-Chalamish S, Breaker RR: An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci USA. 2002, 99: 15908-15913.
Article
PubMed
PubMed Central
Google Scholar
Jørgensen F, Bally M, Chapon-Hervé V, Michel G, Lazdunski A, Williams P, Stewart GS: RpoS-dependent stress tolerance in Pseudomonas aeruginosa. Microbiology. 1999, 145: 835-844.
Article
PubMed
Google Scholar
Typas A, Becker G, Hengge R: The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase. Mol Microbiol. 2007, 63: 1296-1306.
Article
PubMed
Google Scholar
Wexler M, Sargent F, Jack RL, Stanley NR, Bogsch EG, Robinson C, Berks BC, Palmer T: TatD is a cytoplasmic protein with DNase activity. No requirement for TatD family proteins in Sec-independent protein export. J Biol Chem. 2000, 275: 16717-16722.
Article
PubMed
Google Scholar
Valverde C, Lindell M, Wagner EG, Haas D: A repeated GGA motif is critical for the activity and stability of the riboregulator RsmY of Pseudomonas fluorescens. J Biol Chem. 2004, 279: 25066-25074.
Article
PubMed
Google Scholar
Heurlier K, Williams F, Heeb S, Dormond C, Pessi G, Singer D, Cámara M, Williams P, Haas D: Positive control of swarming, rhamnolipid synthesis, and lipase production by the posttranscriptional RsmA/RsmZ system in Pseudomonas aeruginosa PAO1. J Bacteriol. 2004, 186: 2936-2945.
Article
PubMed
PubMed Central
Google Scholar
Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000, 16: 276-277.
Article
PubMed
Google Scholar
Voisard C, Bull CT, Keel C, Laville J, Maurhofer M, Schnider M, Défago G, Haas D: Biocontrol of root diseases by Pseudomonas fluorescens CHA0: current concepts and experimental approaches. Molecular ecology of rhizosphere microorganisms. Edited by: O'Gara F, Dowling DN, Boesten B. 1994, Weinheim, Germany: VCH Publisher, 67-89.
Chapter
Google Scholar
Laville J, Voisard C, Keel C, Maurhofer M, Défago G, Haas D: Global control in Pseudomonas fluorescens mediating antibiotic synthesis and suppression of black root rot of tobacco. Proc Natl Acad Sci USA. 1992, 89: 1562-1566.
Article
PubMed
PubMed Central
Google Scholar
Blumer C, Heeb S, Pessi G, Haas D: Global GacA-steered control of cyanide and exoprotease production in Pseudomonas fluorescens involves specific ribosome binding sites. Proc Natl Acad Sci USA. 1999, 96: 14073-14078.
Article
PubMed
PubMed Central
Google Scholar
Sambrook J, Russell DW: Molecular cloning: A Laboratory Manual. 2001, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 3
Google Scholar
Carmi R, Carmeli S, Levy E, Gough FJ: (+)-(S)-dihydroaeruginoic acid, an inhibitor of Septoria tritici and other phytopathogenic fungi and bacteria, produced by Pseudomonas fluorescens. J Nat Prod. 1994, 57: 1200-1205.
Article
PubMed
Google Scholar
Vogel HJ, Bonner DM: Acetylornithinase of Escherichia coli : partial purification and some properties. J Biol Chem. 1956, 218: 97-106.
PubMed
Google Scholar
Del Sal G, Manfioletti G, Schneider C: A one-tube plasmid DNA mini-preparation suitable for sequencing. Nucleic Acids Res. 1988, 16: 9878-
Article
PubMed
PubMed Central
Google Scholar
Farinha MA, Kropinski AM: High efficiency electroporation of Pseudomonas aeruginosa using frozen cell suspensions. FEMS Microbiol Lett. 1990, 58: 221-225.
PubMed
Google Scholar
Schnider-Keel U, Seematter A, Maurhofer M, Blumer C, Duffy B, Gigot-Bonnefoy C, Reimmann C, Notz R, Défago G, Haas D: Autoinduction of 2,4-diacetylphloroglucinol biosynthesis in the biocontrol agent Pseudomonas fluorescens CHA0 and repression by the bacterial metabolites salicylate and pyoluteorin. J Bacteriol. 2000, 182: 1215-1225.
Article
PubMed
PubMed Central
Google Scholar
Voisard C, Rella M, Haas D: Conjugative transfer of plasmid RP1 to soil isolates of Pseudomonas fluorescens is facilitated by certain large RP1 deletions. FEMS Microbiol Lett. 1988, 55: 9-14.
Article
Google Scholar
Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M, Holmes M: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol. 2002, 4: 799-808.
Article
PubMed
Google Scholar
Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, Deboy RT, Durkin AS, Kolonay JF: The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA. 2003, 100: 10181-10186.
Article
PubMed
PubMed Central
Google Scholar
Pseudomonas fluorescens SBW25. [http://www.sanger.ac.uk/Projects/P_fluorescens]
Pseudomonas fluorescens Pf0-1. [http://genome.jgi-psf.org/finished_microbes/psefl/psefl.home.html]
Pseudomonas fluorescens Pf-5. [http://cmr.tigr.org/tigr-scripts/CMR/GenomePage.cgi?org=gpf]
Barrios H, Valderrama B, Morett E: Compilation and analysis of sigma(54)-dependent promoter sequences. Nucleic Acids Res. 1999, 27: 4305-4313.
Article
PubMed
PubMed Central
Google Scholar
Lacour S, Kolb A, Landini P: Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase. J Biol Chem. 2003, 278: 37160-37168.
Article
PubMed
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680.
Article
PubMed
PubMed Central
Google Scholar
Pseudomonas aeruginosa PAO1. [http://v2.pseudomonas.com/]
Massé E, Escorcia FE, Gottesman S: Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev. 2003, 17: 2374-2383.
Article
PubMed
PubMed Central
Google Scholar
Miller JH: Assay of β-galactosidase. Experiments in Molecular Genetics. 1972, New York: Cold Spring Harbor Laboratory Press, 352-355.
Google Scholar
Ding Y, Chan CY, Lawrence CE: Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 2004, 32: W135-141.
Article
PubMed
PubMed Central
Google Scholar