title: Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element.
abstract: BACKGROUND
  Small bacterial RNAs (sRNAs) have been shown to participate in the regulation of gene expression and have been identified in numerous prokaryotic species. Some of them are involved in the regulation of virulence in pathogenic bacteria. So far, little is known about sRNAs in Bordetella, and only very few sRNAs have been identified in the genome of Bordetella pertussis, the causative agent of whooping cough.
  
  
  RESULTS
  An in silico approach was used to predict sRNAs genes in intergenic regions of the B. pertussis genome. The genome sequences of B. pertussis, Bordetella parapertussis, Bordetella bronchiseptica and Bordetella avium were compared using a Blast, and significant hits were analyzed using RNAz. Twenty-three candidate regions were obtained, including regions encoding the already documented 6S RNA, and the GCVT and FMN riboswitches. The existence of sRNAs was verified by Northern blot analyses, and transcripts were detected for 13 out of the 20 additional candidates. These new sRNAs were named Bordetella pertussis RNAs, bpr. The expression of 4 of them differed between the early, exponential and late growth phases, and one of them, bprJ2, was found to be under the control of BvgA/BvgS two-component regulatory system of Bordetella virulence. A phylogenetic study of the bprJ sequence revealed a novel, so far undocumented repeat of ~90 bp, found in numerous copies in the Bordetella genomes and in that of other Betaproteobacteria. This repeat exhibits certain features of mobile elements.
  
  
  CONCLUSIONS
  We shown here that B. pertussis, like other pathogens, expresses sRNAs, and that the expression of one of them is controlled by the BvgA/BvgS system, similarly to most virulence genes, suggesting that it is involved in virulence of B. pertussis.
authors.affiliation: Center for Infection and Immunity of Lille, Institut Pasteur de Lille, France. david.hot@pasteur-lille.fr
authors.forename: David
authors.initials: D
authors.lastname: Hot
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Slupek
authors.forename: Bérénice
authors.initials: B
authors.lastname: Wulbrecht
authors.forename: Anthony
authors.initials: A
authors.lastname: D'Hondt
authors.forename: Christine
authors.initials: C
authors.lastname: Hubans
authors.forename: Rudy
authors.initials: R
authors.lastname: Antoine
authors.forename: Camille
authors.initials: C
authors.lastname: Locht
authors.forename: Yves
authors.initials: Y
authors.lastname: Lemoine
mesh_terms: D001483:Base Sequence; D015152:Blotting, Northern; D001886:Bordetella pertussis / Q000235:genetics* / Q000472:pathogenicity; D021901:DNA, Intergenic / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D010641:Phenotype; D012329:RNA, Bacterial / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D015203:Reproducibility of Results; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated