In silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes

J Bacteriol. 2014 Jan;196(2):325-36. doi: 10.1128/JB.00806-13. Epub 2013 Nov 1.


The small RNAs CsrB and CsrC of Salmonella indirectly control the expression of numerous genes encoding widespread cellular functions, including virulence. The expression of csrB and csrC genes, which are located in different chromosomal regions, is coordinated by positive transcriptional control mediated by the two-component regulatory system BarA/SirA. Here, we identified by computational analysis an 18-bp inverted repeat (IR) sequence located far upstream from the promoter of Salmonella enterica serovar Typhimurium csrB and csrC genes. Deletion analysis and site-directed mutagenesis of the csrB and csrC regulatory regions revealed that this IR sequence is required for transcriptional activation of both genes. Protein-DNA and protein-protein interaction assays showed that the response regulator SirA specifically binds to the IR sequence and provide evidence that SirA acts as a dimer. Interestingly, whereas the IR sequence was essential for the SirA-mediated expression of csrB, our results revealed that SirA controls the expression of csrC not only by binding to the IR sequence but also by an indirect mode involving the Csr system. Additional computational, biochemical, and genetic analyses demonstrated that the integration host factor (IHF) global regulator positively controls the expression of csrB, but not of csrC, by interacting with a sequence located between the promoter and the SirA-binding site. These findings contribute to the better understanding of the regulatory mechanism controlling the expression of CsrB and CsrC.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism
  • Computational Biology
  • DNA Mutational Analysis
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • Gene Expression Regulation, Bacterial*
  • Genes, Bacterial*
  • Mutagenesis, Site-Directed
  • Protein Binding
  • Protein Multimerization
  • RNA, Small Untranslated / biosynthesis*
  • RNA, Small Untranslated / genetics
  • Regulatory Elements, Transcriptional*
  • Salmonella typhimurium / genetics*
  • Sequence Deletion
  • Trans-Activators / metabolism


  • Bacterial Proteins
  • DNA, Bacterial
  • RNA, Small Untranslated
  • SirA protein, Salmonella
  • Trans-Activators