title: In silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes.
abstract: 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.
authors.affiliation: Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
authors.forename: Luary C
authors.initials: LC
authors.lastname: Martínez
authors.forename: Irma
authors.initials: I
authors.lastname: Martínez-Flores
authors.forename: Heladia
authors.initials: H
authors.lastname: Salgado
authors.forename: Marcos
authors.initials: M
authors.lastname: Fernández-Mora
authors.forename: Alejandra
authors.initials: A
authors.lastname: Medina-Rivera
authors.forename: José L
authors.initials: JL
authors.lastname: Puente
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
authors.forename: Víctor H
authors.initials: VH
authors.lastname: Bustamante
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D019295:Computational Biology; D004252:DNA Mutational Analysis; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D055503:Protein Multimerization; D058727:RNA, Small Untranslated / Q000096:biosynthesis* / Q000235:genetics; D050436:Regulatory Elements, Transcriptional; D012486:Salmonella typhimurium / Q000235:genetics*; D017384:Sequence Deletion; D015534:Trans-Activators / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D058727:RNA, Small Untranslated; C104847:SirA protein, Salmonella; D015534:Trans-Activators