Different requirements for σ Region 4 in BvgA activation of the Bordetella pertussis promoters P(fim3) and P(fhaB)

J Mol Biol. 2011 Jun 24;409(5):692-709. doi: 10.1016/j.jmb.2011.04.017. Epub 2011 Apr 22.


Bordetella pertussis BvgA is a global response regulator that activates virulence genes, including adhesin-encoding fim3 and fhaB. At the fhaB promoter, P(fhaB), a BvgA binding site lies immediately upstream of the -35 promoter element recognized by Region 4 of the σ subunit of RNA polymerase (RNAP). We demonstrate that σ Region 4 is required for BvgA activation of P(fhaB), a hallmark of Class II activation. In contrast, the promoter-proximal BvgA binding site at P(fim3) includes the -35 region, which is composed of a tract of cytosines that lacks specific sequence information. We demonstrate that σ Region 4 is not required for BvgA activation at P(fim3). Nonetheless, Region 4 mutations that impair its typical interactions with core and with the -35 DNA affect P(fim3) transcription. Hydroxyl radical cleavage using RNAP with σD581C-FeBABE positions Region 4 near the -35 region of P(fim3); cleavage using RNAP with α276C-FeBABE or α302C-FeBABE also positions an α subunit C-terminal domain within the -35 region, on a different helical face from the promoter-proximal BvgA~P dimer. Our results suggest that the -35 region of P(fim3) accommodates a BvgA~P dimer, an α subunit C-terminal domain, and σ Region 4. Molecular modeling suggests how BvgA, σ Region 4, and α might coexist within this DNA in a conformation that suggests a novel mechanism of activation.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Binding Sites
  • Bordetella pertussis / genetics*
  • DNA, Bacterial / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Hydroxyl Radical / metabolism
  • Molecular Sequence Data
  • Mutation
  • Promoter Regions, Genetic*
  • Sequence Homology, Amino Acid
  • Sequence Homology, Nucleic Acid
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Transcription, Genetic / genetics


  • Bacterial Proteins
  • BvgA protein, Bacteria
  • DNA, Bacterial
  • Transcription Factors
  • Hydroxyl Radical
  • DNA-Directed RNA Polymerases