Investigating the DNA-Binding Site for VirB, a Key Transcriptional Regulator of Shigella Virulence Genes, Using an In Vivo Binding Tool

Genes (Basel). 2019 Feb 15;10(2):149. doi: 10.3390/genes10020149.


The transcriptional anti-silencing and DNA-binding protein, VirB, is essential for the virulence of Shigella species and, yet, sequences required for VirB-DNA binding are poorly understood. While a 7-8 bp VirB-binding site has been proposed, it was derived from studies at a single VirB-dependent promoter, icsB. Our previous in vivo studies at a different VirB-dependent promoter, icsP, found that the proposed VirB-binding site was insufficient for regulation. Instead, the required site was found to be organized as a near-perfect inverted repeat separated by a single nucleotide spacer. Thus, the proposed 7-8 bp VirB-binding site needed to be re-evaluated. Here, we engineer and validate a molecular tool to capture protein-DNA binding interactions in vivo. Our data show that a sequence organized as a near-perfect inverted repeat is required for VirB-DNA binding interactions in vivo at both the icsB and icsP promoters. Furthermore, the previously proposed VirB-binding site and multiple sites found as a result of its description (i.e., sites located at the virB, virF, spa15, and virA promoters) are not sufficient for VirB to bind in vivo using this tool. The implications of these findings are discussed.

Keywords: DNA-binding site; Shigella; VirB; anti-silencing; in vivo binding; transcription; virulence.

Publication types

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

MeSH terms

  • Bacterial Proteins / genetics*
  • Binding Sites
  • DNA-Binding Proteins / genetics
  • Dysentery, Bacillary / genetics*
  • Dysentery, Bacillary / microbiology
  • Gene Expression Regulation, Bacterial / genetics
  • Molecular Chaperones / genetics
  • Promoter Regions, Genetic
  • Protein Domains / genetics
  • Shigella flexneri / genetics*
  • Shigella flexneri / pathogenicity
  • Transcription Factors / genetics
  • Transcription, Genetic*
  • Virulence Factors / genetics


  • Bacterial Proteins
  • DNA-Binding Proteins
  • Molecular Chaperones
  • Spa15 protein, Shigella flexneri
  • Transcription Factors
  • VirA protein, Shigella flexneri
  • Virulence Factors
  • virG protein, Shigella flexneri