VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae

Nucleic Acids Res. 2018 Sep 28;46(17):8876-8887. doi: 10.1093/nar/gky606.


The small molecule cyclic di-GMP (c-di-GMP) is known to affect bacterial gene expression in myriad ways. In Vibrio cholerae in vivo, the presence of c-di-GMP together with the response regulator VpsR results in transcription from PvpsL, a promoter of biofilm biosynthesis genes. VpsR shares homology with enhancer binding proteins that activate σ54-RNA polymerase (RNAP), but it lacks conserved residues needed to bind to σ54-RNAP and to hydrolyze adenosine triphosphate, and PvpsL transcription does not require σ54 in vivo. Consequently, the mechanism of this activation has not been clear. Using an in vitro transcription system, we demonstrate activation of PvspL in the presence of VpsR, c-di-GMP and σ70-RNAP. c-di-GMP does not significantly change the affinity of VpsR for PvpsL DNA or the DNase I footprint of VpsR on the DNA, and it is not required for VpsR to dimerize. However, DNase I and KMnO4 footprints reveal that the σ70-RNAP/VpsR/c-di-GMP complex on PvpsL adopts a different conformation from that formed by σ70-RNAP alone, with c-di-GMP or with VpsR. Our results suggest that c-di-GMP is required for VpsR to generate the specific protein-DNA architecture needed for activated transcription, a previously unrecognized role for c-di-GMP in gene expression.

Publication types

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

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / physiology*
  • Biofilms / growth & development*
  • Cyclic GMP / analogs & derivatives*
  • Cyclic GMP / physiology
  • DNA Footprinting
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / physiology*
  • DNA-Directed RNA Polymerases / metabolism
  • Enzyme Activation
  • Gene Expression Regulation, Bacterial / genetics*
  • Promoter Regions, Genetic / genetics*
  • Protein Binding
  • Sigma Factor / metabolism
  • Structure-Activity Relationship
  • Transcription Initiation, Genetic*
  • Vibrio cholerae / genetics*
  • Vibrio cholerae / metabolism


  • Bacterial Proteins
  • DNA, Bacterial
  • DNA-Binding Proteins
  • Sigma Factor
  • VpsR protein, Vibrio cholerae
  • bis(3',5')-cyclic diguanylic acid
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases
  • Cyclic GMP