The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity

Nucleic Acids Res. 2012 Jun;40(11):4783-93. doi: 10.1093/nar/gks055. Epub 2012 Feb 9.

Abstract

FliZ, a global regulatory protein under the control of the flagellar master regulator FlhDC, was shown to antagonize σ(S)-dependent gene expression in Escherichia coli. Thereby it plays a pivotal role in the decision between alternative life-styles, i.e. FlhDC-controlled flagellum-based motility or σ(S)-dependent curli fimbriae-mediated adhesion and biofilm formation. Here, we show that FliZ is an abundant DNA-binding protein that inhibits gene expression mediated by σ(S) by recognizing operator sequences that resemble the -10 region of σ(S)-dependent promoters. FliZ does so with a structural element that is similar to region 3.0 of σ(S). Within this element, R108 in FliZ corresponds to K173 in σ(S), which contacts a conserved cytosine at the -13 promoter position that is specific for σ(S)-dependent promoters. R108 as well as C(-13) are also crucial for DNA binding by FliZ. However, while a number of FliZ binding sites correspond to known σ(S)-dependent promoters, promoter activity is not a prerequisite for FliZ binding and repressor function. Thus, we demonstrate that FliZ also feedback-controls flagellar gene expression by binding to a site in the flhDC control region that shows similarity only to a -10 element of a σ(S)-dependent promoter, but does not function as a promoter.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / antagonists & inhibitors
  • Bacterial Proteins / metabolism*
  • Binding Sites
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism*
  • DNA-Directed RNA Polymerases / antagonists & inhibitors
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / growth & development
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial*
  • Operon
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Structure, Secondary
  • Repressor Proteins / chemistry
  • Repressor Proteins / metabolism*
  • Sigma Factor / antagonists & inhibitors
  • Sigma Factor / metabolism*

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Escherichia coli Proteins
  • FliZ protein, E coli
  • Repressor Proteins
  • Sigma Factor
  • sigma factor KatF protein, Bacteria
  • DNA-Directed RNA Polymerases