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

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. © 2012 The Author(s).