The −10 Region Is a Key Promoter Specificity Determinant for the Bacillus subtilis Extracytoplasmic-Function ς Factors ς X and ς W

Abstract

Transcriptional selectivity derives, in large part, from the sequence-specific DNA-binding properties of the ς subunit of RNA polymerase. There are 17 ς factors in Bacillus subtilis which, in general, recognize distinct sets of promoters. However, some ς factors have overlapping promoter selectivity. We hypothesize that the overlap between the regulons activated by the ς ^X and ς ^W factors can be explained by overlapping specificity for the −10 region: ς ^X recognizes −10 elements with the sequence CGAC and ς ^W recognizes CGTA, while both can potentially recognize CGTC. To test this model, we mutated the ς ^X -specific autoregulatory site (P _X ), containing the −10 element CGAC, to either CGTC or GCTA. Conversely, the ς ^W autoregulatory site (P _W ) was altered from CGTA to CGTC or CGAC. Transcriptional analyses, both in vitro and in vivo, indicate that changes to the −10 element are sufficient to switch a promoter from the ς ^X to the ς ^W regulon or, conversely, from the ς ^W to the ς ^X regulon, but context effects clearly play an important role in determining promoter strength. It seems likely that these subtle differences in promoter selectivity derive from amino acid differences in conserved region 2 of ς, which contacts the −10 element. However, we were unable to alter promoter selectivity by replacements of two candidate recognition residues in ς ^W .