The -10 region is a key promoter specificity determinant for the Bacillus subtilis extracytoplasmic-function sigma factors sigma(X) and sigma(W).

Transcriptional selectivity derives, in large part, from the sequence-specific DNA-binding properties of the sigma subunit of RNA polymerase. There are 17 sigma factors in Bacillus subtilis which, in general, recognize distinct sets of promoters. However, some sigma factors have overlapping promoter selectivity. We hypothesize that the overlap between the regulons activated by the sigma(X) and sigma(W) factors can be explained by overlapping specificity for the -10 region: sigma(X) recognizes -10 elements with the sequence CGAC and sigma(W) recognizes CGTA, while both can potentially recognize CGTC. To test this model, we mutated the sigma(X)-specific autoregulatory site (P(X)), containing the -10 element CGAC, to either CGTC or GCTA. Conversely, the sigma(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 sigma(X) to the sigma(W) regulon or, conversely, from the sigma(W) to the sigma(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 sigma, which contacts the -10 element. However, we were unable to alter promoter selectivity by replacements of two candidate recognition residues in sigma(W).