The core-independent promoter-specific binding of Bacillus subtilis σB

Bacillus subtilis σ(D) is an alternative σ factor that possesses a core-independent promoter -10 element binding specificity despite the lack of a distinct footprint on its cognate promoter. We wished to determine whether this property is common to alternative σ factors. To this end, we over-expressed B. subtilis σ(B) in Escherichia coli and analyzed its DNA binding ability by electrophoretic mobility shift assay and DNase I footprinting. The major complex formed by σ(B) and its cognate promoter DNA is heparin-sensitive. However, in contrast to the -10 element binding specificity observed for B. subtilis σ(D) , the promoter binding of σ(B) is specific for the -35 element. These and other results clearly demonstrate that alternative σ factors possess different promoter-binding characteristics, and make core-independent contributions to recognition of their cognate promoters.