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

Bacillussubtilis sigma(D) is an alternative sigma 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 sigma factors. To this end, we over-expressed B.subtilis sigma(B) in Escherichiacoli and analyzed its DNA binding ability by electrophoretic mobility shift assay and DNaseI footprinting. The major complex formed by sigma(B) and its cognate promoter DNA is heparin-sensitive. However, in contrast to the -10 element binding specificity observed for B.subtilis sigma(D), the promoter binding of sigma(B) is specific for the -35 element. These and other results clearly demonstrate that alternative sigma factors possess different promoter-binding characteristics, and make core-independent contributions to recognition of their cognate promoters.