Nucleotide sequences of two Bacillus subtilis promoters used by Bacillus subtilis sigma-28 RNA polymerase

RNA polymerase holoenzymes from many bacterial species share a common promoter recognition specificity since they use the same promoter sites on a variety of templates. These promoters generally include sequences homologous to the average sequences -TTGACA- and -TATAATA-, located -35 and -10 base pairs, respectively, upstream of the transcriptional state site. We have isolated a minor form of B. subtilis RNA polymerase in which the normal sigma subunit (sigma 55) is replaced by a smaller polypeptide (sigma 28) and which is highly specific for a class of promoter sites not used by the sigma 55-holoenzyme. Sequencing of two B. subtilis promoter sites used by the sigma 28-holoenzyme reveals identical sequences at -35 and -10 base pairs from the start site, which are -CTAAA- and -CCGATAT-, respectively. These results confirm that sigma subunit plays a major direct role in promoter sequence recognition, and support a model in which sigma interacts sequentially with -35 and -10 regions, respectively.