Role of the sigma factor in transcription initiation in the absence of core RNA polymerase

Sigma factors (sigmas) are bacterial transcription factors that bind core RNA polymerase (RNAP) and direct transcription initiation at cognate promoter sites. However, most of their functions have been investigated in the context of RNAP. This has made the exact function of sigma, and the importance of core RNAP in modulating sigma function, ambiguous. Here we identify a Bacillus subtilis mutant sigma(A) that is independently capable of specific binding and melting of the promoter DNA. Interestingly, specific and independent promoter binding of sigma is sufficient for the temperature- and Mg(2+)-independent melting of promoter DNA around the transcription start site, in contrast to the temperature- and Mg(2+)-dependent melting by RNAP around the promoter -10 element. Thus core RNAP is able to negatively modulate the sigma-initiated melting of the transcription start site and, by sensing the changes in temperature and Mg(2+) concentration, to regulate the efficiency of promoter -10 melting.