Definition of the σW Regulon of Bacillus subtilis in the Absence of Stress

Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that activate the different ECF sigma factors. Here we have employed tiling arrays to single out the ECF sigma(W) regulon of the Gram-positive bacterium Bacillus subtilis from the overlapping ECF sigma(X), sigma(Y), and sigma(M) regulons. For this purpose, we profiled the transcriptome of a B. subtilis sigW mutant under non-stress conditions to select candidate genes that are strictly sigma(W)-regulated. Under these conditions, sigma(W) exhibits a basal level of activity. Subsequently, we verified the sigma(W)-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental B. subtilis strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of rasP or prsW mutant strains that lack the proteases involved in the degradation of the sigma(W) anti-sigma factor RsiW and subsequent activation of the sigma(W)-regulon. Taken together, our studies identify 89 genes as being strictly sigma(W)-regulated, including several genes for non-coding RNAs. The effects of rasP or prsW mutations on the expression of sigma(W)-dependent genes were relatively mild, which implies that sigma(W)-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of rasP mutant cells, which have defects in competence development, protein secretion and membrane protein production, is not mirrored in the transcript profile of these cells. This implies that RasP is not only important for transcriptional regulation via sigma(W), but that this membrane protease also exerts other important post-transcriptional regulatory functions.