Definition of the σ^W Regulon of <em>Bacillus subtilis</em> in the Absence of Stress

<div><p>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 σ^W regulon of the Gram-positive bacterium <em>Bacillus subtilis</em> from the overlapping ECF σ^X, σ^Y, and σ^M regulons. For this purpose, we profiled the transcriptome of a <em>B. subtilis sigW</em> mutant under non-stress conditions to select candidate genes that are strictly σ^W-regulated. Under these conditions, σ^W exhibits a basal level of activity. Subsequently, we verified the σ^W-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental <em>B. subtilis</em> strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of <em>rasP</em> or <em>prsW</em> mutant strains that lack the proteases involved in the degradation of the σ^W anti-sigma factor RsiW and subsequent activation of the σ^W-regulon. Taken together, our studies identify 89 genes as being strictly σ^W-regulated, including several genes for non-coding RNAs. The effects of <em>rasP</em> or <em>prsW</em> mutations on the expression of σ^W-dependent genes were relatively mild, which implies that σ^W-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of <em>rasP</em> 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 σ^W, but that this membrane protease also exerts other important post-transcriptional regulatory functions.</p>