Overlapping SigH and SigE sigma factor regulons in .

The sigma H (σ) and sigma E (σ) subunits of RNA polymerase belong to Group 4 of sigma factors, also called extracytoplasmic function (ECF) sigma factors. Genes of the σ regulon that are involved in heat and oxidative stress response have already been defined, whereas the genes of the σ regulon, which is involved in cell surface stress response, have not been explored until now. Using the RES167 strain and its derivative Δ with a deletion in the anti-σ gene, differential gene expression was analyzed by RNA sequencing. We found 296 upregulated and 398 downregulated genes in Δ compared to RES167. To confirm the functional link between σ and the corresponding promoters, we tested selected promoters using the two-plasmid system with uv as a reporter gene and by transcription. Analyses with RNAP+σ and RNAP+σ, which were previously shown to recognize similar promoters, proved that the σ and σ regulons significantly overlap. The σ-controlled genes were found to be involved for example in protein quality control (, , , and ), the regulation of Clp proteases (), and membrane integrity maintenance. The single-promoter analyses with σ and σ revealed that there are two groups of promoters: those which are exclusively σ-specific, and the other group of promoters, which are σ/σ-dependent. No exclusively σ-dependent promoter was detected. We defined the consensus sequences of exclusively σ-regulated promotors to be -35 GGAAt and - 10 GTT and σ/σ-regulated promoters to be -35 GGAAC and - 10 cGTT. Fifteen genes were found to belong to the σ/σ regulon. Homology modeling showed that there is a specific interaction between Met170 in σ and the nucleotides -31 and - 30 within the non-coding strand (AT or CT) of the σ-dependent promoters. In σ, Arg185 was found to interact with the nucleotides GA at the same positions in the σ-dependent promoters.