σ from Bacillus subtilis: Impact on Gene Expression and Characterization of σ-Dependent Transcription That Requires New Types of Promoters with Extended -35 and -10 Elements.

The σ sigma factor from is a σ factor associated with RNA polymerase (RNAP) that was previously implicated in adaptation of the cell to elevated temperature. Here, we provide a comprehensive characterization of this transcriptional regulator. By transcriptome sequencing (RNA-seq) of wild-type (wt) and σ-null strains at 37°C and 52°C, we identified ∼130 genes affected by the absence of σ Further analysis revealed that the majority of these genes were affected indirectly by σ The σ regulon, i.e., the genes directly regulated by σ, consists of 16 genes, of which eight (the and operons) are involved in iron metabolism. The involvement of σ in iron metabolism was confirmed phenotypically. Next, we set up an transcription system and defined and experimentally validated the promoter sequence logo that, in addition to -35 and -10 regions, also contains extended -35 and -10 motifs. Thus, σ-dependent promoters are relatively information rich in comparison with most other promoters. In summary, this study supplies information about the least-explored σ factor from the industrially important model organism In bacteria, σ factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these σ factors) is the key for understanding how bacteria cope with the changing environment and could be instrumental for biotechnologically motivated rewiring of gene expression. Here, we characterize the σ regulon from the industrially important model Gram-positive bacterium We reveal that σ affects expression of ∼130 genes, of which 16 are directly regulated by σ, including genes encoding proteins involved in iron homeostasis. Detailed analysis of promoter elements then identifies unique sequences important for σ-dependent transcription. This study thus provides a comprehensive view on this underexplored component of the transcription machinery.