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

Abstract

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.

Impact of high salinity and the compatible solute glycine betaine on gene expression of Bacillus subtilis

“…SigI, which is mainly involved in cell wall metabolism, also directly promotes transcription of genes subject to regulation by the Fur repressor (Baichoo et al ., 2002), namely the dhbACEBF and ykuNOP operons (Ramaniuk et al ., 2018), which were more than 10‐fold induced during growth in high‐salinity medium. Under these conditions, cells apparently experience severe iron limitation, leading to the induction of the Fur regulon (Hoffmann et al ., 2002; Steil et al ., 2003), of which 30 genes were significantly upregulated in B. subtilis BSB1 grown at high versus low salinity (Fig.…”

A regulatory pathway that selectively up-regulates elongasome function in the absence of class A PBPs

“…Next, we sought to identify the σ I -dependent genes important for survival in the absence of aPBPs. Of the genes directly regulated by σ I ( Ramaniuk et al, 2018 ), five ( mreBH , lytE , gsiB , fabI and bcrC) have known or likely roles related to cell envelope functions. GsiB is a general stress response protein ( Michna et al, 2016 ) and FabI is involved in fatty acid synthesis ( Heath et al, 2000 ).…”

Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex

“…The alternative σ I and anti-σ I (i.e. SigI and RsgI) were first discovered in Bacillus subtilis as related to the heat-shock response (11) and they are found widely in Bacilli and Clostridia of Firmicutes (12). Multiple paralogous σ I and anti-σ I pairs have been discovered in many lignocellulolytic bacteria to regulate the components of secreted multi-enzyme complexes, termed cellulosomes, by sensing the status of environmental polysaccharides (13,14).…”