Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth

Abstract

The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using literature-mined data complemented with gene expression kinetic modeling and promoter sequence analysis. This approach allowed us to identify the regulon of Bacillus subtilis sigma factor SigB of RNA polymerase (RNAP) specifically expressed during germination and outgrowth. SigB is critical for the cell’s response to general stress but is also expressed during spore germination and outgrowth, and this specific regulon is not known. This approach allowed us to (i) define a subset of the known SigB regulon controlled by SigB specifically during spore germination and outgrowth, (ii) identify the influence of the promoter sequence binding motif organization on the expression of the SigB-regulated genes, and (iii) suggest additional sigma factors co-controlling other SigB-dependent genes. Experiments then validated promoter sequence characteristics necessary for direct RNAP–SigB binding. In summary, this work documents the potential of computational approaches to unravel new information even for a well-studied system; moreover, the study specifically identifies the subset of the SigB regulon, which is activated during germination and outgrowth.

Arabidopsis thaliana induces multigenerational stress tolerance against biotic and abiotic stressors and memorization of host colonization in Bacillus subtilis

“…However, 278 genes were still differentially expressed in the descendants of pre-exposed bacteria, and many of them belonged to either the general stress response, or c-di-AMP signaling. Both pathways are possibly interlinked, as the diadenylate cyclase DisA is part of the general stress regulon of SigB 67 . Our hypothesis that the plant metabolites actively trigger the general stress response via altering c-di-AMP signaling is supported by our finding that plant secretions can compensate for the loss of the diadenylate cyclase CdaA by inducing DisA (in ancestors) and CdaS (in descendants).…”

Prediction and validation of novel SigB regulon members in Bacillus subtilis and regulon structure comparison to Bacillales members

“…Each promoter hit sequence was manually curated (Supplementary Table S 2 ). Different spacers were screened in this study as Vohradky et al [ 8 ] indicated that genes controlled by SigB must contain both − 35 and − 10 binding motifs in the SigB PBM, and have a spacer length of 15 to 17 bp. Additionally, the similarity of the SigB PBM to the SigB consensus (indicated by the p -value) also took the nucleotide composition of spacers into account in this study.…”

Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation

“…Sigma B (SigB) is a principal stress response sigma factor protecting cells from various stressors such as heat, oxidative, alkaline, acidic or osmotic [ 5 ]. SigB recognizes two sequences in −35 and −10 (numbering relative to the transcription start site) regions GTTTaa and GGG(A/T)A(A/T) [ 6 ]. SigB itself is regulated by a mechanism involving anti-sigma, anti-anti-sigma factors and phosphatases that act upstream of the “anti” factors [ 7 ].…”

“…These interactions form a regulatory network whose activity was previously modeled by a set of chemical equations and rate constants [ 9 ], which explained some of the features observed in the experimental data. A kinetic analysis of the SigB regulon was presented in our previous study [ 6 ].…”