Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in under Stationary Phase Stress Condition.

can regulate and fine-tune gene expression, to adapt to diverse stress conditions encountered during foodborne transmission. To further understand the contributions of alternative sigma (σ) factors to the regulation of gene expression, RNA-Seq was performed on strain 10403S and five isogenic mutants (four strains bearing in-frame null mutations in three out of four alternative σ factor genes, ΔCHL, ΔBHL, ΔBCL, and ΔBCH, and one strain bearing null mutations in all four genes, ΔBCHL), grown to stationary phase. Our data showed that 184, 35, 34, and 20 genes were positively regulated by σ, σ, σ, and σ (posterior probability > 0.9 and Fold Change (FC) > 5.0), respectively. Moreover, σ-dependent genes showed the highest FC (based on comparisons between the ΔCHL and the ΔBCHL strain), with 44 genes showing an FC > 100; only four σ-dependent, and no σ- or σ-dependent genes showed FC >100. While σ-regulated genes identified in this study are involved in stress-associated functions and metabolic pathways, σ appears to largely regulate genes involved in a few specific metabolic pathways, including positive regulation of operons encoding phosphoenolpyruvate (PEP)-dependent phosphotransferase systems (PTSs). Overall, our data show that (i) σ and σ directly and indirectly regulate genes involved in several energy metabolism-related functions; (ii) alternative σ factors are involved in complex regulatory networks and appear to have epistatic effects in stationary phase cells; and (iii) σ regulates multiple stress response pathways, while σ and σ positively regulate a smaller number of specific pathways.