Expanding the RpoS/σ^S-Network by RNA Sequencing and Identification of σ^S-Controlled Small RNAs in <i>Salmonella</i>

<div><p>The RpoS/σ^S sigma subunit of RNA polymerase (RNAP) controls a global adaptive response that allows many Gram-negative bacteria to survive starvation and various stresses. σ^S also contributes to biofilm formation and virulence of the food-borne pathogen <i>Salmonella enterica</i> serovar Typhimurium (<i>S</i>. Typhimurium). In this study, we used directional RNA-sequencing and complementary assays to explore the σ^S-dependent transcriptome of <i>S</i>. Typhimurium during late stationary phase in rich medium. This study confirms the large regulatory scope of σ^S and provides insights into the physiological functions of σ^S in <i>Salmonella</i>. Extensive regulation by σ^S of genes involved in metabolism and membrane composition, and down-regulation of the respiratory chain functions, were important features of the σ^S effects on gene transcription that might confer fitness advantages to bacterial cells and/or populations under starving conditions. As an example, we show that arginine catabolism confers a competitive fitness advantage in stationary phase. This study also provides a firm basis for future studies to address molecular mechanisms of indirect regulation of gene expression by σ^S. Importantly, the σ^S-controlled downstream network includes small RNAs that might endow σ^S with post-transcriptional regulatory functions. Of these, four (RyhB-1/RyhB-2, SdsR, SraL) were known to be controlled by σ^S and deletion of the <i>sdsR</i> locus had a competitive fitness cost in stationary phase. The σ^S-dependent control of seven additional sRNAs was confirmed in Northern experiments. These findings will inspire future studies to investigate molecular mechanisms and the physiological impact of post-transcriptional regulation by σ^S.</p>