Expanding the RpoS/σS-Network by RNA Sequencing and Identification of σS-Controlled Small RNAs in Salmonella

Abstract

The RpoS/σS sigma subunit of RNA polymerase (RNAP) controls a global adaptive response that allows many Gram-negative bacteria to survive starvation and various stresses. σS also contributes to biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). In this study, we used directional RNA-sequencing and complementary assays to explore the σS-dependent transcriptome of S. Typhimurium during late stationary phase in rich medium. This study confirms the large regulatory scope of σS and provides insights into the physiological functions of σS in Salmonella. Extensive regulation by σS of genes involved in metabolism and membrane composition, and down-regulation of the respiratory chain functions, were important features of the σS 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 σS. Importantly, the σS-controlled downstream network includes small RNAs that might endow σS with post-transcriptional regulatory functions. Of these, four (RyhB-1/RyhB-2, SdsR, SraL) were known to be controlled by σS and deletion of the sdsR locus had a competitive fitness cost in stationary phase. The σS-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 σS.

Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12

“…RpoS also drives the downregulation of genes involved in the tricarboxylic acid (TCA) cycle. These patterns of metabolic regulation are very similar to those identified in late stationary phase in Salmonella enterica (21). The only significant GO term not explicitly linked to metabolism (GO:0006970, response to osmotic stress) also includes metabolic genes, such as otsA and otsB, that are involved in trehalose biosynthesis.…”

“…Not all of the regulation is identical between E. coli and S. enterica, however. For example, Lévi-Meyrueis et al (21) noted that RpoS appears to direct switching between many pairs of isozymes, where one isozyme is expressed under conditions when RpoS is abundant and its partner isozyme is expressed when RpoS levels are low. While some pairs show a similar pattern in E. coli (such as tktA and tktB and acnA and acnB), others (such as fumA and fumC) do To determine sites where RpoS binds (and hence likely plays a direct role in transcription), we used ChIP-seq to map the association of RpoS across the E. coli chromosome during stationary-phase growth in minimal medium.…”

Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella

“…E. coli and Salmonella control the production of σ S at multiple levels (16,17), and in turn σ S controls a large regulon (66,67). Nonetheless, even though a variety of environmental stresses activate σ S production, not every of these stress conditions requires repression of plasmid transfer.…”

“…1D). Indeed, cross-comparison with a recently published list of σ S -dependent Salmonella genes (66) revealed that 22 of the 34 activated targets are regulated by σ S ; further experiments will tell which of these genes are directly regulated by σ S , RprA, or both. This notwithstanding, our study suggests that the widely conserved RprA sRNA has a more complex biological role than previously anticipated.…”

Small RNAs in Bacteria and Archaea

“…The four sRNAs OxyS, DsrA, RprA, and OxyR are induced by different TFs (Section 4.6). They, in turn, posttranscriptionally regulate s S , which, at least in Salmonella, transcriptionally controls many (possibly z40) sRNAs (Levi-Meyrueis et al, 2014). Some of the s S -dependent sRNAs, in turn, reach into other regulons.…”