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

Abstract

The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli. The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS ("sensitive" genes), and genes whose expression changes very little with the production of a little RpoS ("insensitive"). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS. IMPORTANCEThe sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli. Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses. KEYWORDS RpoS, promoters, S , stress response, transcriptional regulation, transcriptome G enome-wide measurements of RNA levels have revolutionized our understanding of how cells organize their patterns of transcription. These studies have given us snapshots of how patterns of gene expression change in response to changes in the external environment. They have also allowed us to define the regulons controlled by specific transcription factors (TFs). A major weakness of the vast majority of these

Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase

“…It is possible that the promoter of RSP_3095 can only be activated at optimal protein levels of this sigma factor, a phenomenon that also affects regulation by RpoS in E . coli (Wong et al ., ). Another possibility is the cotranscription of RSP_3094, encoding a predicted trans‐membrane anti‐sigma factor, which is likely in the same operon as RSP_3095, along with two other genes of unknown function, RSP_3093 and RSP_3092.…”

“…In contrast, in both the knockdown and constitutive expression strains, the promoter activity remained low, suggesting that the presence of this protein is somehow important for the activity of the promoter. It is possible that the promoter of RSP_3095 can only be activated at optimal protein levels of this sigma factor, a phenomenon that also affects regulation by RpoS in E. coli (Wong et al, 2017). Another possibility is the cotranscription of RSP_3094, encoding a predicted trans-membrane anti-sigma factor, which is likely in the same operon as RSP_3095, along with two other genes of unknown function, RSP_3093 and RSP_3092.…”

Experimental Evolution of Escherichia coli K-12 at High pH and with RpoS Induction

“…The high-pH-evolved isolates showed a striking pattern of point mutations in the RpoS stress sigma factor, whose fitness contributions remain unclear. RpoS is required for survival at extremely high pH (pH 9.8) (15), and it mediates regulation of base resistance proteins (10,13). This connection may be related to the fact that the pH rises during culture growth to stationary phase in unbuffered tryptone-yeast extract medium Fig.…”

“…Another way that E. coli acclimates to pH stress is by inducing the global stress sigma factor rpoS, which regulates ϳ500 stress-associated genes and 1,044 genes in total (12,13). RpoS is expressed at high levels under a variety of stress conditions, such as nutrient starvation associated with stationary phase (14), as well as during exponential phase if the cells face other external stresses such as temperature shock, osmotic stress, or acid stress (12).…”

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

“…The specific nature of the starvation (i.e., the type of nutrient that has become limiting for growth) and the time spent under nutrient limiting conditions affect the accumulation of these modulators of transcription, presumably allowing cells to target their stress response to best compensate for the shortage of particular metabolites. 58,67-70 Similarly, we reckon that tRNA degradation may only be beneficial during exposure to a subset of the possible stressors a bacterium may encounter. In our study 14 (as in most other studies on the stringent response, reviewed in refs.…”