Genome-Wide Analysis of the General Stress Response Network inEscherichia coli: σ^S-Dependent Genes, Promoters, and Sigma Factor Selectivity

Abstract

The S (or RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli. While nearly absent in rapidly growing cells, S is strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of the E. coli genes are under direct or indirect control of S and that S should be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a S consensus promoter in silico. Moreover, our results suggest that S -dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect S and/or 70 selectivity of many promoters. These observations indicate that certain modules of the S -dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with 70 RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.The general stress sigma factor S (or RpoS) is strongly induced when Escherichia coli cells are exposed to various stress conditions, which include starvation, hyperosmolarity, pH downshift, or nonoptimal high or low temperature (for a review of S regulation, see reference 24). By standard genetic and molecular biology methods, more than 80 S -controlled genes have been identified to date, indicating that S is the master regulator of a rather large regulon which represents the genetic basis of the E. coli general stress response (for summaries, see references 23 and 41).In their regulatory patterns, many S -controlled genes just follow the cellular S level; i.e., they are activated whenever S and therefore S -containing RNA polymerase (E S ) accumulate in the cell. Other S -dependent genes, however, exhibit highly specific regulation, with a narrow window of expression only under some sort of stress condition. The best-studied example of this type of S -controlled gene is the csiD gene, which is mainly induced by carbon starvation because the cyclic AMP (cAMP)-cAMP receptor protein (CRP) acts as an essential activator for S -containing RNA polymerase at the csiD promoter (21,46,49). Also, the leucine-responsive regulatory protein (Lrp) is involved in the regulation of certain S -dependent genes (9,13,33,64). These findings indicate that the S -containing RNA polymerase holoenzyme has the ability to cooperate with additional regulatory factors, just as the vegetative RNA polymerase containing 70 does. ...

Elevated levels of σ S inhibit biofilm formation in Escherichia coli: a role for the Rcs phosphorelay

“…For example, different deletion mutations in rpoS have been reported to have opposite effects on the ability of cells to attach to surfaces (Adams & McLean, 1999;CoronaIzquierdo & Membrillo-Hernandez, 2002). However, given that cells are likely to be exposed to a variety of stresses during the development of a biofilm and s S has been shown to regulate the expression of many genes encoding proteins involved in biofilm formation, an important role for s S in biofilm formation would not be surprising (Bougdour et al, 2008;Hengge, 2008;Patten et al, 2004;Weber et al, 2005). In our genetic background, the introduction of the rpoS : : Km allele negatively affected biofilm formation which explains why rpoS was not picked up in our screen.…”

“…Consistent with this role, the Rcs phosphorelay has been shown to regulate the general stress response-associated sigma factor, s S , through the activation of RprA, a small non-coding RNA that positively controls the level of s S in the cell by base-pairing with the 59 end of the rpoS mRNA (Majdalani et al, 2001(Majdalani et al, , 2002. s S is involved in the adaptation of the bacteria to starvation, hyperosmotic shock, pH downshift and low temperature, and controls many genes during the transition from the exponential to the stationary phase of growth (Patten et al, 2004;Weber et al, 2005;White-Ziegler et al, 2008). Recent studies have reported that s S influences global gene expression and protein production within E. coli biofilms, suggesting that this alternative sigma factor may have an important function during biofilm formation (Collet et al, 2008;Ito et al, 2009).…”

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

“…The E. coli K12 MG1655 genome and gene coordinate annotations were downloaded from the KEGG database 55 . A list of 140 genes regulated by RpoS were obtained from Weber et al 38 . RNA-seq data for stationary and mid-exponential phase 40 were generated in our lab as reported previously and RPKM 56 values obtained from this were used.…”

Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

“…4), we have allowed the cells to regularly reach an extended stationary phase, which is typically characterized by an extreme growth arrest, depletion of the carbon source, amino acid and oxygen limitations, pH shifts, secondary metabolite production, and profound gene expression changes (Kolter et al 1993). Under such conditions, many Proteobacteria strongly upregulate the rpoSencoded general stress response sigma factor σ S , which is known to control the transcription of up to 10 % of the genome (Weber et al 2005) and to play a key role in the adaptation to new environments. A further observation is that previous reports have implicated σ S in the regulation of transcription from the Tn4652 transposase promoter of Pseudomonas putida (Ilves et al 2001) and in stress-induced transposition-mediated deletions in E. coli (Gomez-Gomez et al 1997).…”