Control of RpoS in global gene expression of

Department of Biology, McMaster University, Life Sciences Building, Rm. 433, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
Molecular Genetics and Genomics (Impact Factor: 2.73). 11/2008; 281(1):19-33. DOI: 10.1007/s00438-008-0389-3
Source: PubMed

ABSTRACT RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli. The RpoS regulon expression has been well characterized in rich media that support fast growth and high growth yields. In contrast, though RpoS levels are high in minimal media, how RpoS functions under such conditions has not been clearly resolved. In this study, we compared the global transcriptional profiles of wild type and an rpoS mutant of E. coli grown in glucose minimal media using microarray analyses. The expression of over 200 genes was altered by loss of RpoS in exponential and stationary phases, with only 48 genes common to both conditions. The nature of the RpoS-controlled regulon in minimal media was substantially different from that expressed in rich media. Specifically, the expression of many genes encoding regulatory factors (e.g., hfq, csrA, and rpoE) and genes in metabolic pathways (e.g., lysA, lysC, and hisD) were regulated by RpoS in minimal media. In early exponential phase, protein levels of RpoS in minimal media were much higher than that in Luria-Bertani media, which may at least partly account for the observed difference in the expression of RpoS-controlled genes. Expression of genes required for flagellar function and chemotaxis was elevated in the rpoS mutant. Western blot analyses show that the flagella sigma factor FliA was expressed much higher in rpoS mutants than in WT in all phase of growth. Consistent with this, the motility of rpoS mutants was enhanced relative to WT. In conclusion, RpoS and its controlled regulators form a complex regulatory network that mediates the expression of a large regulon in minimal media.

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    • "The −35 region within the σ S promoter family is varying as well, with only a small set of σ S promoters known to be induced by osmolarity (Lee and Gralla, 2004). Many E. coli genes are under the control of both σ factors, including those for stress response (e.g., compatible solute synthesis, DNA repair or protein folding), iron acquisition or the transport, biosynthesis, and metabolism of sugars, amino acids, and fatty acids, among others (Weber et al., 2005; Dong and Schellhorn, 2009). "
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    ABSTRACT: Chromohalobacter salexigens is a halophilic γ-proteobacterium that responds to osmotic and heat stresses by accumulating ectoine and hydroxyectoine, respectively. Evolution has optimized its metabolism to support high production of ectoines. We analyzed the effect of an rpoS mutation in C. salexigens metabolism and ectoines synthesis. In long-term adapted cells, the rpoS strain was osmosensitive but not thermosensitive and showed unaltered ectoines content, suggesting that RpoS regulates ectoine(s)-independent osmoadaptive mechanisms. RpoS is involved in the regulation of C. salexigens metabolic adaptation to stress, as early steps of glucose oxidation through the Entner-Doudoroff pathway were de-regulated in the rpoS mutant, leading to improved metabolic efficiency at low salinity. Moreover, a reduced pyruvate (but not acetate) overflow was displayed by the rpoS strain at low salt, probably linked to a slowdown in gluconate production and/or subsequent metabolism. Interestingly, RpoS does not seem to be the main regulator triggering the immediate transcriptional response of ectoine synthesis to osmotic or thermal upshifts. However, it contributed to the expression of the ect genes in cells previously adapted to low or high salinity. This article is protected by copyright. All rights reserved.
    Environmental Microbiology Reports 11/2014; 7(2). DOI:10.1111/1758-2229.12249 · 3.29 Impact Factor
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    • "ppGpp bound to DksA also induces the expression of the stationary phase sigma factor (RpoS or sσ) [72], however, the induction of the RpoS regulon requires high ppGpp concentrations, namely famine conditions [56]. RpoS controls the expression of many stationary phase genes including the genes encoding transport proteins for better nutrient scavenging [73,74] and degradation of less favorable substrates [75-79] as well as genes of the oxidative stress response [56] and other genes related to general cell protection [80] (Additional file 1: Table S4). RpoS also exerts positive control on the expression of metabolic pathway genes, namely the genes of the lower and upper glycolytic pathway [56,81] and, importantly, also on acs[52,81,82] and poxB[56,81,83] (Figure 6, Additional file 1: Table S4). "
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    ABSTRACT: The proteome reflects the available cellular machinery to deal with nutrients and environmental challenges. The most common E. coli strain BL21 growing in different, commonly employed media was evaluated using a detailed quantitative proteome analysis. The presence of preformed biomass precursor molecules in rich media such as Luria Bertani supported rapid growth concomitant to acetate formation and apparently unbalanced abundances of central metabolic pathway enzymes, e.g. high levels of lower glycolytic pathway enzymes as well as pyruvate dehydrogenase, and low levels of TCA cycle and high levels of the acetate forming enzymes Pta and AckA. The proteome of cells growing exponentially in glucose-supplemented mineral salt medium was dominated by enzymes of amino acid synthesis pathways, contained more balanced abundances of central metabolic pathway enzymes, and a lower portion of ribosomal and other translational proteins. Entry into stationary phase led to a reconstruction of the bacterial proteome by increasing e.g. the portion of proteins required for scavenging rare nutrients and general cell protection. This proteomic reconstruction during entry into stationary phase was more noticeable in cells growing in rich medium as they have a greater reservoir of recyclable proteins from the translational machinery. The proteomic comparison of cells growing exponentially in different media reflected the antagonistic and competitive regulation of central metabolic pathways through the global transcriptional regulators Cra, Crp, and ArcA. For example, the proteome of cells growing exponentially in rich medium was consistent with a dominating role of phosphorylated ArcA most likely a result from limitations in reoxidizing reduced quinones in the respiratory chain under these growth conditions. The proteomic alterations of exponentially growing cells into stationary phase cells were consistent with stringent-like and stationary phase responses and a dominating control through DksA-ppGpp and RpoS.
    Microbial Cell Factories 03/2014; 13(1):45. DOI:10.1186/1475-2859-13-45 · 4.22 Impact Factor
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    • "Other proteins affecting rpoS transcript levels are LrhA and the CspC and CspE proteins. LrhA negatively regulates rpoS translation while positively affecting motility and transcription of flagellar and chemotaxis genes (Lehnen et al., 2002), which underlines the negative correlation between cellular motility and rpoS expression (Dong and Schellhorn, 2009; Dudin et al., 2013). LrhA is a transcriptional repressor of the RprA small RNA, which acts as a positive regulator for rpoS mRNA translation, thus suggesting that its regulation of rpoS might be indirect (Peterson et al., 2006). "
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    ABSTRACT: Bacterial cells often face hostile environmental conditions, to which they adapt by activation of stress responses. In Escherichia coli, environmental stresses resulting in significant reduction in growth rate stimulate the expression of the rpoS gene, encoding the alternative σ factor σ(S). The σ(S) protein associates with RNA polymerase, and through transcription of genes belonging to the rpoS regulon allows the activation of a 'general stress response', which protects the bacterial cell from harmful environmental conditions. Each step of this process is finely tuned in order to cater to the needs of the bacterial cell: in particular, selective promoter recognition by σ(S) is achieved through small deviations from a common consensus DNA sequence for both σ(S) and the housekeeping σ(70). Recognition of specific DNA elements by σ(S) is integrated with the effects of environmental signals and the interaction with regulatory proteins, in what represents a fascinating example of multifactorial regulation of gene expression. In this report, we discuss the function of the rpoS gene in the general stress response, and review the current knowledge on regulation of rpoS expression and on promoter recognition by σ(S).
    Environmental Microbiology Reports 02/2014; 6(1):1-13. DOI:10.1111/1758-2229.12112 · 3.29 Impact Factor
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