RpoS and the bacterial general stress response

Abstract

SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.

Keywords: RssB; small RNAs.

Fig 1

The bacterial general stress response. (A) Multiple stresses feed into synthesis and stabilization of RpoS, the primary regulator of the E. coli GSR, and (B) RpoS regulates multiple stress response pathways. Stress resistance pathways are represented in purple, within shaded blue region, metabolic changes in gold and in blue-green, other physiological changes upon RpoS induction. Induction by any of the stresses in A can lead to many of the outcomes in B.

Fig 2

Sigma factors and RpoS structure/function. (A) Domain organization of different sigma factor groups. Examples of sigma factors belonging to each group are in parenthesis, in black for those found in E. coli and in green examples of GSR sigma factors of Bacillus subtilis (σ^B) and of α-proteobacteria (σ^ECFG). (B) Key features in RpoS-recognized promoters and the RpoS sigma factor. Consensus sequence as defined in Peano et al. (4); see text for additional references (3, 5, 6). Length of spacer, shown in pink, includes extended −10 region.

Fig 3

Translational regulation of RpoS by sRNAs. (A) Genome context of rpoS. The major rpoS promoter is located within the upstream nlpD gene, forming a 567-nucleotide 5′ UTR. Another promoter is located upstream of nlpD and drives nlpD transcription but contributes very little to the expression of rpoS. Transcriptional activators and repressors shown are those discussed in the text and noted with an asterisk in Table 1. (B) (i) Translational regulation of rpoS. Closed hairpin structure of the 5′ UTR of rpoS mRNA inhibits translation initiation. This is overcome by base-pairing of the Hfq-dependent sRNAs ArcZ, DsrA, and RprA (in turquoise), with the upper strand of the hairpin, leading to the opening of hairpin and subsequent ribosome binding and activation of translation. Negative regulation of translation by the sRNAs OxyS through Hfq titration, and by CyaR by direct base-pairing to rpoS mRNA are shown. Other sRNAs implicated in rpoS regulation are discussed briefly in the text but not shown. (ii) Inducing signals leading to sRNA transcription. See text for references and further details.

Fig 4

Regulation of RpoS proteolysis by RssB, ClpXP, and anti-adaptors. (A) Genome context for rssB, encoding an adaptor for RpoS degradation. One rssB promoter is located upstream of rssA; the other is downstream of rssA, immediately upstream of rssB. Both are controlled by RpoS and RpoD, with RpoD providing the basal level expression of RssB. (B) Activators, repressors, and inducing signals for the anti-adaptors IraM, IraP, and IraD are shown. See text for references. (C) Degradation of RpoS mediated by RssB and ClpXP and inhibition of RpoS degradation by the core RNAP and the anti-adaptors. Each of these anti-adaptors has a different interaction with RssB (not shown here), with only IraP preferring the phosphorylated form of RssB (as shown); binding of RssB to RpoS is also favored by phosphorylation.

Fig 5

Regulators of RpoS activity and roles of ppGpp for RpoS levels. (A) Regulators of RpoS activity. Direct or indirect activators of RpoS appear in turquoise and repressors in red. Crl promotes RpoS binding to the core RNAP, shown in brown, while FliZ can associate with some RpoS-dependent promoters, inhibiting their recognition by RpoS. Rsd, DksA, ppGpp, and 6S RNA inhibit RpoD activity through different mechanisms highlighted in the text, indirectly favoring RpoS. (B) Positive effects of ppGpp on RpoS levels. DksA and ppGpp induce the expression of four positive regulators of RpoS, including the anti-adaptors IraD and IraP, the sRNA DsrA, and the RNA chaperone Hfq. Increased levels of anti-adaptors protect RpoS from degradation (Fig. 4); DsrA together with its chaperone Hfq promotes the translation of rpoS mRNA (Fig. 3). RssB phosphorylation favors RpoS binding; it aids but is not required for IraP activity.

Fig 6

Input signals at different levels of RpoS regulation. High cell density or starvation for some nutrients leads to an increase in ppGpp levels, affecting multiple levels of RpoS control (Fig. 5B), by promoting transcription and translation and/or inhibiting degradation. High pH also impacts multiple levels of RpoS control. Upstream regulators for transcription of the sRNAs DsrA, ArcZ, and RprA sense multiple signals leading to RpoS translation. Anti-adaptor induction upon various stresses leads to RpoS protein stabilization. This figure combines the detailed analysis shown in parts of Fig. 3 to 5.

Fig 7

RpoS-dependent acid stress response. RpoS induces the expression of genes involved in glutamate decarboxylation (AR2 pathway), chaperones, acid and proton export, and in membrane structure. Shown are RpoS-dependent proteins with known roles and involvement in acid resistance. Regulators and other proteins whose roles are unclear are not mentioned here.

Fig 8

RpoS-dependent glutamate synthesis pathways. Glu stands for glutamate, Gln for glutamine, and Arg for arginine. GABA is γ-aminobutyric acid. In blue are proteins under RpoS control (strong evidence), in darker blue are proteins potentially under RpoS control (GltB, GltD, and SpeA; less compelling evidence). (1) The glutaminase GlsA converts glutamine into glutamate, releasing ammonia. (2) Glutamate biosynthesis pathway through GltB and GltD; these convert glutamine to glutamate and also convert the ammonia and oxoglutarate into glutamate. (3) GABA degradation pathway. GabT converts GABA into glutamate; GabD converts the products of the reaction into succinate. (4) Putrescine import and degradation pathways. The transporters Pot and PuuP import putrescine, which is further degraded by PatA and PuuABCD, leading to succinate, glutamate, and GABA production. (5) Arginine import and degradation pathways. Arginine is imported through the Art transporter and subsequently degraded into glutamate and succinate by the Ast pathway. Arginine can also be converted into putrescine by the SpeA and SpeB enzymes.