Trouble is coming: Signaling pathways that regulate general stress responses in bacteria

Abstract

Bacteria can rapidly and reversibly respond to changing environments via complex transcriptional and post-transcriptional regulatory mechanisms. Many of these adaptations are specific, with the regulatory output tailored to the inducing signal (for instance, repairing damage to cell components or improving acquisition and use of growth-limiting nutrients). However, the general stress response, activated in bacterial cells entering stationary phase or subjected to nutrient depletion or cellular damage, is unique in that its common, broad output is induced in response to many different signals. In many different bacteria, the key regulator for the general stress response is a specialized sigma factor, the promoter specificity subunit of RNA polymerase. The availability or activity of the sigma factor is regulated by complex regulatory circuits, the majority of which are post-transcriptional. In Escherichia coli, multiple small regulatory RNAs, each made in response to a different signal, positively regulate translation of the general stress response sigma factor RpoS. Stability of RpoS is regulated by multiple anti-adaptor proteins that are also synthesized in response to different signals. In this review, the modes of signaling to and levels of regulation of the E. coli general stress response are discussed. They are also used as a basis for comparison with the general stress response in other bacteria with the aim of extracting key principles that are common among different species and highlighting important unanswered questions.

Keywords: ClpXP; Escherichia coli (E. coli); Hfq protein; RNA; RNA polymerase; RpoS; anti-adaptor; general stress response; prokaryotic signal-transduction; proteolysis.

Figure 1.

Specific stress responses versus general stress responses. A, specific stress responses respond to environmental signals to change the state of the specific regulator; the set of induced and repressed genes (the regulon) includes those encoding proteins that help the cell avoid or repair damage or reduce the need for and increase import for a limiting nutrient in the case of a starvation response. B, in contrast, general stress responses are triggered by multiple different stresses, and the output is multipronged, leading to cross-resistance to stresses not used in the original induction. In all cases studied thus far, the global regulator that mediates the general stress response is a specialized sigma factor.

Figure 2.

Multiple levels of regulation affect availability of the RpoS (σ^S) general stress response sigma factor in E. coli. The major regulators of RpoS synthesis and function are outlined here. Transcription is primarily from the prpoS promoter, embedded within the upstream nlpD gene. The resulting transcript includes a long 5′ UTR, which folds back to occlude ribosome entry. sRNAs, made in response to specific signals (see Fig. 3 and text), open this structure, promoting translation. Other stress signals lead to synthesis of anti-adaptors (green shapes) that block the rapid degradation of RpoS. When levels of RpoS (yellow spheres, σ^S) rise as a consequence of these changes in regulation, RpoS combines with core RNA polymerase (blue), inducing transcription of the genes of the RpoS regulon; Crl helps to promote RpoS capture of core polymerase.

Figure 3.

Translational activation by sRNAs. In the absence of the activating sRNAs or the RNA chaperone Hfq (not shown), translation of RpoS is low, reflecting both occlusion of ribosome entry and Rho-dependent termination within the long leader. Each of the sRNAs shown has been found to pair with the upper region of the hairpin, as shown, to allow translation. The red portion of each sRNA has been predicted to pair with the rpoS 5′ UTR, although in all cases only a subset of the predicted pairs has been tested for function. ArcZ is rapidly processed to a short sRNA; only the processed form is shown here. Each sRNA is regulated at the level of transcription, by the signals and regulators shown to the left, and discussed in the text.

Figure 4.

Anti-adaptor regulation of RpoS degradation. A, three differently characterized anti-adaptors are shown in green, with their known upstream transcriptional regulators. The regulator mediating the response to DNA damage is not known. B, pathway for adaptor-mediated degradation of RpoS and anti-adaptor regulation of this process is shown. RpoS (σ^S) is shown in yellow. Adaptor RssB is shown in blue, both in phosphorylated and unphosphorylated form. The ClpXP protease is shown in gray; the details of binding of RpoS and RssB to ClpXP are not fully understood.

Figure 5.

Anti-sigmas and anti-anti–sigmas in general stress responses. On this chart, sigma factors mediating general stress responses are shown in shades of yellow and brown. Alphaproteobacteria use an ECF family sigma factor, named SigT in C. crescentus, shown here, and are referred to more generally as σ^EcfG in other alphaproteobacteria, to mediate their general stress response. RpoS (E. coli and S. oneidensis) and sigma B (in B. subtilis and some other Gram-positive bacteria) are related to the vegetative sigma factors. Blue symbols show general organization of the proteins that operate as “anti-sigmas,” although RssB, as noted, targets RpoS for proteolysis rather than simply binding it, as for other anti-sigmas. RR domains are response regulators. The PP2C domain in RssB is inactive as a phosphatase (pale blue oval). Some of the anti-anti–sigmas have sigma-like domains, providing mimics for binding to the anti-sigmas. STAS stands for sulfate transporter and anti-sigma factor antagonist domain; CrsA is also a STAS protein. PP2C domains (ovals in anti-sigmas) are also found in the upstream signaling pathways of many of these organisms (for more detail see Ref. 117). Not shown here is the signaling pathway upstream of PhyR–P, in which multiple histidine kinases converge on response regulator MrrA, which in turns transfers phosphate via PhyK to PhyR (131).