Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase

Abstract

The sigma(S) (RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli and related bacteria. While rapidly growing cells contain very little sigma(S), exposure to many different stress conditions results in rapid and strong sigma(S) induction. Consequently, transcription of numerous sigma(S)-dependent genes is activated, many of which encode gene products with stress-protective functions. Multiple signal integration in the control of the cellular sigma(S) level is achieved by rpoS transcriptional and translational control as well as by regulated sigma(S) proteolysis, with various stress conditions differentially affecting these levels of sigma(S) control. Thus, a reduced growth rate results in increased rpoS transcription whereas high osmolarity, low temperature, acidic pH, and some late-log-phase signals stimulate the translation of already present rpoS mRNA. In addition, carbon starvation, high osmolarity, acidic pH, and high temperature result in stabilization of sigma(S), which, under nonstress conditions, is degraded with a half-life of one to several minutes. Important cis-regulatory determinants as well as trans-acting regulatory factors involved at all levels of sigma(S) regulation have been identified. rpoS translation is controlled by several proteins (Hfq and HU) and small regulatory RNAs that probably affect the secondary structure of rpoS mRNA. For sigma(S) proteolysis, the response regulator RssB is essential. RssB is a specific direct sigma(S) recognition factor, whose affinity for sigma(S) is modulated by phosphorylation of its receiver domain. RssB delivers sigma(S) to the ClpXP protease, where sigma(S) is unfolded and completely degraded. This review summarizes our current knowledge about the molecular functions and interactions of these components and tries to establish a framework for further research on the mode of multiple signal input into this complex regulatory system.

FIG. 1.

Various levels of σ^S regulation are differentially affected by various stress conditions. An increase of the cellular σ^S level can be obtained either by stimulating σ^S synthesis at the levels of rpoS transcription or rpoS mRNA translation or by inhibiting σ^S proteolysis (which under nonstress conditions is extraordinarily rapid). The most rapid and strongest reaction can be achieved by a combination of these processes (as observed, e.g., on hyperosmotic or pH shifts). For further details, see the text.

FIG. 2.

Transcriptional control regions upstream of the rpoS gene. (A) The nlpD-rpoS operon is located at 61.76 min on the E. coli chromosome, where it is trancribed in counterclockwise direction. (B) The operon promoters (nlpDp1 and nlpDp2) contribute to basal expression of rpoS but are not regulated by growth rate or growth phase (115). (C) The major rpoS promoter (rpoSp) is located within the nlpD gene, is flanked by two putative cAMP-CRP binding sites (CRP box I and II), and is subject to stationary-phase induction when cells are grown on rich medium (112). Broken lines in panel A indicate the relative positions of the sequences shown in panels B and C.

FIG. 3.

The rpoS translational control network. rpoS mRNA is thought to occur in at least two different conformations, one being a more closed structure with the translation initiation region base paired to an upstream internal antisense element, and the other being a more open and translationally competent structure. The translation-stimulating factors Hfq, HU, and DsrA RNA can bind to rpoS mRNA (indicated by broken heavy lines) and together probably drive it into the translationally competent structure. The other components shown are likely to act more indirectly (for further details, see the text).

FIG. 4.

Role of RssB-ClpXP and putative signal input in the σ^S recognition and degradation pathway. The response regulator RssB is an essential, specific, and direct σ^S recognition factor. RssB delivers σ^S to the ClpXP protease, where σ^S is unfolded and completely degraded whereas RssB is released. σ^S binding requires RssB phosphorylation, but it is unclear whether the catalytic cycle of RssB involves obligatory dephosphorylation during release and subsequent rephosphorylation. Stress signals may affect (i) the phosphorylation of RssB and therefore RssB-σ^S complex formation; (ii) the cellular level of RssB (which in growing cells is rate limiting for σ^S proteolysis); (iii) the synthesis of σ^S such that RssB becomes titrated on σ^S overproduction; (iv) σ^S association with RNA polymerase core enzyme, which protects against binding by RssB; and (v) the function of the ClpXP protease itself (see the text for details). However, the molecular details of the stress signal input pathways involved are still largely unknown.