Small Regulatory RNAs in the Enterobacterial Response to Envelope Damage and Oxidative Stress

Abstract

The ability of bacteria to thrive in diverse habitats and to adapt to ever-changing environmental conditions relies on the rapid and stringent modulation of gene expression. It has become evident in the past decade that small regulatory RNAs (sRNAs) are central components of networks controlling the bacterial responses to stress. Functioning at the posttranscriptional level, sRNAs base-pair with cognate mRNAs to alter translation, stability, or both to either repress or activate the targeted transcripts; the RNA chaperone Hfq participates in stabilizing sRNAs and in promoting pairing between target and sRNA. In particular, sRNAs act at the heart of crucial stress responses, including those dedicated to overcoming membrane damage and oxidative stress, discussed here. The bacterial cell envelope is the outermost protective barrier against the environment and thus is constantly monitored and remodeled. Here, we review the integration of sRNAs into the complex networks of several major envelope stress responses of Gram-negative bacteria, including the RpoE (σ^E), Cpx, and Rcs regulons. Oxidative stress, caused by bacterial respiratory activity or induced by toxic molecules, can lead to significant damage of cellular components. In Escherichia coli and related bacteria, sRNAs also contribute significantly to the function of the RpoS (σ^S)-dependent general stress response as well as the specific OxyR- and SoxR/S-mediated responses to oxidative damage. Their activities in gene regulation and crosstalk to other stress-induced regulons are highlighted.

FIGURE 1

Activity of sRNAs in the general stress response. (A) Together with Hfq, the sRNAs DsrA, ArcZ, and RprA activate translation of the rpoS transcript by alleviating a self-inhibitory structure within the 5′ UTR of the mRNA. The sRNA OxyS functions as an indirect, negative regulator of rpoS expression. The major alternative sigma factor RpoS governs the general stress response and controls >400 genes in E. coli and related enterobacteria, including at least four sRNAs (SdsR, SdsN, GadY, and SraL). (B) Transcription factors which are restricted to function as either activators or repressors utilize sRNAs to facilitate opposite regulation.

FIGURE 2

The role of sRNAs in the major envelope stress responses. Gram-negative bacteria are diderm, with the OM and IM being separated by the periplasmic space containing the PG cell wall. (A) OM homeostasis is regulated by the RpoE response. A series of proteolysis steps results in the degradation of the anti-sigma factor RseA and concomitant release of RpoE. The large regulon of the alternative sigma factor also comprises at least three sRNAs: MicA and RybB function to downregulate the transcripts of all major OMPs to reduce the accumulation of misfolded porins within the periplasm. MicL specifically represses translation of the lpp mRNA. (B) Maintenance of the IM relies on the CpxA-CpxR TCS, which amongst other targets controls expression of at least three sRNAs, CyaR, RprA, and CpxQ. CpxQ is a stable fragment released by RNase E processing from the 3′ end of the cpxP mRNA. In association with Hfq, CpxQ functions to repress translation of several transcripts including skp mRNA, which encodes a periplasmic chaperone promoting the mistargeting of OMPs into the IM. (C) The IM-associated histidine kinase RcsC, phosphotransfer protein RcsD, and response regulator RcsB constitute the core of the Rcs system. The sRNA RprA is one highly induced component of the Rcs response, which is activated by LPS damage and perturbations of the cell wall. While acting as a negative regulator of the csgD mRNA, RprA also promotes translation of both the rpoS and the ricI messages. As transcription of ricI (encoding an inhibitor of the conjugation machinery) is dependent on RpoS, RprA functions at the heart of a posttranscriptional feedforward loop for RicI activity.

FIGURE 3

Posttranscriptional regulation of LPS modification. The PhoQ-PhoP TCS, a major determinant of LPS modifications, is activated in response to Mg²⁺ starvation as well as by AMPs. Translation of the phoPQ bicistronic transcript is repressed by two sRNAs, MicA and GcvB. PhoQ-PhoP controls expression of MgrR, which, together with ArcZ, inhibits phosphoethanolamine (PEA) addition to the LPS oligosaccharide core by EptB. Both GcvB and MgrR are regulated at the posttranscriptional level by the sRNA SroC, which acts as a sponge and induces decay of its target sRNAs. Downregulation of lpxR mRNA by MicF decreases lipid A deacylation.

FIGURE 4

The OxyS and MicF sRNAs are integrated into the enterobacterial response to oxidative stress. OxyS, induced by the hydrogen peroxide-responsive OxyR, downregulates fhlA mRNA (encoding a transcription factor regulating formate metabolism) and indirectly represses rpoS expression. In addition, OxyS-mediated repression of nusG results in increased expression of kilR, encoded in the cryptic Rac prophage. KilR sequesters FtsZ, thereby leading to inhibition of cell division and growth arrest, which allows the cell to facilitate DNA damage repair. MicF contributes to increased bacterial resistance against antibiotics of different classes by repressing the major porin OmpF. Additional targets of MicF include lpxR mRNA (encoding an LPS modification enzyme), as well as lrp mRNA (encoding a transcriptional regulator of amino acid metabolism and transport). Expression of MicF is positively controlled by the transcription factors OmpR, MarA, Rob, and SoxS, with the last being induced in the presence of superoxide.