Target activation by regulatory RNAs in bacteria

Abstract

Bacterial small regulatory RNAs (sRNAs) are commonly known to repress gene expression by base pairing to target mRNAs. In many cases, sRNAs base pair with and sequester mRNA ribosome-binding sites, resulting in translational repression and accelerated transcript decay. In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets. However, the mechanisms underlying activation differ substantially from repression. Base pairing resulting in target activation can involve sRNA interactions with the 5(') untranslated region (UTR), the coding sequence or the 3(') UTR of the target mRNAs. Frequently, the activities of protein factors such as cellular ribonucleases and the RNA chaperone Hfq are required for activation. Bacterial sRNAs, including those that function as activators, frequently control stress response pathways or virulence-associated functions required for immediate responses to changing environments. This review aims to summarize recent advances in knowledge regarding target mRNA activation by bacterial sRNAs, highlighting the molecular mechanisms and biological relevance of regulation.

Keywords: Hfq; RNase E; anti-antisense; degradation interference; sRNA; sponge RNA.

Graphical Abstract Figure.

This review discusses recent advances in understanding of positive regulation of gene expression by small RNAs in bacteria.

Figure 1.

Mechanisms of target activation at the 5^′ end. (A) General scheme of anti-antisense regulation for activation of mRNA translation. An mRNA with a long 5^′ UTR forms a translation-inhibitory hairpin in the absence of any sRNA activator. The sRNA forms base pairing interactions that prevent formation of the inhibitory structure, thus allowing ribosomes to access the SD sequence and initiate translation. (B) In group A Streptococcus, FasX sRNA base pairs with sequences in the 5^′ UTR of ska mRNA to prevent RNase E-mediated degradation. Increased stability of ska mRNA promotes enhanced translation and production of the encoded streptokinase. (C) In C. perfringens, the colA mRNA forms a translation-inhibitory structure. The VR-RNA base pairs with colA mRNA and promotes processing by an unknown RNase. Processed colA mRNA forms an alternative structure at the 5^′ end that stabilizes it and allows enhanced production of the encoded collagenase. (D) In E. coli and Salmonella, the cfa mRNA is inherently unstable due to RNase E-dependent degradation. The RydC sRNA base pairs with an RNase E-sensitive site, stabilizing the cfa mRNA and promoting synthesis of the encoded cyclopropane fatty acid synthase.

Figure 2.

Anti-antisense activation of rpoS by DsrA. In E. coli and related species, the long 5^′UTR of the rpoS mRNA forms a complex secondary structure that blocks RBS and thereby inhibits ribosome binding. In addition, this RNA structure is subject to RNase III-mediated cleavage. Together with Hfq, DsrA can base pair with the rpoS 5^′ UTR inducing structural rearrangements in the RNA allowing ribosome binding. Interaction with DsrA also creates an alternative RNase III cleavage site in the distal part of the stem-loop structure. At low temperatures, DsrA also requires the DEAD box helicase CsdA for rpoS activation.

Figure 3.

SgrS regulates carbon metabolism and virulence. SgrS represses three mRNA targets, ptsG, manXYZ and sopD, and activates one mRNA target, yigL mRNA. Activation of yigL depends on base pairing of SgrS with the pldB ORF preventing mRNA degradation through RNase E. The result of these activities is inhibition of sugar uptake (via repression of ptsG and manXYZ) and activation of sugar efflux (via activation of yigL), which promotes recovery from glucose-phosphate stress.

Figure 4.

Regulation at the 3^′ end through GadY. The GadY sRNA is encoded in cis and antisense to gadX mRNA. GadY base pairing interaction with the gadX–gadW mRNA promotes RNase III-dependent processing, yielding individual gadX and gadW transcripts that are more stable than the full-length mRNA.

Figure 5.

Indirect mechanisms of activation by bacterial sRNAs. (A) Titration of a repressor. CsrB, CsrC and McaS bind the translational regulatory protein CsrA to inhibit its activity and relieve repression of CsrA target genes. (B) Decoy RNAs. GlmY acts as a decoy for the active sRNA regulator GlmZ and binds the adaptor protein RapZ, which would otherwise promote RNase E-dependent processing and inactivation of GlmZ. In the presence of GlmY, GlmZ is able to accumulate and activate glmS to promote synthesis of GlcN6P synthase. (C and D) Sponge RNAs. (C) In the presence of chitosugars, chbBCARFG mRNA is produced and sequences in the intergenic region act as a sponge for ChiX sRNA, sequestering it away from another target, chiP mRNA, encoding the chitoporin. The net effect is activation of chitoporin synthesis in the presence of chitosugars. (D) SroC sRNA is a decay product of polycistronic gltIJKL mRNA and base pairs with GcvB sRNA to promote its turnover by RNase E. The activity of SroC results in activation of GcvB-repressed targets.