Review
Regulatory RNAs and target mRNA decay in prokaryotes

https://doi.org/10.1016/j.bbagrm.2013.02.013Get rights and content

Highlights

  • Many small RNAs regulate translation initiation in prokaryotes.

  • Small RNAs interact with the RNA chaperone Hfq for stability and function.

  • Some small RNAs also initiate mRNA decay through RNAse E recruitment.

  • New mechanisms including Rho termination factor and riboswitches are discussed.

Abstract

Recent advances in prokaryote genetics have highlighted the important and complex roles of small regulatory RNAs (sRNAs). Although blocking mRNA translation is often the main function of sRNAs, these molecules can also induce the degradation of target mRNAs using a mechanism that drastically differs from eukaryotic RNA interference (RNAi). Whereas RNAi relies on RNase III-like machinery that is specific to double-strand RNAs, sRNA-mediated mRNA degradation in Escherichia coli and Samonella typhimurium depends on RNase E, a single-strand specific endoribonuclease. Surprisingly, the latest descriptions of sRNA-mediated mRNA degradation in various bacteria suggest a variety of previously unsuspected mechanisms. In this review, we focus on recently characterized mechanisms in which sRNAs can bind to target mRNAs to induce decay. These new mechanisms illustrate how sRNAs and mRNA structures, including riboswitches, act cooperatively with protein partners to initiate the decay of mRNAs. This article is part of a Special Issue entitled: RNA Decay mechanisms.

Introduction

Post-transcriptional gene regulation mediated by small regulatory RNAs (sRNAs) is commonly found in both prokaryotic and eukaryotic kingdoms. Small RNAs in these systems act to down-regulate target genes by decreasing translation and/or increasing mRNA turnover [1], [2], [3]. Eukaryotic microRNAs (miRNA) or small interfering RNAs (siRNA) are assembled into ribonucleoprotein complexes known as RNA-induced silencing complex (RISC) [1], [2]. RISCs are composed of a variety of proteins such as RNA-binding proteins, RNA helicases, and nucleases. These characteristics are reminiscent of bacterial sRNAs and RNA-binding protein Hfq, both of which form ribonucleoprotein complexes with the endoribonuclease RNase E [4]. Although there are multiple functional similarities between eukaryote and prokaryote processes, this review will focus on prokaryotic systems of mRNA decay, notably in Escherichia coli.

In bacteria, sRNAs are usually non-coding and smaller than 300 nucleotides. At present, ~ 100 sRNAs have been identified, located either on E. coli plasmid or its chromosome [3], [5]. Antisense sRNAs, which act by base-pairing with mRNA to inhibit translation of their targets, represent the major class of sRNAs in bacteria. This group can be subdivided as true antisense RNAs or cis-encoded sRNAs, synthesized from the strand complementary to the mRNA they regulate, or trans-encoded sRNAs, synthesized at a different genomic location. The latter type of sRNA possesses limited complementarity with mRNA targets (about 7 to 12 bases) that enables trans-encoded sRNAs to modulate the activity and stability of multiple mRNAs [3]. The segment of contiguous base-pairing is called “seed region” by comparison to eukaryotic microRNA system [6]. Basically, base-pairing between sRNA and mRNA targets can lead to the activation or inhibition of mRNA translation (RNAIII, [7]), mRNA stabilization (GadY, [8]) or mRNA degradation (RyhB, [9]).

Section snippets

sRNAs as mRNA translation modulators

Most sRNAs characterized to date block translation by direct binding to the ribosome-binding site (RBS) in the 5′-UTR (UnTranslated Region) of target mRNAs (Fig. 1A). Basically, sRNA sequester and mask the RBS through interactions involving short regions (7–12 bases) of imperfect complementarity, to prevent 30S ribosome binding and translation initiation.

In contrast, some sRNAs activate translation by binding to the 5′-untranslated region (5′-UTR) of the target mRNA. Usually, these target mRNAs

The RNA chaperone Hfq and mRNA translation repression

In E. coli, most sRNAs that bind to mRNAs depend on the 11 kDa RNA chaperone Hfq. In vivo, Hfq monomers assemble to form hexamers and dodecamers, which stabilize sRNAs and modulate base-pairing with target mRNAs [13], [14], [15]. Several studies have shown similarities in both protein sequence and structure between bacterial Hfq and eukaryotic Sm proteins, which bind small nucleolar RNAs and are components of the spliceosome in eukaryotes [16]. Recently, a number of studies, using Hfq as bait,

Hfq antagonizes RNase E activity

Hfq is also a key player in the modulation of mRNA stability. In fact, Hfq can protect transcripts against ribonuclease E (RNase E) attacks due to coincident Hfq binding sites and RNase E cleavage sites on mRNA (AU-rich single-strand regions) [4]. RNase E is a single-strand-specific endoribonuclease that initiates the decay of many mRNAs in E. coli. Subsequently to RNase E-dependent cleavage, the resulting intermediate products are degraded by endo- and exoribonucleases (e.g. polynucleotide

sRNA-mediated mRNA decay

A new family of sRNAs with a more complex mechanism of action was first characterized ten years ago [9]. This group of sRNAs, which quickly became a paradigm in sRNA mechanism, was shown to base-pair with target mRNAs to trigger their degradation by RNase E (Fig. 1B and C). Incidently, RNA-binding Hfq was also shown to be involved in the recruitment of RNase E and sRNA-mediated mRNA decay [27], [28]. The first example of sRNA involved in sRNA-mediated mRNA degradation was RyhB, which

RNase III can replace RNase E

RNase E is not the only RNase involved in mRNA decay. Other RNases directly process and degrade mRNA transcripts like RNase III, which cleaves double-stranded RNA [52]. For example, S. aureus sRNA RNAIII is involved in the control of virulence by regulating several mRNAs encoding exotoxins and exoproteases [53]. RNAIII base-pairs with a couple of mRNA target independently of Hfq and induce degradation by RNase III instead of RNase E [54]. A same mechanism is observed for tisAB mRNA

Modulation of RNA stability is a widespread regulatory mechanism for sRNAs

The sRNA GadY is a member of the cis-encoded RNA class. GadY positively regulates the levels of gadW and gadX mRNA that are involved in response to acid stress [57]. Base-pairing of GadY with the intergenic region of the gadX-gadW mRNA results in targeted cleavage within the region of complementarity and in the stabilization of each transcript [58], [59], [60]. In E. coli, the activity of the pleiotropic/global regulator CsrA (carbon storage regulator) is regulated by two sRNAs CsrB and CsrC,

Small RNAs and the termination factor Rho

A Rho-dependent mechanism of transcriptional termination by trans-acting sRNAs has recently been proposed [68]. In bacteria, there are two types of transcriptional termination, Rho-dependent and Rho-independent termination. In the case of Rho-independent termination, the mRNA generally presents a stem–loop structure followed by a poly-uracil sequence, which facilitates dissociation of RNA polymerase from the DNA template. In this connection, Rho-independent transcription termination is a

Riboswitches

Riboswitches are RNA structures located within the 5′-UTR of mRNAs that regulate gene expression at the level of transcription, translation or splicing [72], [73]. These RNA structures can change conformation by directly binding intracellular metabolites (e.g. vitamins or amino acids). Depending on the concentration of the metabolite, riboswitches will adopt either activating (ON) or repressing (OFF) conformations (Fig. 3A). Whereas riboswitches normally regulate in cis, recent results suggest

Riboswitches as targets for RNase E-based mRNA decay

Although every riboswitch is known, to date, to regulate either transcription elongation, translation initiation or splicing, it was recently shown that the E. coli lysC riboswitch controls both translation initiation and mRNA decay (Fig. 3B). When bound to the amino acid lysine, the lysC riboswitch adopts the OFF conformation, which simultaneously blocks translation initiation and rapidly induces RNase E degradation [75]. This rapid degradation suggests an active recruitment mechanism whereby

Conclusions

An increasing body of evidence supports the interpretation that, in many organisms including humans, mice, yeasts, and bacteria, transcription does not always map to genes [76], [77], [78]. In fact, it has become clearer that transcripts originate throughout the whole genome, including regions previously thought to be silent. This “pervasive” transcription also implies extensive post-transcriptional RNA regulation and processing, as suggested recently in bacteria [77]. Therefore, it is very

Acknowledgements

Work in our respective laboratories was funded by an operating grant (MOP69005) to E.M. and (MOP82877) to D.A.L. from the Canadian Institute for Health Research (CIHR). E.M. is a Senior Scholar from the Fonds de la Recherche en Santé du Québec (FRSQ). DAL is a CIHR New Investigator scholar.

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    This article is part of a Special Issue entitled: RNA Decay mechanisms.

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