Abstract
Small non-coding RNAs (sRNAs) are critical post-transcriptional regulators of gene expression. Distinct RNA-binding proteins (RBPs) influence the processing, stability and activity of bacterial small RNAs. The vast majority of bacterial sRNAs interact with mRNA targets, affecting mRNA stability and/or its translation rate. The assistance of RNA-binding proteins facilitates and brings accuracy to sRNA-mRNA basepairing and the RNA chaperones Hfq and ProQ are now recognized as the most prominent RNA matchmakers in bacteria. These RBPs exhibit distinct high affinity RNA-binding surfaces, promoting RNA strand interaction between a trans-encoding sRNA and its mRNA target. Nevertheless, some organisms lack ProQ and/or Hfq homologs, suggesting the existence of other RBPs involved in sRNA function. Along this line of thought, the global regulator CsrA was recently shown to facilitate the access of an sRNA to its target mRNA and may represent an additional factor involved in sRNA function. Ribonucleases (RNases) can be considered a class of RNA-binding proteins with nucleolytic activity that are responsible for RNA maturation and/or degradation. Presently RNase E, RNase III, and PNPase appear to be the main players not only in sRNA turnover but also in sRNA processing. Here we review the current knowledge on the most important bacterial RNA-binding proteins affecting sRNA activity and sRNA-mediated networks.
Introduction
The majority of small non-coding RNAs (sRNAs) interact with a complementary mRNA through an antisense mechanism, leading to the formation of a duplex sRNA-mRNA region. Consequently, expression from the target mRNA is affected and frequently repressed (Storz et al., 2011). sRNA-mediated networks are cost efficient and often more rapid in the reprogramming of gene expression than pathways that rely exclusively on regulatory proteins (Shimoni et al., 2007). However, the interaction between sRNAs and RNA-binding proteins (RBPs) is often critical for the regulatory activity of sRNAs. RNA-binding proteins are a diverse class of proteins ubiquitously found in all living organisms and that control all steps of the life of an RNA (Smirnov et al., 2017a). The capacity of these proteins to recognize and bind RNA molecules arises from the presence of well-defined RNA-binding domains, such as the canonical S1 domain, cold shock domain (CSD), K homology (KH) domain, amongst others (). Additional regions may also contribute to RNA-protein interactions, like the disordered regions that confer flexibility to proteins. The overall fold of the protein and the recognition of different RNA-binding motifs determines the interaction with RNA in a sequence- and/or structure-specific dependent manner. RBPs and sRNAs networks have been extensively studied in Eukarya and Bacteria, with a current lack of information about this regulation in Archaea (). Though many RBPs can be found in bacteria only few have been shown to associate with sRNAs. However, these participate in a variety of reactions that affect the catalytic and molecular recognition properties of sRNAs.
RNA chaperones constitute a specific group of RBPs that transiently bind and induce structural changes in RNA substrates by melting RNA secondary structures (Woodson et al., 2018). Such structural rearrangements influence not only the stability of sRNA and mRNA molecules but also facilitate the basepairing of sRNAs and mRNAs. Moreover, RNA chaperones that bind simultaneously the sRNA and the target mRNA, bring them closely together in a complex, promoting the annealing and formation of stable RNA-RNA interactions. Though sRNA-mRNA basepairing can occur in the absence of RNA chaperones, their presence greatly accelerates this process (Rajkowitsch and Schroeder, 2007; Panja et al., 2013). Three major RNA chaperones that assist sRNA function in bacteria are currently known: the Sm family member Hfq (Santiago-Frangos and Woodson, 2018), the FinO family member ProQ (Smirnov et al., 2016) and the prototype of its family CsrA (Müller et al., 2019). Despite being widespread, these RBPs are not evenly present in bacteria and the interactome studies of these RNA chaperones indicate they preferably bind different sRNAs (Figure 1), suggesting more specialized roles for each of them (, ; Smirnov et al., 2016; Melamed et al., 2019).
FIGURE 1
Ribonucleases (RNases) are another group of specific RBPs that interact with sRNAs. These enzymes are responsible for the catalytic cleavage of all classes of RNA (
RNA Chaperones
Hfq
Hfq is widely recognized as a global regulator and key element of sRNA-based networks. Hundreds of sRNA molecules have been reported in Escherichia coli, and ∼30% rely on Hfq to carry on their functions (Vogel and Luisi, 2011). Hfq is particularly important for the action of trans-encoded sRNAs (which are expressed from a different genomic region than their mRNA targets), stabilizing the imperfect basepairing between sRNA/mRNA pairs. At least in Gram-negative bacteria, Hfq primary role is to promote the annealing of sRNA-mRNA duplexes, acting as a molecular “matchmaker,” but its role in Gram-positive bacteria is more controversial (Woodson et al., 2018;
Interactome studies identified thousands of Hfq-bound RNA pairs, dominated by mRNA-sRNA pairs exhibiting sequence complementarity (
sRNAs have been classified in two major classes according to their dependence on Hfq contact surfaces. The vast majority of bacterial sRNAs belong to class I. Hfq contacts these transcripts through binding of its proximal face to the unstructured U-rich stretches present at the 3′-end of sRNAs. On the other hand, the distal face of the Hfq ring preferentially interacts with ARN motifs in mRNAs. The basic patched rim surface may then interact with UA-rich sites present in both RNAs, coordinating the successful annealing between the sRNA-mRNA pair (Panja et al., 2013; Zhang et al., 2013; Schu et al., 2015). As an example, the iron-responsive class I sRNA RyhB relies on Hfq for successful interaction with its targets (
Hfq remodels RNA conformation by disrupting secondary structures, without the need to hydrolyze ATP. This intrinsic RNA chaperone capability is important to unfold structured RNAs, exposing unpaired RNA stretches for basepairing between complementary strands. One of the best characterized Hfq-dependent sRNAs is MicA, which was found to target the ompA mRNA (Udekwu et al., 2005). The RNA chaperone activity of Hfq is also important for remodeling MicA structural elements, altering its stability and binding specificities. Hfq binding rearranges MicA fold to allow exposure of the ompA-binding site for pairing that leads to translation repression (
ProQ
ProQ is a recently identified RNA chaperone of the FinO family of RNA-binding proteins commonly found in Proteobacteria (Olejniczak and Storz, 2017). Most of the work on ProQ RNA substrates came from studies performed in E. coli, Salmonella enterica, and Legionella pneumophila, which identified a hundred mRNA transcripts and more than fifty sRNAs as ProQ ligands (
Most sRNAs that bind ProQ have unknown functions so far. In contrast to Hfq, the majority of known ProQ-associated sRNAs act in cis promoting extensive perfect basepairing with the target mRNA encoded on the opposite strand (Smirnov et al., 2017b). However, ProQ was also found to regulate trans-acting sRNAs, assisting the imperfect basepairing with their target mRNAs. Two well characterized examples in Salmonella are known: the RaiZ sRNA-hupA mRNA and STnc540 sRNA-mgtB mRNA (Smirnov et al., 2017b; Westermann et al., 2019). ProQ binds RaiZ through its 3′-terminal stem-loops and promotes interaction of a linear region of this sRNA with the hupA mRNA. This three-partner ProQ/RaiZ/hupA mRNA complex results in impairment of hupA mRNA translation by preventing loading of the 30S ribosome subunit (Smirnov et al., 2017b). STnc540 sRNA also represses the expression of its target mRNA in a ProQ-dependent manner (Westermann et al., 2019). In both examples, ProQ is absolutely required for stability of the sRNAs, affecting their abundance.
Recent work in E. coli explores the RNA-RNA interactomes of Hfq and ProQ chaperones using RIL-seq (Melamed et al., 2019). Even though the interactome of ProQ was smaller than the one of Hfq, about a third of the RNA-RNA interactions were common between the two RNA chaperones, with examples like RybB and MalM sRNAs. This suggests complementary or competitive roles for these RBPs. An additional example is found in Salmonella, in the regulation mediated by the SraL sRNA. This sRNA binds to the 5′-UTR of the rho mRNA, an interaction that can be mediated by ProQ and/or Hfq (Silva et al., 2019). However, the RNAs bound by ProQ generally differ from those bound by Hfq. RIL-seq data revealed that while Hfq-bound RNAs were enriched in both sRNAs and mRNAs, ProQ-bound RNAs were mainly enriched for coding sequences (Melamed et al., 2019). This suggests that the RNA-RNA matchmaking activity of ProQ may not be generalized, unlike observed with Hfq that is primarily involved in sRNA-mediated regulation of mRNA translation. Additional roles for ProQ may include RNA protection from RNase attack or a participation in RNA modification.
CsrA
The CsrA protein was first discovered in E. coli and its function attributed to carbon storage and glycogen production, acting as a translational repressor of the glgC mRNA (Romeo et al., 1993; Romeo and Babitzke, 2018). In Pseudomonas aeruginosa the homolog protein is termed RsmA (for regulator of secondary metabolism) with paralogs (RsmF/N, RsmE, and RsmI) found in different Pseudomonas species (Reimmann et al., 2005;
The E. coli CsrA is a ∼7 kDa RNA-binding protein and consists of a homodimer, each subunit with five β-strands, one α-helix and an unstructured C-terminal (
CsrA was recently described to act as an RNA chaperone that indirectly promotes the basepairing between the trans-acting SR1 sRNA and its primary target the ahrC mRNA, which encodes the transcription activator of the arginine catabolic operons in Bacillus subtilis (Müller et al., 2019). In vitro binding studies demonstrated that CsrA binds these RNAs with high affinity, in the nanomolar range, even in the presence of an mRNA competitor. Further mutational analysis of the SR1 sRNA and the ahrC mRNA confirmed binding of CsrA to both transcripts. CsrA facilitates the binding of the SR1 sRNA downstream the start codon of the ahrC mRNA and induces conformational changes in the RBS preventing its translation (Müller et al., 2019). Importantly, Hfq was not found to catalyze this interaction and ProQ is not expressed in B. subtilis. Interestingly, this suggests that CsrA may act as an alternative RNA chaperone to Hfq and ProQ in assisting sRNA-mRNA basepairing.
RNA- and DNA-Binding Multifunctional Proteins as RNA Chaperones
While Hfq, ProQ, and CsrA may be considered the major RNA chaperones interacting with sRNAs, additional RBPs are known to assist RNA folding and bind sRNAs. Two of such examples include the cold shock proteins (CSPs) and the StpA protein. CSPs are a group of small proteins that display the RNA-binding cold shock domain (CSD) (Phadtare and Severinov, 2010) and can passively remodel RNA structures (Woodson et al., 2018). The major cold shock protein of E. coli is CspA that binds RNA with low sequence specificity and in a cooperative fashion (
RNases
RNase E
Homologs of E. coli RNase E have been identified in the majority of Proteobacteria classes (
RNase III
RNase III is a widely distributed endoribonuclease involved in the processing of double-stranded RNAs (dsRNAs). E. coli RNase III acts as a 52 kDa homodimer, with the catalytic N-terminal domain connected by a short linker to the C-terminal dsRNA-binding domain (
PNPase
Polynucleotide phosphorylase (PNPase) is a highly conserved 3′–5′ exoribonuclease that processively degrades RNA (Saramago et al., 2014;
Although to a lesser extent, additional RNases are involved in the regulation of sRNAs. The degradative enzymes YbeY and RNase R are illustrative examples. YbeY is a highly conserved endoribonuclease commonly associated with rRNA processing (
Conclusion
RNA chaperones can modify sRNA structure, facilitate the basepairing of sRNAs to their target mRNAs and together with RNases control sRNA stability (Figure 2). However, some RNA chaperones seem to be specific of some species and the activities performed by these regulators may be compensated by other still unidentified RNA-binding proteins. Several RBPs with unorthodox RNA-binding domains have been identified in humans, expanding the number of proteins that can associate with RNA (
FIGURE 2

RNA chaperone and RNase activities on sRNAs. Simplified scheme that illustrates the effect of these RNA-binding proteins in different aspects of the sRNA lifetime, namely on the folding of sRNA secondary structures, promotion of sRNA/mRNA basepairing and control of sRNA stability.
Statements
Author contributions
JA outlined the manuscript. AQ, AS, and RS prepared the figures. CA and JA supervised the work. All authors wrote and participated in preparation of the final manuscript.
Funding
This work was supported by Project LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) and by FCT—Fundação para a Ciência e a Tecnologia (Portugal), including Program IF (IF/00961/2014) and Grants PTDC/IMI-MIC/4463/2014 and PTDC/BIA-MIC/32525/2017 to JA, Grant PTDC/BIA-MIC/1399/2014 to CA, the Doctoral fellowships PD/BD/135487/2018 to AQ, and PD/BD/146136/2019 to AS.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Summary
Keywords
RNA-binding proteins, RNA chaperone, ribonucleases, small non-coding RNAs, CsrA, Hfq, ProQ
Citation
Quendera AP, Seixas AF, dos Santos RF, Santos I, Silva JPN, Arraiano CM and Andrade JM (2020) RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria. Front. Mol. Biosci. 7:78. doi: 10.3389/fmolb.2020.00078
Received
20 January 2020
Accepted
06 April 2020
Published
13 May 2020
Volume
7 - 2020
Edited by
Olga N. Ozoline, Institute of Cell Biophysics (RAS), Russia
Reviewed by
Irina Masulis, Institute of Cell Biophysics (RAS), Russia; Claudio Valverde, National University of Quilmes, Argentina
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© 2020 Quendera, Seixas, dos Santos, Santos, Silva, Arraiano and Andrade.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: José M. Andrade, andrade@itqb.unl.pt
This article was submitted to Protein and RNA Networks, a section of the journal Frontiers in Molecular Biosciences
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