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.
Highlights
The majority of small non-coding RNAs interact with a complementary mRNA through an antisense mechanism, leading to the formation of a duplex sRNA-mRNA region
Polynucleotide phosphorylase (PNPase) adopts a homotrimeric organization with a ring-like structure, each monomer having a molecular weight of 78 kDa and holding two RNA-binding domains, K homology (KH) and S1, on the C-terminal (Shi et al, 2008)
In E. coli, PNPase is the main enzyme involved in the degradation of sRNAs that are not bound to Hfq, as shown for the regulation of different Hfq-dependent sRNAs, such as MicA, GlmY, RyhB, and SgrS levels (Andrade et al, 2012, 2013)
Summary
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. 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 (Holmqvist et al, 2016, 2018; Smirnov et al, 2016; Melamed et al, 2019). We summarize the current information on the major RNA chaperones and RNases governing the activity of bacterial sRNAs
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