RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria

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.

Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas

“…Prokaryotic genomes encode over a hundred of RNA-binding proteins, being the majority of them devoted to scaffold the ribosomal subunits or to catalytically process RNA molecules for maturation or defense (Holmqvist and Vogel, 2018 ). A third functional class of RNA-binding proteins is involved in posttranscriptional control of gene expression (Quendera et al, 2020 ), with some outstanding cases acting as global regulators of major influence in the fate of hundreds of mRNAs, as is the case of the broadly studied chaperone Hfq (Vogel and Luisi, 2011 ; Sobrero and Valverde, 2012 ; Kavita et al, 2018 ; Santiago-Frangos and Woodson, 2018 ), or the members of the CsrA family (Romeo and Babitzke, 2019 ), which is the subject of this article. Here, we will review the features of the RNA-binding proteins of the CsrA superfamily, with an emphasis on the representatives of the genus Pseudomonas , for which our comparative genome analysis revealed a prolific evolutionary spreading of multiple paralogues.…”

A survey of non-coding RNAs in the social and predatory myxobacterium Myxococcus xanthus DK1622

“…Nevertheless, the M. xanthus DK1622 genome does encode six homologues of CspA, which has RNA chaperone activity. 13 Predicted mRNA targets Prediction of the regulatory targets of antisense ncRNAs is trivial. However, currently available algorithms for the identification of the regulatory targets of trans-acting ncRNAs are prone to false positives.…”

“…12 In addition, matchmaking between ncRNAs and their mRNA targets is often stimulated by RNA chaperone proteins such as Hfq, ProQ and CsrA. 13 The myxobacteria are a family of proteobacteria that are particularly noted for their complex gene regulatory networks. 14 Nevertheless, with two notable exceptions (Pxr and MsDNA), their ncRNAs have received little research attention.…”

Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA–DNA adapter protein

“…Bacteria are capable of exquisite control of gene expression in response to cellular or environmental stress (Gottesman and Storz 2011;Wagner and Romby 2015;Dersch et al 2017). Small RNAs (sRNAs) are a class of trans-acting non-coding RNAs in bacteria that are expressed under specific conditions to regulate groups of messenger RNAs (mRNAs) (Gottesman and Storz 2011;Wagner and Romby 2015;Hör et al 2020;Quendera et al 2020).…”