Keeping up with RNA-based regulation in bacteria: new roles for RNA binding proteins

Bacterial RNA binding proteins (RBPs) are ubiquitous, versatile molecules, involved in post-transcriptional regulation of gene expression. With other effectors, especially RNA regulators, they form an intricate regulatory network that coordinates the reshaping of bacterial transcriptomes in response to stress. Emergence of high-throughput transcriptome-wide methods aimed at the study of RNA–RNA or RNA–protein interactions led to major discoveries. Thanks to these advances, the roles of three major bacterial RBPs, Hfq, ProQ, and CsrA have been revisited and redefined. Hfq and ProQ perform highly similar functions, yet, striking differences render each molecule unique. The interactomes of Hfq and ProQ overlap, inevitably creating a hierarchization or a competition between both proteins. Cas proteins are RBPs central to cell survival against invading nucleic acids. They are critical actors of the clustered regularly interspaced short palindromic repeats (CRISPR) system, the immune defense of bacterial organisms. Cas RBPs enable protection of the bacterial population over several generations. RNA binding proteins (RBPs) are ubiquitously found in all kingdoms of life. They are involved in a plethora of regulatory events, ranging from direct regulation of gene expression to guiding modification of RNA molecules. As bacterial regulators, RBPs can act alone or in concert with RNA-based regulators, such as small regulatory RNAs (sRNAs), riboswitches, or clustered regularly interspaced short palindromic repeats (CRISPR) RNAs. Various functions of RBPs, whether dependent or not on an RNA regulator, have been described in the past. However, the past decade has been a fertile ground for the development of novel high-throughput methods. These methods acted as stepping-stones for the discovery of new functions of RBPs and helped in the understanding of the molecular mechanisms behind previously described regulatory events. Here, we present an overview of the recently identified roles of major bacterial RBPs from different model organisms. Moreover, the tight relationship between RBPs and RNA-based regulators will be explored.

Английский

Trends in Genetics. – 2021. – Vol. 37, № 1. – P. 86–97.