RNA-binding proteins in bacteria

Abstract

RNA-binding proteins (RBPs) are central to most if not all cellular processes, dictating the fate of virtually all RNA molecules in the cell. Starting with pioneering work on ribosomal proteins, studies of bacterial RBPs have paved the way for molecular studies of RNA-protein interactions. Work over the years has identified major RBPs that act on cellular transcripts at the various stages of bacterial gene expression and that enable their integration into post-transcriptional networks that also comprise small non-coding RNAs. Bacterial RBP research has now entered a new era in which RNA sequencing-based methods permit mapping of RBP activity in a truly global manner in vivo. Moreover, the soaring interest in understudied members of host-associated microbiota and environmental communities is likely to unveil new RBPs and to greatly expand our knowledge of RNA-protein interactions in bacteria.

Long noncoding RNA MAPKAPK5‐AS1 promotes colorectal cancer proliferation by partly silencing p21 expression

“…Many lncRNAs can regulate the expression of downstream target genes by forming complexes with RNA‐binding proteins, then acts as an oncogene or a suppressor oncogene . In this study, we found that knockdown of MAPKAPK5‐AS1 in CRC cells could lead to changes in related downstream genes, including p15 , p21 , p27 , p57 , KLF2 , and Trail .…”

“…26 Therefore, the discovery of new CRC-related lncRNAs is of great significance for further understanding the molecular mechanisms of CRC progression and providing clinical therapeutic targets. In this study, we analyzed 2 sources Many lncRNAs can regulate the expression of downstream target genes by forming complexes with RNA-binding proteins, [27][28][29][30] then acts as an oncogene or a suppressor oncogene. [31][32][33][34][35] In this study, we found that knockdown of MAPKAPK5-AS1 in CRC cells could lead to changes in related downstream genes, including p15, p21, p27, p57, KLF2, and Trail.…”

Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

“…In many but not all bacteria, trans-encoded sRNAs require the RNA chaperone Hfq for efficient regulation (Vogel & Luisi, 2011;Holmqvist & Vogel, 2018;Woodson et al, 2018). Hfq is a ring-like homohexamer with at least three distinct RNA-binding surfaces (Updegrove et al, 2016;.…”

The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs

“…To complicate things further, these RNA sequence elements involve usually short (between 8 and less than 50 nts) and noncontinuous base pairings, and can be involved in alternative intramolecular secondary structures competing with the intermolecular interaction. Moreover, interacting proteins such as the RNA chaperones Hfq (Dos Santos, Arraiano, & Andrade, ) and ProQ (Smirnov et al, ) frequently mediate these interactions in Enterobacteriaceae (Holmqvist & Vogel, ). All these factors make the simple bioinformatic search for complementary segments in a given sRNA versus the pool of coding sequences inadequate (Backofen & Hess, ).…”