Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells.

Seongjin Park,Eric Massé,Wei Liu,Jingyi Fei,Emily M Heideman,Marie-Claude Carrier,Karine Prévost,Matthew A Reyer,Muhammad S Azam

doi:10.7554/elife.64207

Abstract

RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face.

Highlights

In all kingdoms of life, RNA-binding proteins (RBPs) orchestrate the post-transcriptional fates of RNAs by modulating their turnover, structure, and localization, and often as a companion of regulatory RNAs
The speed map and quantification of the average osd speed suggest that Hfq diffuses within the nucleoid and cytoplasmic region, but slightly more slowly in the membrane (Figure 1d), which could be due to the association with RNase E in the inner membrane
As our model suggests that binding of Hfq to the mRNA through the distal face can regulate the mRNA turnover, we reasoned that small RNAs (sRNAs) that can effectively compete for Hfq binding against mRNAs may decoy Hfq from this regulatory function

Summary

Introduction

In all kingdoms of life, RNA-binding proteins (RBPs) orchestrate the post-transcriptional fates of RNAs by modulating their turnover, structure, and localization, and often as a companion of regulatory RNAs. Biochemistry and Chemical Biology Microbiology and Infectious Disease eLife digest Messenger RNAs or mRNAs are molecules that the cell uses to transfer the information stored in the cell’s DNA so it can be used to make proteins Bacteria can regulate their levels of mRNA molecules, and they can control how many proteins are being made, by producing a different type of RNA called small regulatory RNAs or sRNAs. Each sRNA can bind to several specific mRNA targets, and lead to their degradation by an enzyme called RNase E. Certain bacterial RNA-binding proteins, such as Hfq, protect sRNAs from being degraded, and help them find their mRNA targets. It is critical for bacterial growth under harsh conditions and it is involved in the process through which pathogenic bacteria infect cells It is outnumbered by the many different RNA molecules in the cell, which compete for binding to the protein. Our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner

Results

Discussion

Materials and methods

Funding Funder National Institutes of Health