Recognition of the small regulatory RNA RydC by the bacterial Hfq protein.

Daniela Dimastrogiovanni,Kathrin S Fröhlich,Jörg Vogel,Heather A Bruce,Ben F Luisi,Susann Hohensee,Katarzyna J Bandyra

doi:10.7554/elife.05375

Daniela Dimastrogiovanni, Kathrin S Fröhlich + Show 5 more

Open Access

https://doi.org/10.7554/elife.05375

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Abstract

Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. The sRNA RydC of Salmonella sp. and Escherichia coli is an example of this class of riboregulators. Like many other sRNAs, RydC bears a 'seed' region that recognises specific transcripts through base-pairing, and its activities are facilitated by the RNA chaperone Hfq. The crystal structure of RydC in complex with E. coli Hfq at a 3.48 Å resolution illuminates how the protein interacts with and presents the sRNA for target recognition. Consolidating the protein-RNA complex is a host of distributed interactions mediated by the natively unstructured termini of Hfq. Based on the structure and other data, we propose a model for a dynamic effector complex comprising Hfq, small RNA, and the cognate mRNA target.

Highlights

The expression of genetic information is controlled and synchronised through intricate regulatory networks
We describe the structure of the small RNAs (sRNAs) RydC in complex with the full-length Hfq protein of E. coli
It seems unlikely that one RydC can find two Hfq hexamers when the protein is limiting to total RNA (Wagner, 2013), and we suggest that the 1:1 complex is likely to represent the physiologically relevant species

Summary

Introduction

The expression of genetic information is controlled and synchronised through intricate regulatory networks. The kinetics of target pairing seem an essential aspect of sRNA action in vivo, as many of these sRNAs affect rates of translation or decay, either positively or negatively depending on target and context (Storz et al, 2004; Fröhlich and Vogel, 2009; Desnoyers and Massé, 2012; Papenfort et al, 2013). It can be envisaged how Hfq acts as a catalyst for such recognition in vivo, but the question naturally arises how sRNAs generally achieve precision, accuracy, and speed in producing their effects and avoid undesired offtarget consequences. The key to understanding these fundamental processes of sRNA-based regulation is to determine how RNAs are bound and presented by Hfq and other effector proteins

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