Multi-scale ensemble properties of the Escherichia coli RNA degradosome.

Tom Dendooven,Md Saiful Islam,Alister Burt,Alexander V Shkumatov,Giulia Paris,Steven W Hardwick,Tai Yuchen Yang,Ben F Luisi,Marta A Kubańska

doi:10.1111/mmi.14800

Abstract

In organisms from all domains of life, multi-enzyme assemblies play central roles in defining transcript lifetimes and facilitating RNA-mediated regulation of gene expression. An assembly dedicated to such roles, known as the RNA degradosome, is found amongst bacteria from highly diverse lineages. About a fifth of the assembly mass of the degradosome of Escherichia coli and related species is predicted to be intrinsically disordered – a property that has been sustained for over a billion years of bacterial molecular history and stands in marked contrast to the high degree of sequence variation of that same region. Here, we characterize the conformational dynamics of the degradosome using a hybrid structural biology approach that combines solution scattering with ad hoc ensemble modelling, cryo-electron microscopy, and other biophysical methods. The E. coli degradosome can form punctate bodies in vivo that may facilitate its functional activities, and based on our results, we propose an electrostatic switch model to account for the propensity of the degradosome to undergo programmable puncta formation.

Highlights

The fate of cellular mRNAs often has as much importance in the control of gene expression as the processes of transcription and translation themselves (Felden & Paillard, 2017)
Over the past 25 years, many studies have investigated the functional roles of bacterial RNA degradosome assemblies in post transcriptional gene regulation (Bandyra & Luisi, 2018; Bayas et al, 2018; Chao et al, 2017; Commichau et al, 2009; Tejada-Arranz et al, 2020)
It is likely that this inherent flexibility in the RNase E core adds only a small contribution to the overall flexibility of the RNA degradosome due to the natively unstructured character of the RNase E scaffold domain

Summary

| INTRODUCTION

The fate of cellular mRNAs often has as much importance in the control of gene expression as the processes of transcription and translation themselves (Felden & Paillard, 2017). The resulting distribution functions of the Rg and Dmax metrics for selected ensembles were plotted and compared to the corresponding distribution functions for the random pool (Figure 3c,d) These distribution functions show that the ensemble models are significantly more extended than the overall pool, meaning that the RNase E scaffold domain and its partner enzymes extend away from the catalytic core of RNase E in solution, ruling out a closed configuration of the degradosome components in the absence of RNA. Previous studies showed that the interaction between the RNA degradosome and ribosomes is mediated mainly by RhlB and the two RNA binding sites on the RNase E scaffold domain (RBD and AR2, Figure 1b; Tsai et al, 2012). Attempts at reliable docking models for enolase and RhlB were unsuccessful

| DISCUSSION

Findings

| MATERIAL AND METHODS