Multi‐scale ensemble properties of the Escherichia coli RNA degradosome. Issue 1 (25th September 2021)

• Record Type: Journal Article
• Authors: Dendooven, Tom; Paris, Giulia; Shkumatov, Alexander V.; Islam, Md. Saiful; Burt, Alister; Kubańska, Marta A.; Yang, Tai Yuchen; Hardwick, Steven W.; Luisi, Ben F.
• Other Names: Papenfort Kai guestEditor.; Woodson Sarah A. guestEditor.; Schmitz Ruth A. guestEditor.; Winkler Wade C. guestEditor.
• Is Part Of: Molecular microbiology. Volume 117:Issue 1(2022)
• Page Start: 102
• Page End: 120
• Publication Date: 2021-09-25
• Subjects: colloidal polymer -- intrinsically disordered protein -- post‐transcriptional gene regulation -- ribonuclease -- riboregulation -- RNA condensates -- RNA metabolism -- RNA surveillance -- RNase E; Molecular microbiology -- Periodicals; 572.829
• DOI: 10.1111/mmi.14800
• Languages: English
• ISSNs: 0950-382X

Abstract

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. Abstract : Integrated structural biology approaches used to study the conformational landscape of the RNA degradosome and its sub‐assemblies. Cryo‐EM single particle analysis and 3D variability analysis revealed potential modes of conformational accommodation of the catalytic domain of RNase E. Different biophysical techniques (DLS, AUC, SEC‐SAXS) were employed to explore the conformational behavior of the truncated degradosome in solution, and SAXS ensemble optimization modelling revealed that the complex is highly flexible and extended, but compacts upon engaging an RNA substrate. Finally, the structural organization of the RNA degradosome tethered to lipid membranes was investigated by cryo‐electron tomography, which suggests a more compact assembly in its native environment.