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In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways

Published version
Peer-reviewed

Type

Article

Change log

Authors

Chao, Yanjie 
Li, Lei 
Girodat, Dylan 
Förstner, Konrad U 
Said, Nelly 

Abstract

Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small RNAs whereby RNase E acts together with the RNA chaperone Hfq to liberate stable 3′ fragments from various precursor RNAs. Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post-transcriptional regulators.

Description

Keywords

3′ UTR, ArcZ, Hfq, RNA degradome, RNase E, RprA, TIER-seq, non-coding RNA, sRNA maturation, uridine ruler, 3' Untranslated Regions, Bacterial Proteins, Catalysis, Computational Biology, Databases, Genetic, Endoribonucleases, Gene Expression Regulation, Bacterial, Host Factor 1 Protein, Molecular Dynamics Simulation, Nucleic Acid Conformation, RNA Precursors, RNA, Bacterial, RNA, Messenger, RNA, Small Untranslated, Salmonella enterica, Structure-Activity Relationship, Transcriptome, Uridine

Journal Title

Molecular Cell

Conference Name

Journal ISSN

1097-2765
1097-4164

Volume Title

65

Publisher

Elsevier
Sponsorship
Wellcome Trust (200873/Z/16/Z)
This study was funded by DFG ( Vo875/14-1 ) and BioSysNet grants. B.F.L. is supported by the Wellcome Trust. K.P. was supported by the Human Frontiers Science Program (CDA00024/2016-C) .