title: In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways.
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.
authors.affiliation: Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Yanjie
authors.initials: Y
authors.lastname: Chao
authors.affiliation: Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.affiliation: Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
authors.forename: Dylan
authors.initials: D
authors.lastname: Girodat
authors.affiliation: Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Konrad U
authors.initials: KU
authors.lastname: Förstner
authors.affiliation: Laboratory of Structural Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.
authors.forename: Nelly
authors.initials: N
authors.lastname: Said
authors.affiliation: Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Colin
authors.initials: C
authors.lastname: Corcoran
authors.affiliation: Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
authors.forename: Michał
authors.initials: M
authors.lastname: Śmiga
authors.affiliation: Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Department of Biology I, Microbiology, Ludwig-Maximilians-Universität Munich, 82152 Martinsried, Germany.
authors.forename: Kai
authors.initials: K
authors.lastname: Papenfort
authors.affiliation: Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.affiliation: Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
authors.forename: Hans-Joachim
authors.initials: HJ
authors.lastname: Wieden
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
authors.forename: Ben F
authors.initials: BF
authors.lastname: Luisi
authors.affiliation: Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany. Electronic address: joerg.vogel@uni-wuerzburg.de.
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
mesh_terms: D020413:3' Untranslated Regions; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D002384:Catalysis; D019295:Computational Biology; D030541:Databases, Genetic; D004722:Endoribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000235:genetics / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019779:Salmonella enterica / Q000201:enzymology* / Q000235:genetics; D013329:Structure-Activity Relationship; D059467:Transcriptome; D014529:Uridine / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D001426:Bacterial Proteins; D035001:Host Factor 1 Protein; D012322:RNA Precursors; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D004722:Endoribonucleases; C022537:ribonuclease E; D014529:Uridine
keywords: 3′ UTR; ArcZ; Hfq; RNA degradome; RNase E; RprA; TIER-seq; non-coding RNA; sRNA maturation; uridine ruler