In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways
| Autor: | Jörg Vogel, Bonaventura Francesco Luisi, Dylan Girodat, Nelly Said, Kai Papenfort, Michał Śmiga, Konrad U. Förstner, Lei Li, Yanjie Chao, Hans-Joachim Wieden, Richard Reinhardt, Colin P. Corcoran |
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| Přispěvatelé: | Luisi, Ben [0000-0003-1144-9877], Apollo - University of Cambridge Repository, HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße 2, 97080 Würzburg, Germany. |
| Rok vydání: | 2017 |
| Předmět: |
ArcZ
0301 basic medicine RNase E RNase P 3′ UTR non-coding RNA Science program Host Factor 1 Protein Molecular Dynamics Simulation Biology RNA degradome Cleavage (embryo) Article Hfq RprA Catalysis Structure-Activity Relationship 03 medical and health sciences Bacterial Proteins In vivo Databases Genetic Endoribonucleases RNA Precursors RNA Messenger 3' Untranslated Regions Uridine Molecular Biology Genetics 030102 biochemistry & molecular biology Computational Biology Salmonella enterica Gene Expression Regulation Bacterial Cell Biology Non-coding RNA sRNA maturation TIER-seq uridine ruler 3. Good health RNA Bacterial RNase MRP 030104 developmental biology Nucleic Acid Conformation RNA Small Untranslated Transcriptome |
| Zdroj: | Molecular Cell |
| ISSN: | 1097-2765 |
| DOI: | 10.1016/j.molcel.2016.11.002 |
| Popis: | Summary 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. Graphical Abstract Highlights • TIER-seq precisely maps ∼22,000 endogenous RNase E cleavage sites in Salmonella • Consensus motif of RNase E reveals a 2-nt uridine ruler-and-cut mechanism • RNase E is a central component in both maturation and degradation of small RNAs • There is a general small-RNA biogenesis pathway requiring RNase E and Hfq Chao et al. discover that the essential bacterial RNase E cleaves numerous transcripts at preferred sites by sensing uridine as a 2-nt ruler. RNase E processing of various precursor RNAs produces many small regulatory RNAs, constituting a major small-RNA biogenesis pathway in bacteria. |
| Databáze: | OpenAIRE |
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