Format

Send to

Choose Destination
Mol Cell. 2017 Jan 5;65(1):39-51. doi: 10.1016/j.molcel.2016.11.002.

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

Author information

1
Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.
2
Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany.
3
Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
4
Laboratory of Structural Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.
5
Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany; Department of Biology I, Microbiology, Ludwig-Maximilians-Universität Munich, 82152 Martinsried, Germany.
6
Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
7
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
8
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.

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.

KEYWORDS:

3′ UTR; ArcZ; Hfq; RNA degradome; RNase E; RprA; TIER-seq; non-coding RNA; sRNA maturation; uridine ruler

PMID:
28061332
PMCID:
PMC5222698
DOI:
10.1016/j.molcel.2016.11.002
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Elsevier Science Icon for PubMed Central
Loading ...
Support Center