Molecular Cell
Volume 65, Issue 1, 5 January 2017, Pages 39-51
Journal home page for Molecular Cell

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

https://doi.org/10.1016/j.molcel.2016.11.002Get rights and content
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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

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.

Keywords

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

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