The PIN domain plays a central role in cellular RNA biology and is involved in processes as diverse as rRNA maturation, mRNA decay and telomerase function. Here, we solve the crystal structure of the Rae1 (YacP) protein of Bacillus subtilis, a founding member of the NYN (Nedd4‐BP1/YacP nuclease) subfamily of PIN domain proteins, and identify potential substrates in vivo. Unexpectedly, degradation of a characterised target mRNA was completely dependent on both its translation and reading frame. We provide evidence that Rae1 associates with the B. subtilis ribosome and cleaves between specific codons of this mRNA in vivo. Critically, we also demonstrate translation‐dependent Rae1 cleavage of this substrate in a purified translation assay in vitro. Multiple lines of evidence converge to suggest that Rae1 is an A‐site endoribonuclease. We present a docking model of Rae1 bound to the B. subtilis ribosomal A‐site that is consistent with this hypothesis and show that Rae1 cleaves optimally immediately upstream of a lysine codon (AAA or AAG) in vivo.
A new bacterial endoribonuclease Rae1/YacP, founding member of the NYN subfamily of PIN domain proteins, cleaves mRNAs at specific codons through its association with the ribosome.
The crystal structure of Bacillus subtilis RNase Rae1 reveals an N‐terminal NYN domain that can be docked into the ribosome A‐site.
Potential substrates of Rae1 cleavage are revealed by RNA sequencing.
Translation activity and correct reading frame are required for Rae1 cleavage of mRNA encoding a 17‐ amino acid peptide.
Rae1 cleavage preferentially occurs immediately upstream of a lysine (AAG/AAA) codon.
- Received January 16, 2017.
- Revision received March 2, 2017.
- Accepted March 2, 2017.
- © 2017 The Authors
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