Bacterial noncoding Y RNAs are widespread and mimic tRNAs
- 1Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
- 2Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06510, USA
- Corresponding author: sandra.wolin{at}yale.edu
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↵3 These authors contributed equally to this work.
Abstract
Many bacteria encode an ortholog of the Ro60 autoantigen, a ring-shaped protein that is bound in animal cells to noncoding RNAs (ncRNAs) called Y RNAs. Studies in Deinococcus radiodurans revealed that Y RNA tethers Ro60 to polynucleotide phosphorylase, specializing this exoribonuclease for structured RNA degradation. Although Ro60 orthologs are present in a wide range of bacteria, Y RNAs have been detected in only two species, making it unclear whether these ncRNAs are common Ro60 partners in bacteria. In this study, we report that likely Y RNAs are encoded near Ro60 in >250 bacterial and phage species. By comparing conserved features, we discovered that at least one Y RNA in each species contains a domain resembling tRNA. We show that these RNAs contain nucleotide modifications characteristic of tRNA and are substrates for several enzymes that recognize tRNAs. Our studies confirm the importance of Y RNAs in bacterial physiology and identify a new class of ncRNAs that mimic tRNA.
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Footnotes
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.047241.114.
- Received July 10, 2014.
- Accepted July 30, 2014.
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