title: Bacterial noncoding Y RNAs are widespread and mimic tRNAs.
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.
authors.affiliation: Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA.
authors.forename: Xinguo
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA.
authors.forename: Soyeong
authors.initials: S
authors.lastname: Sim
authors.affiliation: Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA.
authors.forename: Elisabeth J
authors.initials: EJ
authors.lastname: Wurtmann
authors.affiliation: Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA.
authors.forename: Ann
authors.initials: A
authors.lastname: Feke
authors.affiliation: Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA sandra.wolin@yale.edu.
authors.forename: Sandra L
authors.initials: SL
authors.lastname: Wolin
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D030541:Databases, Genetic; D006801:Humans; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000378:metabolism; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D000099207:SS-A Antigen
chemical_list: D012329:RNA, Bacterial; D012343:RNA, Transfer; D022661:RNA, Untranslated; D012261:Ribonucleoproteins; D000099207:SS-A Antigen
keywords: Ro60 autoantigen; noncoding RNAs; tRNA-like domain