title: Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.
abstract: 5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator.
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada matus.a.valach@gmail.com.
authors.forename: Matus
authors.initials: M
authors.lastname: Valach
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada.
authors.forename: Gertraud
authors.initials: G
authors.lastname: Burger
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4B2, Canada.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Gray
authors.affiliation: Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada franz.lang@umontreal.ca.
authors.forename: B Franz
authors.initials: BF
authors.lastname: Lang
mesh_terms: D003044:Coccidia / Q000235:genetics; D030561:Databases, Nucleic Acid; D050259:Genes, Mitochondrial; D020459:Genes, rRNA; D054629:Genome, Mitochondrial; D054627:Genome, Plastid; D009690:Nucleic Acid Conformation; D000459:Phaeophyceae / Q000235:genetics; D012313:RNA / Q000737:chemistry / Q000235:genetics; D000077278:RNA, Mitochondrial; D012341:RNA, Ribosomal, 5S / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D017423:Sequence Analysis, RNA; D058009:Stramenopiles / Q000235:genetics
chemical_list: D000077278:RNA, Mitochondrial; D012341:RNA, Ribosomal, 5S; D012313:RNA