title: Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes.
abstract: Remolding of tRNAs is a well-documented process in mitochondrial genomes that changes the identity of a tRNA. It involves a duplication of a tRNA gene, a mutation that changes the anticodon and the loss of the ancestral tRNA gene. The net effect is a functional tRNA that is more closely related to tRNAs of a different alloacceptor family than to tRNAs with the same anticodon in related species. Beyond being of interest for understanding mitochondrial tRNA function and evolution, tRNA remolding events can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. Therefore, it is important to identify and catalog these events. Here we describe novel methods to detect tRNA remolding in large-scale data sets and apply them to survey tRNA remolding throughout animal evolution. We identify several novel remolding events in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived from ancestral events.
authors.affiliation: Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany Bioinformatics Unit and Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany sahyoun@ie-freiburg.mpg.de.
authors.forename: Abdullah H
authors.initials: AH
authors.lastname: Sahyoun
authors.affiliation: RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Hölzer
authors.affiliation: Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Jühling
authors.affiliation: Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Höner zu Siederdissen
authors.affiliation: Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon.
authors.forename: Marwa
authors.initials: M
authors.lastname: Al-Arab
authors.affiliation: Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon.
authors.forename: Kifah
authors.initials: K
authors.lastname: Tout
authors.affiliation: RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany Michael Stifel Center Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.affiliation: Parallel Computing and Complex Systems Group, Department of Computer Science, Leipzig University, Augustusplatz 10, D-04109 Leipzig, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Middendorf
authors.affiliation: Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany Fraunhofer Institut für Zelltherapie und Immunologie Perlickstraße 1, D-04103 Leipzig, Germany Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: Parallel Computing and Complex Systems Group, Department of Computer Science, Leipzig University, Augustusplatz 10, D-04109 Leipzig, Germany bernt@informatik.uni-leipzig.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Bernt
mesh_terms: D000818:Animals; D000926:Anticodon; D003062:Codon; D003445:Crustacea / Q000235:genetics; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D009154:Mutation; D011161:Porifera / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics*; D012356:RNA, Transfer, Leu / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D000926:Anticodon; D003062:Codon; D012356:RNA, Transfer, Leu; D012343:RNA, Transfer