title: Distribution and frequencies of post-transcriptional modifications in tRNAs.
abstract: Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.
authors.affiliation: a International Institute of Molecular and Cell Biology ; Warsaw , Poland.
authors.forename: Magdalena A
authors.initials: MA
authors.lastname: Machnicka
authors.forename: Anna
authors.initials: A
authors.lastname: Olchowik
authors.forename: Henri
authors.initials: H
authors.lastname: Grosjean
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D019605:Euryarchaeota / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005658:Fungi / Q000145:classification / Q000235:genetics / Q000378:metabolism; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D018087:Plastids / Q000235:genetics / Q000378:metabolism; D014176:Protein Biosynthesis; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012984:Software; D057948:Viridiplantae / Q000145:classification / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D012343:RNA, Transfer
keywords: RNA maturation; comparative analysis; evolution; modified nucleotides; post-transcriptional modification; tRNA; tRNA modifications; tRNA sequence; web server