title: Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes.
abstract: Transfer RNA (tRNA) is essential for the translation of genetic information into proteins, and understanding its molecular evolution is important if we are to understand the genetic code. In general, long variable-arm (V-arm) structures form in tRNA(Leu), tRNA(Ser), and bacterial and organellar tRNA(Tyr). However, as we have previously reported, noncanonical V-arms occur in nematode tRNA(Gly) and tRNA(Ile), and potentially affect translational fidelity. Here, we comprehensively analyzed 69 eukaryotic genome sequences and examined the evolutionary divergence of the V-arm-containing tRNAs. In total, 253 V-arm-containing tRNAs, with neither leucine nor serine anticodons, were identified in organisms ranging from nematodes to fungi, plants, and vertebrates. We defined them as "noncanonical V-arm-containing tRNAs" (nov-tRNAs). Moreover, 2,415 nov-tRNA-like sequences lacking some of the conserved features of tRNAs were also identified, largely in vertebrate genomes. These nov-tRNA/nov-tRNA-like sequences can be categorized into three types, based on differences in their possible evolutionary origins. The type A nov-tRNAs in nematodes probably evolved not only from tRNA(Leu) but also from tRNA(Ser) and other isotypes on several independent occasions. The type B nov-tRNAs are dispersed abundantly throughout vertebrate genomes, and seem to have originated from retrotransposable elements. The type C nov-tRNAs may have been acquired from plant chloroplasts or from bacteria through horizontal transfer. Our findings provide unexpected insight into the evolution of the tRNA molecule, which was diverse and occurred independently in nematodes, vertebrates, and plants.
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
authors.forename: Kiyofumi
authors.initials: K
authors.lastname: Hamashima
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan akio@sfc.keio.ac.jp.
authors.forename: Akio
authors.initials: A
authors.lastname: Kanai
mesh_terms: D049148:Aminoacylation; D000818:Animals; D002335:Carnivora / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D056890:Eukaryota / Q000235:genetics*; D019143:Evolution, Molecular; D018628:Gene Dosage; D009348:Nematoda / Q000235:genetics; D009690:Nucleic Acid Conformation; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics*; D018626:Retroelements; D020086:Short Interspersed Nucleotide Elements
chemical_list: D018626:Retroelements; D012343:RNA, Transfer
keywords: chloroplast; molecular evolution; phylogenetics; retrotransposable element; transfer RNA; variable arm