title: Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs.
abstract: The faithful translation of the genetic code requires the highly accurate aminoacylation of transfer RNAs (tRNAs). However, it has been shown that nematode-specific V-arm-containing tRNAs (nev-tRNAs) are misacylated with leucine in vitro in a manner that transgresses the genetic code. nev-tRNA(Gly) (CCC) and nev-tRNA(Ile) (UAU), which are the major nev-tRNA isotypes, could theoretically decode the glycine (GGG) codon and isoleucine (AUA) codon as leucine, causing GGG and AUA codon ambiguity in nematode cells. To test this hypothesis, we investigated the functionality of nev-tRNAs and their impact on the proteome of Caenorhabditis elegans. Analysis of the nucleotide sequences in the 3' end regions of the nev-tRNAs showed that they had matured correctly, with the addition of CCA, which is a crucial posttranscriptional modification required for tRNA aminoacylation. The nuclear export of nev-tRNAs was confirmed with an analysis of their subcellular localization. These results show that nev-tRNAs are processed to their mature forms like common tRNAs and are available for translation. However, a whole-cell proteome analysis found no detectable level of nev-tRNA-induced mistranslation in C. elegans cells, suggesting that the genetic code is not ambiguous, at least under normal growth conditions. Our findings indicate that the translational fidelity of the nematode genetic code is strictly maintained, contrary to our expectations, although deviant tRNAs with misacylation properties are highly conserved in the nematode genome.
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.
authors.forename: Masaru
authors.initials: M
authors.lastname: Mori
authors.affiliation: Genome Biology Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, SOKENDAI, Mishima, Japan.
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Andachi
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: Genome Biology Laboratory, National Institute of Genetics, Mishima, Japan; Department of Genetics, SOKENDAI, Mishima, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kohara
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: Akio
authors.initials: A
authors.lastname: Kanai
mesh_terms: D000818:Animals; D000926:Anticodon / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism; D003062:Codon / Q000235:genetics; D005815:Genetic Code / Q000235:genetics; D009348:Nematoda / Q000235:genetics / Q000378:metabolism*; D012343:RNA, Transfer / Q000235:genetics*
chemical_list: D000926:Anticodon; D003062:Codon; D012343:RNA, Transfer