title: Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix.
abstract: The genetic code is one of the most highly conserved characters in living organisms. Only a small number of genomes have evolved slight variations on the code, and these non-canonical codes are instrumental in understanding the selective pressures maintaining the code. Here, we describe a new case of a non-canonical genetic code from the oxymonad flagellate Streblomastix strix. We have sequenced four protein-coding genes from S.strix and found that the canonical stop codons TAA and TAG encode the amino acid glutamine. These codons are retained in S.strix mRNAs, and the legitimate termination codons of all genes examined were found to be TGA, supporting the prediction that this should be the only true stop codon in this genome. Only four other lineages of eukaryotes are known to have evolved non-canonical nuclear genetic codes, and our phylogenetic analyses of alpha-tubulin, beta-tubulin, elongation factor-1 alpha (EF-1 alpha), heat-shock protein 90 (HSP90), and small subunit rRNA all confirm that the variant code in S.strix evolved independently of any other known variant. The independent origin of each of these codes is particularly interesting because the code found in S.strix, where TAA and TAG encode glutamine, has evolved in three of the four other nuclear lineages with variant codes, but this code has never evolved in a prokaryote or a prokaryote-derived organelle. The distribution of non-canonical codes is probably the result of a combination of differences in translation termination, tRNAs, and tRNA synthetases, such that the eukaryotic machinery preferentially allows changes involving TAA and TAG.
authors.affiliation: Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4. pkeeling@interchange.ubc.ca
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Keeling
authors.forename: Brian S
authors.initials: BS
authors.lastname: Leander
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D018388:Codon, Terminator / Q000235:genetics; D017931:DNA Primers / Q000737:chemistry; D016054:DNA, Protozoan; D056890:Eukaryota / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D017125:Genes, Protozoan; D005815:Genetic Code; D005973:Glutamine / Q000235:genetics; D018841:HSP90 Heat-Shock Proteins / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010445:Peptide Elongation Factors / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D014176:Protein Biosynthesis; D016053:RNA, Protozoan / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer; D017386:Sequence Homology, Amino Acid; D014404:Tubulin / Q000235:genetics
chemical_list: D018388:Codon, Terminator; D017931:DNA Primers; D016054:DNA, Protozoan; D018841:HSP90 Heat-Shock Proteins; D010445:Peptide Elongation Factors; D016053:RNA, Protozoan; D012335:RNA, Ribosomal; D014404:Tubulin; D005973:Glutamine; D012343:RNA, Transfer