title: A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.
abstract: The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects.
authors.affiliation: Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
authors.forename: Stefanie
authors.initials: S
authors.lastname: Mühlhausen
authors.affiliation: Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
authors.forename: Peggy
authors.initials: P
authors.lastname: Findeisen
authors.affiliation: Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
authors.forename: Uwe
authors.initials: U
authors.lastname: Plessmann
authors.affiliation: Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Bioanalytics Group, Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.
authors.forename: Henning
authors.initials: H
authors.lastname: Urlaub
authors.affiliation: Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
authors.forename: Martin
authors.initials: M
authors.lastname: Kollmar
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics; D003062:Codon; D019143:Evolution, Molecular; D005815:Genetic Code; D058977:Molecular Sequence Annotation; D012343:RNA, Transfer / Q000235:genetics; D004718:Saccharomycetales / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D003062:Codon; D012343:RNA, Transfer