ArticleGenome research2016
A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 84 citations in OpenAlex.
- Predicting the Structural Effects of CUG Codon Translation on Uncharacterized Proteins inJournal of fungi (Basel, Switzerland) · 2025Article
- Ancient origin and high diversity of zymocin-like killer toxins in the budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates.PLoS genetics · 2024Article
- Genomic factors shaping codon usage across the Saccharomycotina subphylum.G3 (Bethesda, Md.) · 2024Article
- Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids.Chemical reviews · 2024Review
- Evolution of the Genetic Code in the Ascoideales (CUG-Ser2) Yeast Clade: The Ancestral tRNA-Leu(CAG) Gene Is Retained in Most Saccharomycopsis Species but Is Nonessential and Not Used for Translation.Genome biology and evolution · 2024Article
- A systematic screen for co-option of transposable elements across the fungal kingdom.Mobile DNA · 2024Article
- Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids.PLoS genetics · 2023Article
- A genome-informed higher rank classification of the biotechnologically important fungal subphylumStudies in mycology · 2023Article
- The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes.International journal of molecular sciences · 2023Article
- Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing.Frontiers in plant science · 2022Article
- Proteogenomics analysis of CUG codon translation in the human pathogen Candida albicans.BMC biology · 2021Article
- Article
- tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes.Nucleic acids research · 2021Article
- The role of non-standard translation in Candida albicans pathogenesis.FEMS yeast research · 2021Review
- Transfer RNAs: diversity in form and function.RNA biology · 2021Review
- tRNAs as a Driving Force of Genome Evolution in Yeast.Frontiers in microbiology · 2021Review
- Fungal evolution: diversity, taxonomy and phylogeny of the Fungi.Biological reviews of the Cambridge Philosophical Society · 2019Article
- The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae.FEMS yeast research · 2019Article
- Variation and selection on codon usage bias across an entire subphylum.PLoS genetics · 2019Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.