ArticleGenome biology and evolution2014
Molecular phylogeny of sequenced Saccharomycetes reveals polyphyly of the alternative yeast codon usage.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Functional mapping of the N-terminal region of the yeast moonlighting protein Sis2/Hal3 reveals crucial residues for Ppz1 regulation.The FEBS journal · 2022Article
- Proteogenomics analysis of CUG codon translation in the human pathogen Candida albicans.BMC biology · 2021Article
- Survival Strategies of PathogenicmBio · 2020Article
- Fungal evolution: diversity, taxonomy and phylogeny of the Fungi.Biological reviews of the Cambridge Philosophical Society · 2019Article
- Review
- Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes.Molecular biology and evolution · 2019Article
- Development of a Transformation Method for Metschnikowia borealis and other CUG-Serine Yeasts.Genes · 2019Article
- Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica.Current biology : CB · 2018Article
- Synthetic genome recoding: new genetic codes for new features.Current genetics · 2018Review
- A CTG Clade Candida Yeast Genetically Engineered for the Genotype-Phenotype Characterization of Azole Antifungal Resistance in Human-Pathogenic Yeasts.Antimicrobial agents and chemotherapy · 2018Article
- Whole Genome Sequence of the Heterozygous Clinical IsolateG3 (Bethesda, Md.) · 2017Article
- How tRNAs dictate nuclear codon reassignments: Only a few can capture non-cognate codons.RNA biology · 2017Review
- Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data.G3 (Bethesda, Md.) · 2016Article
- Evolutionary genomics of yeast pathogens in the Saccharomycotina.FEMS yeast research · 2016Review
- Comparative genomics of biotechnologically important yeasts.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.Genome research · 2016Article
- The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata.FEMS yeast research · 2016Review
- The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts.BMC genomics · 2015Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The universal genetic code defines the translation of nucleotide triplets, called codons, into amino acids. In many Saccharomycetes a unique alteration of this code affects the translation of the CUG codon, which is normally translated as leucine. Most of the species encoding CUG alternatively as serine belong to the Candida genus and were grouped into a so-called CTG clade. However, the "Candida genus" is not a monophyletic group and several Candida species are known to use the standard CUG translation. The codon identity could have been changed in a single branch, the ancestor of the Candida, or to several branches independently leading to a polyphyletic alternative yeast codon usage (AYCU). In order to resolve the monophyly or polyphyly of the AYCU, we performed a phylogenomics analysis of 26 motor and cytoskeletal proteins from 60 sequenced yeast species. By investigating the CUG codon positions with respect to sequence conservation at the respective alignment positions, we were able to unambiguously assign the standard code or AYCU. Quantitative analysis of the highly conserved leucine and serine alignment positions showed that 61.1% and 17% of the CUG codons coding for leucine and serine, respectively, are at highly conserved positions, whereas only 0.6% and 2.3% of the CUG codons, respectively, are at positions conserved in the respective other amino acid. Plotting the codon usage onto the phylogenetic tree revealed the polyphyly of the AYCU with Pachysolen tannophilus and the CTG clade branching independently within a time span of 30–100 Ma.
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