ArticleMolecular biology and evolution2023
Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 34 citations in OpenAlex.
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- Alternative Approaches and Plant-Based Remedies for Livestock Health Management Among the Batswana of Southern Africa: A Review.Chemistry & biodiversity · 2026Review
- Genomic and physiological signatures of adaptation in pathogenic fungi.Nature communications · 2026Article
- Xylose Metabolism Perturbation in Yarrowia lipolytica for Efficient Succinic Acid Bioproduction from Lignocellulosic Biomass.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Taxogenomic Analysis of a Novel Yeast Species, Lachancea rosae Sp. Nov. F.A., Isolated From the Wild Rose Rosa californica.Yeast (Chichester, England) · 2025Article
- Beyond Sugar: A Holistic Review of Sweeteners and Their Role in Modern Nutrition.Foods (Basel, Switzerland) · 2025Review
- Convergent reductive evolution in bee-associated lactic acid bacteria.Applied and environmental microbiology · 2024Article
- Genomic factors shaping codon usage across the Saccharomycotina subphylum.G3 (Bethesda, Md.) · 2024Article
- Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework.Yeast (Chichester, England) · 2024Review
- Convergent reductive evolution in bee-associated lactic acid bacteria.bioRxiv : the preprint server for biology · 2024Article
- Machine learning enables identification of an alternative yeast galactose utilization pathway.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.Science (New York, N.Y.) · 2024Article
- Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces.Biotechnology for biofuels and bioproducts · 2024Article
- Natural trait variation across Saccharomycotina species.FEMS yeast research · 2024Review
- Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov.Yeast (Chichester, England) · 2023Article
- Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism.PLoS biology · 2023Article
- Genomic and ecological factors shaping specialism and generalism across an entire subphylum.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
8 authors at 3 institutions in 1 country.
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Abstract
Xylose is the second most abundant monomeric sugar in plant biomass. Consequently, xylose catabolism is an ecologically important trait for saprotrophic organisms, as well as a fundamentally important trait for industries that hope to convert plant mass to renewable fuels and other bioproducts using microbial metabolism. Although common across fungi, xylose catabolism is rare within Saccharomycotina, the subphylum that contains most industrially relevant fermentative yeast species. The genomes of several yeasts unable to consume xylose have been previously reported to contain the full set of genes in the XYL pathway, suggesting the absence of a gene-trait correlation for xylose metabolism. Here, we measured growth on xylose and systematically identified XYL pathway orthologs across the genomes of 332 budding yeast species. Although the XYL pathway coevolved with xylose metabolism, we found that pathway presence only predicted xylose catabolism about half of the time, demonstrating that a complete XYL pathway is necessary, but not sufficient, for xylose catabolism. We also found that XYL1 copy number was positively correlated, after phylogenetic correction, with xylose utilization. We then quantified codon usage bias of XYL genes and found that XYL3 codon optimization was significantly higher, after phylogenetic correction, in species able to consume xylose. Finally, we showed that codon optimization of XYL2 was positively correlated, after phylogenetic correction, with growth rates in xylose medium. We conclude that gene content alone is a weak predictor of xylose metabolism and that using codon optimization enhances the prediction of xylose metabolism from yeast genome sequence data.
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