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Nalabothu RL, Fisher KJ, LaBella AL, Meyer TA, Opulente DA, Wolters JF, Rokas A, Hittinger CT. Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts. Mol Biol Evol 2023; 40:msad111. [PMID: 37154525 PMCID: PMC10263009 DOI: 10.1093/molbev/msad111] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/28/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
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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Affiliation(s)
- Rishitha L Nalabothu
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Kaitlin J Fisher
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC
| | - Taylor A Meyer
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
- Department of Biology, Villanova University, Villanova, PA
| | - John F Wolters
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI
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