Signatures of optimal codon usage in metabolic genes inform budding yeast ecology

LaBella, Abigail Leavitt; Opulente, Dana A.; Steenwyk, Jacob L.; Hittinger, Chris Todd; Rokas, Antonis

doi:10.1371/journal.pbio.3001185

Signatures of optimal codon usage in metabolic genes inform budding yeast ecology

Journal Article · Mon Apr 19 00:00:00 EDT 2021 · PLoS Biology (Online)

DOI:https://doi.org/10.1371/journal.pbio.3001185· OSTI ID:1804455

^[1]; Opulente, Dana A. ^[2]; ^[3]; ^[4]; ^[3]

Vanderbilt Univ., Nashville, TN (United States); Vanderbilt University Department of Biological Sciences
Villanova Univ., PA (United States)
Vanderbilt Univ., Nashville, TN (United States)
Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States)

Reverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism (GAL) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in the GAL pathway is positively correlated with quantitative growth on galactose, suggesting that GAL codon optimization reflects increased capacity to grow on galactose. Optimal codon usage in the GAL pathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage of GAL genes is greater than 85% of all genes in the genome of the major human pathogen Candida albicans (CUG-Ser1 clade) and greater than 75% of genes in the genome of the dairy yeast Kluyveromyces lactis (family Saccharomycetaceae). We further find a correlation between optimization in the GALactose pathway genes and several genes associated with nutrient sensing and metabolism. This work suggests that codon optimization harbors information about the metabolic ecology of microbial eukaryotes. This information may be particularly useful for studying fungal dark matter—species that have yet to be cultured in the lab or have only been identified by genomic material.

Research Organization:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); USDA

Grant/Contract Number:: SC0018409

OSTI ID:: 1804455

Journal Information:: PLoS Biology (Online), Journal Name: PLoS Biology (Online) Journal Issue: 4 Vol. 19; ISSN 1545-7885

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Ecological niches
Enzyme metabolism
Galactose
Gene expression
Genomics
Glucose
Mannose
Saccharomyces cerevisiae

Signatures of optimal codon usage in metabolic genes inform budding yeast ecology

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