ABSTRACT
Budding yeasts are a diverse group of microbes that inhabit a range of environments by exploiting various metabolic traits. The complete genetic basis of these traits are mostly unknown, preventing their addition or removal in a chassis organism for fermentation, including the removal of aerobic ethanol accumulation in Saccharomyces cerevisiae for biomass-derived products. To help understand the molecular evolution of aerobic fermentation in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open source database of manually curated and predicted orthologs in 33 Dikarya fungi (https://github.com/kcorreia/aybrah). AYbRAH was used to evaluate the gain and loss of orthologs in budding yeast central metabolism and refine the topology of recently published yeast species trees. The shift from a lipogenic-citrogenic to ethanologenic lifestyle is distinguished by the emergence of the pyruvate dehydrogenase (PDH) bypass in budding yeasts, with a glucose-inducible acetyl-CoA synthetase. Flux balance analysis (FBA) indicates the PDH bypass has a higher protein and phospholipid yield from glucose than ATP citrate lyase, the ancestral acetyl-CoA source in budding yeasts. Complex I subunits and internal alternative NADH dehydrogenase (NDI) orthologs have been independently lost in multiple yeast lineages. FBA simulations demonstrate Complex I has a significantly higher biomass yield than NDI. We propose the repeated loss of Complex I in yeasts is a result of Complex I inhibition by a mitochondrial metabolite. Existing and future genome annotations can be improved by annotating genomes against manually curated ortholog databases, which we believe can improve the understanding of physiology and evolution across the tree of life.
