WGD and yeast carbon metabolism. (a) Illustrated are glycolysis, alcohol fermentation, and the mitochondrial TCA cycle. We denote the enzymes catalyzing a reaction with circled gene names. Products of SSD events are indicated by single lines joining the pair of enzymes. Enzymes duplicated at WGD are joined by three lines. WGD pairs in red are preserved in duplicate in four extant yeasts: S. cerevisiae, S. bayanus, C. glabrata, and S. castellii. Protein localization for CIT, ADH, and ALD is taken from Huh et al. [46]. We indicate the pyruvate dehydrogenase (PDH) multienzyme complex with a darker blue enclosure. There is a clear bias in where the duplicated enzymes lie, particularly if only those preserved in duplicate across four species are considered. From [47]. (b) Duplicated enzymes losses immediately after WGD were biased toward enzymes catalyzing low-flux reactions. The fluxes through all reactions in the yeast metabolic network [48] were computed under a variety of nutrient conditions as previously described [49]. Then, using our tool for estimating the timing of gene loss after WGD [50], we identified enzymes likely to have been lost along the short branch separating the WGD from the divergence of K. polysporus from the remaining four yeast species. We compared the fluxes of those enzymes to that of enzymes retained in duplicate along that same branch. The genes lost immediately after WGD were more likely to code for enzymes of low flux (, permutation analysis; unpublished data).
