Figure 8

Proposed routes for raffinose utilization in S. cerevisiae. (a) Based on annotation in KEGG and reactions already present in the yeast models, our initial implementation of the raffinose utilization pathway began with the intracellular cleavage of the α-galactosidic bond in raffinose (blue diamond + yellow triangle + brown square) by the protein product of YBR184W to produce sucrose (yellow triangle + brown square) and galactose (blue diamond). Subsequently, the β-fructosidic bond in sucrose is cleaved by SUC2, resulting in the formation of glucose (yellow triangle) and fructose (brown square). Finally, the glucose and fructose produced from sucrose hydrolysis can enter glycolysis and meet cells' metabolic needs. (b) Based on literature citing the lack of an α-galactosidase in the strain of S. cerevisiae studied here, we implemented a raffinose utilization pathway lacking the α-galactosidase reaction. The two different pathways for raffinose utilization were each implemented separately in the iLL672 model, and assessed based on the relative concordance of the phenotypic predictions made by the different builds, with the experimentally determined gene deletion phenotypes. We found an increased concordance with the iLL672 build lacking YBR184W, suggesting that the pathway depicted in (b) is correct.