Figure 6. Examples of epistatic interactions (red dashed lines) with respect to flux phenotypes (red circles), overlaid on the corresponding metabolic pathways.

(A) In Figure 5B, there is an abundance of synergistic interactions between complex II of the electron transport chain (ETC II) and various other biological processes, with respect to succinate secretion. The basis for these interactions is the fact that ETC II catalyzes the succinate dehydrogenase reaction (SDH), which is the major flux consuming succinate under the modeled condition. If SDH is deleted, succinate is predicted to be secreted from the cell. Therefore, a gene deletion resulting in an increase in flux through SDH, will be observed to interact synergistically with SDH relative to succinate secretion. (B) A second predicted interaction is a positive synergistic interaction between glt1 and cox1 relative to glycerol secretion as a phenotype. The metabolic basis for this interaction is the involvement of both the genes and the phenotype in NADH/NAD balancing. Specifically, glt1 is an NADH dependent reaction, and in its absence, glutamate is synthesized by the NADPH dependant glutamate dehydrogenase reaction. Therefore, the deletion of glt1 leaves an excess of NADH, which is in turn oxidized via the respiratory chain. In the cox1 mutant, the respiratory chain is no longer functional, and the redox imbalance is alleviated through glycerol production (Figure S9). Hence, there is an unexpectedly large increase in glycerol secretion in the double mutant, relative to what is observed in the single mutants.