Figure 1

An example network featuring the difference in predicted flux distributions between FBA and MD-FBA. Thick arrows represent metabolic reactions and circular nodes represent metabolites. Narrow arrows represent the growth-associated dilution of their attached metabolites. Note that the stoichiometric coefficients for reaction v₂ are two molecules of A per one molecule of D. v₁ and v₆ represent the uptake for metabolites A and X, respectively. B is the sole metabolite within the biomass, and hence the flux through v₅ represents the growth rate. Blue (dash-dot) and red (solid) arrows represent reactions predicted to be active by MD-FBA and FBA, respectively, while black (dashed) arrows represent all other reactions. The figure illustrates growth on two media: (a) growth on a medium in which both A and X are present; (b) growth on a medium including only metabolite A. FBA predicts the same growth rate, which is equal to v₁ under both media, while MD-FBA predicts a growth rate equal to v₁ when both A and X are present in the medium and a growth rate equal to 0.5v1 when only A is included in the medium. The latter is due to the fact that when X is absent from the growth medium, MD-FBA cannot activate reactions v₄ and v₈, since the dilution of metabolites C and C* cannot be satisfied under this medium. The different flux distributions predicted by the two methods lead to different predictions of enzyme essentiality, as detailed in the main text.