A Method to Constrain Genome-Scale Models with 13C Labeling Data
Fig 6
Cofactor balances show how NADPH and NADH production and consumption change after pgi is knocked out. Arrows pointing inwards on the left indicate fluxes that produce the indicated metabolite and fluxes pointing outwards on the right indicate fluxes that consume it (in units of mMol/gdw/hr). Reaction names are per iJR904 model. Upper panels show NADPH balances for wild type (left) and pgi KO (right) at 5 and 21hr (equivalent growth points due to a lower growth rate in the pgi KO). Lower panels show NADH balances for wild type (left) and pgi KO (right) at the same time points. Note that, unlike FBA, 2S-13C MFA can provide confidence intervals bounded by the data from 13C labeling experiments. These are shown below the reaction name. For some cases (e.g. GND) the experimental data can very effectively constrain the flux value, even if the reaction is not in the core set over which labeling is being tracked (e.g. C181SN). For some others (e.g. THD2), the data can only constrain the flux value in a very limited fashion. Knocking out pgi radically changes NADPH and NADH supply and consumption patterns.