A Method to Constrain Genome-Scale Models with 13C Labeling Data
Fig 8
Robustness with respect to genome reconstruction errors.
A reconstruction error was simulated by changing the NADPH dependence to NADH dependence for the glucose-6-phosphate dehydrogenase (with a large flux value of 2.9 mMol/gdw/hr in the initial 2S-13C MFA calculation). We calculated fluxes again through 2S-13C MFA and FBA (constrained by extracellular flux measurements), and the new fluxes are plotted for the TCA cycle. As can be observed, the change is much larger for FBA than 2S-13C MFA, showing that it is less robust to reconstruction errors (note that squares and circles are almost on top of each other for the 2S-13C MFA case). The transparency in the original flux profile for 2S-13C MFA indicates the confidence intervals. For the 2S-13C MFA case, the NADPH production shift is compensated entirely by the THD2 transhydrogenase. Since the flux value for SUCD1i is negative, the absolute value has been plotted. Similar figures for the glutamate dehydrogenase (GLUDy) and isocitrate dehydrogenase (ICDHyr) reactions are available as S16 Fig.