Extended Data Fig. 8: Thermodynamically constrained model better predicts the cell-cycle dynamics of key metabolic fluxes compared to enzyme-constrained model.
(a) Glucose-uptake flux measurements, described in Fig. 4e. (b) Glycolytic flux measurements, described in Fig. 4f. (c) Glucose-uptake flux predictions of thermodynamically constrained model, described in Fig. 4b. In agreement with independent experimental measurements (a, b), the model predicts the highest fluxes (violet) in G1 and the trough of the flux dynamics in S/G2/M. (d) Glucose-uptake flux predictions of enzyme-constrained model. This model predicts the highest glucose-uptake-flux values in the middle of S/G2/M, contradicting experimental observations (a, b). (e,f) Measurements of carbon dioxide and oxygen exchange rates, described in Extended Data Fig. 6c. (g) O2-uptake and CO2-excretion flux predictions of thermodynamically constrained model, described in Fig. 4b. In agreement with experimental measurements (f), the model predicts that O2-uptake and CO2-excretion rates oscillate almost in antiphase, O2 uptake peaks soon after budding and CO2 excretion peaks in late S/G2/M and G1. (h) O2-uptake and CO2-excretion flux predictions of enzyme-constrained model. This model predicts the highest values of CO2-excretion flux in the middle of S/G2/M and synchronized dynamics of O2-uptake and CO2-excretion fluxes, contradicting independent observations (f). d,h: we predicted metabolic fluxes via the model with constraints over enzyme kinetics and abundance (GECKO, v.2.0.2) [main-text ref. 48] by incorporating the cell-cycle-resolved macromolecular synthesis rates (Fig. 3c, d) identically to how we did it with thermodynamically constrained model. We used the same stoichiometry of macromolecule and biomass reactions (Supplementary Table 7). In GECKO, the total amount of enzyme had an upper limit such that the model could freely distribute individual enzyme amounts under this overall constraint. In model simulations for all cell-cycle time points, we set the upper limit of the total enzyme amount to 0.0445 g/gDW, under which GECKO with modified macromolecule reaction stoichiometries correctly predicts, at the population level, changes of yeast physiology (the rates of growth, oxygen uptake, ethanol and carbon dioxide excretion) across the range of glucose uptake rates [main-text ref. 40]. GECKO was accessed with the help of the Python module geckopy.
