Table 1.
Properties of S. cerevisiae models developed to understand dynamic glucose perturbation response: glycolysis (GLYCO), tricarboxylic acid cycle (TCA), pentose phosphate pathway (PPP), trehalose cycle (TRE). Number of ‘+’ sign according to how advantageous the property is. Cofactor conservation moieties are sumAXP and sumNADX. N/A when reactions were not modeled, or data were not shown in article. Refs. [17,20] fitted different parameter sets to multiple data sets. Other models used a unique parameter set. From the literature pool of articles obtained in the systematic reviewing process, only the works which include glycolysis are displayed.
| Rizzi et al. [19] | Teusink et al. [82] | Teusink et al. [22] | van Eunen et al. [17] | |
|---|---|---|---|---|
| Contribution to glycolytic understanding | Dynamic models can accurately describe glucose perturbation. | ATP surplus can cause the observed overactivation of initial glycolytic steps in DTps1 mutant strains. | In vivo behavior cannot be predicted with in vitro kinetics. | Implementation of allosteric regulation and in vivo measured parameter values is necessary to reproduce GP data. |
| GLYCO | Individual + branch reactions (++) | Lumped reactions (+) | Individual + branch reactions (++) | Individual + branch reactions (++) |
| TRE | N/A | N/A | N/A | T6P regulation (+) |
| TCA | Individual reactions (++) | N/A | N/A | N/A |
| PPP | N/A | N/A | N/A | N/A |
| Cofactors | Conservation moiety (+) | Conservation moiety (+) | Conservation moiety (+) | Conservation moiety (+) |
| Parameters | Computational, in vivo (++) | Computational, toy model (+) | Computational, in vivo (++) | Experimental and computational, in vivo (++) |
| Data | Single GP experiment (++) | Single GP, toy data (+) | SS data point (+) | Single GP experiment and multiple SS (+++) |
| Smallbone et al. [16] | Van Heerden et al. [18] | Messiha et al. [33] | Kesten et al. [20] | |
| Contribution to glycolytic understanding | Broad quantification of enzymatic kinetic constants in in vivo-like conditions. | Glycolytic dynamics combined with cell heterogeneity determine cell fate. | Feasibility of constructing larges network models by merging smaller pathway models. | Cooperativity PYK-PYR and ADH-PDH bypass play a major role in the onset of the Crabtree effect. |
| GLYCO | Individual + branch reactions + isozymes (+++) | Individual + branch reactions (++) | Individual + branch reactions (++) | Individual + branch reactions (++) |
| TRE | N/A | T6P regulation (+) | N/A | N/A |
| TCA | N/A | N/A | N/A | Individual reactions (++) |
| PPP | N/A | N/A | Individual reactions (++) | N/A |
| Cofactors | Conservation moiety (+) | Conservation moiety + dynamic Pi (++) | Conservation moiety (+) | Conservation moiety (+) |
| Parameters | Experimental, in vivo (++) | Experimental, in vivo (++) | Experimental, in vivo (++) | Computational, in vivo (++) |
| Data | N/A | Single GP experiment (++) | Single GP experiment (++) | Single GP experiment (++) |