TABLE 1.
Average residual sum of squares (RSS) for each metabolite in the 12 considered model variants
Shown are the values of RSS for 11 metabolites whose levels have been experimentally measured: sucrose (suc), glucose (gluc), fructose (fru), citrate (cit), 2-oxoglutarate (2OG), succinate (succ), fumarate (fum), malate (mal), glutamate (glu), and GABA. The complete model includes all 30 metabolites and 39 reactions, whereas the reduced model variant excludes reactions 10–14 and 18–21, shown in Fig. 1. The model variant “No phyt-CoA” excludes phytanoyl-CoA as the electron donor via the ETF-ETFQO complex, whereas the model variant “No phyt-CoA and no GABA” excludes in addition the GABA permease (reaction 17) from the complete model. Values for RSS closer to zero indicate a better agreement between time-resolved predictions of metabolite level and the employed experimental data.
| Model | suc | gluc | fru | cit | iso | 2OG | succ | fum | mal | glu | GABA | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| WT | Complete | 159.02 | 221,230.76 | 191,918.84 | 48.34 | 9.38 | 28.93 | 5.57 | 0.82 | 103,723.82 | 26.95 | 0.95 |
| WT | Reduced | 1529.96 | 3005.61 | 2307.22 | 59.57 | 11.93 | 43.70 | 5.90 | 0.19 | 43,305.98 | 104.27 | 0.62 |
| WT | No phyt-CoA | 3415.16 | 5506.61 | 4338.30 | 58.51 | 8.42 | 52.44 | 6.09 | 0.04 | 44,943.25 | 285.25 | 0.95 |
| WT | No phyt-CoA & no GABA | 477.47 | 2065.20 | 819.33 | 19.48 | 0.99 | 14.69 | 1.42 | 0.02 | 43,507.80 | 24.90 | 0.08 |
| d2hgdh1-2 | Complete | 488.61 | 135,187.01 | 155,327.49 | 122.87 | 2.57 | 0.63 | 19.18 | 207.76 | 127,850.79 | 1.22 | 1.51 |
| d2hgdh1-2 | No phyt-CoA | 890.94 | 2482.94 | 947.50 | 165.81 | 64.27 | 2.79 | 28.58 | 307.95 | 852,055.93 | 5.02 | 1.56 |
| etfqo-1 | Complete | 408.56 | 2943.75 | 1138.70 | 176.00 | 24.93 | 2.27 | 54.46 | 15.17 | 469,183.19 | 17.96 | 5.55 |
| etfqo-1 | No phyt-CoA | 146.95 | 1354.74 | 583.71 | 14.16 | 31.34 | 0.91 | 46.62 | 14.74 | 657,855.62 | 3.96 | 2.89 |
| etfqo-2 | Complete | 803.83 | 3524.91 | 1268.16 | 863.69 | 26.61 | 4.26 | 64.24 | 28.35 | 1,256,949.23 | 31.93 | 2.48 |
| etfqo-2 | No phyt-CoA | 813.56 | 3136.59 | 1403.67 | 793.27 | 23.84 | 3.49 | 60.90 | 28.17 | 1,253,703.10 | 36.66 | 1.58 |
| ivdh-1 | Complete | 976.12 | 5556.01 | 4530.74 | 115.37 | 122.38 | 0.89 | 16.64 | 9.37 | 719,997.15 | 4.39 | 0.73 |
| ivdh-1 | No phyt-CoA | 1163.52 | 5959.82 | 4884.76 | 79.20 | 89.29 | 0.31 | 16.59 | 7.70 | 701,012.11 | 4.26 | 0.95 |