Fig 1.
Flowchart describing the steps involved in the evaluation of a given metabolic pathway.
The block within the orange dashed box constitutes the steps of one multi-objective optimisation run. The numbers in blue refer to the corresponding manuscript section with a detailed explanation.
Table 1.
A summary of the multi-objective optimisation components presented in section 2 and the epsilon-constraint solution strategy.
Table 2.
Features of the solvers used to perform the metabolic pathway optimisations.
Fig 2.
Representation of the six pathways selected for propionate oxidation.
Table 3.
Performance of propionate oxidation pathways at Cpro- = 0.01 mol/L, CH2 = 1 nmol/L, pHin = pHout = 7, T = 35°C, ΔGATP = 50 kJ/mol, rH/ATP = 10/3, free CoA = 0.001 mol/L, total CoA pool < 0.01 mol/L.
The available Gibbs energy for the overall reaction (Eq 17) is 63.3 kJ/mol under these conditions (ΔGoverall = -63.3 kJ/mol).
Fig 3.
Pareto curves for propionate oxidation pathways.
The pathways were evaluated at the same parameters as Table 3. The horizontal axis represents the net energy recovered from the pathway, and the vertical axis represents the maximum MDF possible for the pathway with that energy recovery. The various points are obtained by changing the value of ε (number of proton translocations sacrificed) from 0 to 5.
Fig 4.
Detailed bioenergetic breakdown of the via lactate pathway, evaluated at the same parameters as listed in Table 3.
The wide red bars represent proton translocations invested and the bright green bars represent proton translocations recovered. The narrow dark green bars represent SLP. A greyed-out bar indicates a reaction that’s repeated for the sequential listing of species. The species are arranged in the order they react and are produced by the pathway, allowing for visual identification of bottlenecks.
Fig 5.
Anabolic CO2 fixation pathway via reverse TCA cycle.
Fig 6.
Detailed bioenergetic breakdown of the reverse TCA pathway, evaluated at the parameters from Table 4, and Cic = 0.001 mol/L.
The wide red bars represent proton translocations invested and the bright green bars represent proton translocations recovered. The narrow dark green bars represent SLP. A greyed-out bar indicates a reaction that’s repeated for the sequential listing of species. The species are arranged in the order they react and are produced by the pathway, allowing for visual identification of bottlenecks.
Table 4.
Performance of reverse TCA cycle pathway at selected concentrations of inorganic carbon, pHin = pHout = 7, T = 25°C, ΔGATP = 50 kJ/mol, rH/ATP = 10/3, CH2 = 3 μmol/L, free CoA = 0.001 mol/L, total CoA pool < 0.01 mol/L.
Note that the calculation of yield efficiency is inverted for endergonic cases, thus it cannot be directly compared with the exergonic cases.
Fig 7.
Pareto curves for the reverse TCA cycle evaluated at the same parameters as Table 4 excluding Cic.
The horizontal axis represents the net energy spent in the pathway in units of proton translocations, and the vertical axis represents the maximum MDF possible for the pathway with that energy recovery. The various points are obtained by changing the value of epsilon (number of translocations conceded) from 0 to 5.