Simulations with iJR904 were all done using the software package SimPheny™ (Genomatica, San Diego, CA); this software was also used to build iJR904. All calculations were made using the conditions outlined in this section. The biomass reaction was the same as that reported previously [8 (link)] with the addition of intracellular protons and water, and can be found in the additional data files. All flux values reported in this section are in units of mmol/g DW-hr. The flux through the non-growth associated ATP maintenance reaction (ATPM in the additional data files) was fixed to 7.6. Fluxes through all other internal reactions have an upper limit of 1 × 1030; if the reaction is reversible the lower limit is -1 × 1030 and if it is irreversible the lower limit is zero.
In addition to the metabolic reactions listed in the additional data files, reversible exchange reactions for all external metabolites were also included in the simulations to allow external metabolites to cross the system boundaries. If these exchange reactions are used in the forward direction the external metabolites leave the system and if used in the reverse direction (that is, a negative flux value through the reaction) the external metabolites enter the system.
The following external metabolites were allowed to freely enter and leave the system: ammonia, water, phosphate, sulfate, potassium, sodium, iron (II), carbon dioxide and protons (except during the robustness study where proton exchange flux was constrained down to zero). The corresponding exchange fluxes for these metabolites have a lower and upper flux limit of -1 × 1030 and 1 × 1030, respectively. Aerobic conditions were simulated with a maximum oxygen uptake rate of 20 mmol/g DW-hr, by setting the lower and upper limits for the oxygen exchange flux to -20 and 0 respectively, and anaerobic conditions were simulated by fixing the oxygen uptake rate to 0. All other external metabolites, except for the carbon source, were only allowed to leave the system. The lower and upper limits on their corresponding exchange fluxes were 0 and 1 × 1030, respectively. Growth on different carbon sources was simulated by allowing those external metabolites to enter the system; the actual flux values for uptake rates used in the simulations are noted in the text and figures, where the upper limit is 0 and the lower limit is the negative of the uptake rate listed. These constraints are also summarized in the additional data files.
In addition to the metabolic reactions listed in the additional data files, reversible exchange reactions for all external metabolites were also included in the simulations to allow external metabolites to cross the system boundaries. If these exchange reactions are used in the forward direction the external metabolites leave the system and if used in the reverse direction (that is, a negative flux value through the reaction) the external metabolites enter the system.
The following external metabolites were allowed to freely enter and leave the system: ammonia, water, phosphate, sulfate, potassium, sodium, iron (II), carbon dioxide and protons (except during the robustness study where proton exchange flux was constrained down to zero). The corresponding exchange fluxes for these metabolites have a lower and upper flux limit of -1 × 1030 and 1 × 1030, respectively. Aerobic conditions were simulated with a maximum oxygen uptake rate of 20 mmol/g DW-hr, by setting the lower and upper limits for the oxygen exchange flux to -20 and 0 respectively, and anaerobic conditions were simulated by fixing the oxygen uptake rate to 0. All other external metabolites, except for the carbon source, were only allowed to leave the system. The lower and upper limits on their corresponding exchange fluxes were 0 and 1 × 1030, respectively. Growth on different carbon sources was simulated by allowing those external metabolites to enter the system; the actual flux values for uptake rates used in the simulations are noted in the text and figures, where the upper limit is 0 and the lower limit is the negative of the uptake rate listed. These constraints are also summarized in the additional data files.
