2.1. Genome-scale metabolic models
In this study, the genome-scale models of iMM904 (Mo, Palsson, &
HerrgÄrd, 2009), iEM439 (E Motamedian, Saeidi, & Shojaosadati, 2016),
and iJO1366 (Orth et al., 2011) for S. cerevisiae, Z. mobilis,and E. coli were used, respectively. The intracellular reversible
reaction fluxes were constrained between -1000 to 1000 mmol/gDCW/h,
while intracellular irreversible reaction fluxes had zero lower limits.
For the simulation of growth on minimal glucose media by the three
metabolic models, lower bounds of exchange reactions were set to zero
except for glucose, NH4, H2O,
SO4, O2, H+, phosphate
and inorganic ions exchange reactions. Growth on glucose was simulated
by the maximum uptake rate of 10 mmol/gDCW/h. Flux balance analysis
(FBA) was used to simulate the growth, and the biomass reaction was used
as an objective function to be maximized in all in silicoexperiments. MATLAB (R2017b) was used for modeling using the COBRA
Toolbox, and the GLPK (GNU Linear Programming Kit) package was used to
solve linear programming problems. The reconstructed metabolic models
were presented at pH=7 and so, the metabolic models were modified at
other pH levels according to the method presented in the next section.
In this research, pH levels of 5, 6, and 7 were selected for simulation
based on the reported intracellular pH range for S. cerevisiae(Valli et al., 2005), Z. mobilis (Kalnenieks, Pankova, &
Shvinka, 1987), and E. coli (Martinez et al., 2012). The
unrealistic intracellular pH level of 5 for E. coli only was also
assumed for the intracellular medium of the three cells to study the
effect of high acidity.