Figure 1.
Flowchart of dFBA to decipher the dynamic metabolism of S. oneidensis MR-1.
Figure 2.
Monod model for growth kinetics.
The green dots are the measurements, and the blue lines are the simulated growth by the empirical Monod model.
Table 1.
Parameters estimated in the empirical Monod model.
Figure 3.
Prediction of growth rates (h−1).
Blue ○: growth rate determined by the Monod model. Red ○: dFBA prediction using the objective function (maximization of growth rate). Green □: dFBA prediction using dual-objective functions (maximization of growth rate and minimization of overall flux). Yellow ◊: the weight of the dual-objective functions that predicted the measured growth rates. Note: the summation of the square of fluxes (∑v2) was a very large number (total 774 fluxes), so the magnitude of weight w was small.
Figure 4.
Dynamic flux distributions (unit: mmol/g DCW/h) in central metabolic pathways.
The yellow filled cycles are intracellular metabolites; the blue filled cycles are substrates and extracellular metabolites (LAC: extracellular lactate, PYR: extracellular pyruvate, ACT: extracellular acetate); the dashed lines indicate inactive pathways; the green filled boxes are reactions listed in iSO783. All the abbreviations refer to iSO783 [7].
Figure 5.
Experimentally observed and simulated isotopomer labeling patterns [M-57]+ in proteinogenic amino acids.
The standard error for GC-MS measurement was below 0.02. A1: dynamic isotopomer simulation for glutamate from dFBA without considering reaction reversibility (dFBA w/o reversibility). A2: dynamic isotopomer simulation for glutamate from dFBA considering reaction reversibility (dFBA w/ reversibility). Bar plot: comparison of experimentally observed isotopomer labeling to simulated isotopomer labeling patterns of glutamate (A1: without considering reaction reversibility; A2: considering reaction reversibility). B: The model fitting of the isotopomer labeling data of five key amino acids (Ala, Gly, Ser, Asp, and Glu) at t = 24 and 30 h.
Table 2.
Exchange coefficients for key metabolic pathways of MR-1.