Figure 5.

Pathway Model, Elementary Flux Modes, and Flux Estimates.

(A) Pathway model. The model includes the CBC, photorespiration, and Suc, starch synthesis, myo-inositol, and trehalose synthesis. There is explicit separation of cytosolic (blue, subscript c) and plastidic pools (yellow, subscript p) that are not equilibrated by transporters. Plastidic and cytosolic pools of 3PGA and DHAP are treated as a single pool (gray) that is in isotopic equilibrium (Stitt et al., 1983) due to rapid exchange via the triose-phosphate phosphate transporter. Metabolite pools involved in photorespiration are shown in pink. Reactions are set as irreversible (single-headed arrow) or reversible (double-headed arrow), based on experimental data (Bassham and Krause, 1969; Stitt et al., 1980).

(B) to (F) Elementary flux modes of the model: synthesis of starch (B), synthesis of Suc (C), synthesis of myo-inositol (D), synthesis of trehalose (E), and photorespiration (F).

(G) Simulation of best fit. Measured data for the proportion of the total pool present as the ¹²C isotopomer are shown as crosses (±sd) and the predicted decay dynamics of the ¹²C isotopomer modeled using the unadjusted data set (red line) and after excluding the inactive pool (blue line). Gray dotted lines indicate the inactive pool. For Tre6P and myo-inositol (asterisks), which have a small total pool size, the active pool assumption is not applied. The RuBP panel shows the input models for the influx to the pool of 3PGA (purple solid line) and Gly (purple dotted line). The corresponding crosses indicate the data used for parameter estimation.

(H) Selected fluxes and rates for the two scenarios included that were used for benchmarking. The rates of Rubisco carboxylation and oxygenation are given as RuBP consumption (i.e., use of CO₂ or O₂, respectively). Fluxes were estimated for two scenarios (1) All, using unadjusted ¹²C isotopomer decay and metabolite content data sets. (2) Active, using the pool of each metabolite that is actively involved in photosynthetic fluxes. The inactive pool was nominally defined as the proportion that remains as ¹²C isotopomer at 60 min. It was subtracted from the ¹²C isotope kinetic (i.e., the 60-min value is set as zero). The absolute pool (Table 1) was also decreased in the same proportion. For each scenario, flux estimates are denoted by the optimal value obtained with the fit “optimum” and the “lower” and “upper” 95% confidence limits obtained from the Monte-Carlo simulation.