Systematic Comparison Of C3 And C4 Plants Based On ... - NCBI

Improved models by setting the ratio of carboxylation and oxygenation by Rubisco

Rubisco enzyme (EC: 4.1.1.39) catalyzed two different reactions with CO2 and O2 respectively in photosynthesis and photorespiration:

RuBP + CO2 + H2O  -  > 2PGA(1)RuBP + O2 -  > PGA + PGCA(2)

There is constant ratio between rate of carboxylation and oxygenation under specific partial pressure of CO2 and O2 in environment [28]. Therefore, it is hard to accurately simulate the flux change under different CO2 concentration without constraints on rate of the two reactions by Rubisco, which is just the limitation of AraGEM and C4GEM. Here we improved the two models by combining the two reactions into one reaction:

(r + 1)RuBP + r CO2 + r H2O + O2 - > (2r + 1)PGA + PGCA(3)

The ratio r between carboxylation and oxygenation under different CO2 concentration in C3 and C4 model is shown in Table ​Table2.2. The detail calculation of r is in the Methods section.

Table 2

The ratio r between carboxylation and oxygenation under different CO2 concentration in C3 and C4 model

CO2 (μbar) in the air	r in C3	r in C4
100	1.139	22.2282
380	4.33	70.7281
550	6.26	85.9654
800	9.11	87.1062
1000	11.39	88.0189

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In addition, our motivation was to compare the differences between C3 and C4 photosynthesis mechanism and their responses under different environments, therefore we set the objective function as maximization of CO2 fixation and biomass synthesis. Since in previous AraGEM and C4GEM, the objective was to minimize the use of light energy while achieving a specified growth rate, we need to reset some flux constraints according to biochemistry knowledge. For example, the CO2 leakage was blocked from bundle sheath to mesophyll cell with zero flux in C4GEM, which was not consistent with actual situation; here we adjusted the upper bound of this reaction to permit the leakage of CO2. In addition, because starch is not synthesized in mesophyll cell of C4 plants, the biomass components of C4GEM were also reset. The lower and upper bounds of flux in TCA cycle were adjusted as -50 and 50, to restrict flux of respiration in mitochondria. The detail of modified constraints in our improved models can be got from the Additional File.