Comparative analysis of C3 and C4 plants using constraint-based model

To realize the transition from C3 to C4 plants, the systematic comparison of C3 and C4 metabolism is necessary. In this study, we detected their differences using the improved constraint-based models by setting the ratio between carboxylation and oxygenation by Rubisco. We found the C3 model exhibit more dense topology structure than C4. The simulation of enzyme knockouts demonstrated that both C3 and C4 models are very robust, especially when optimizing CO2 fixation. Moreover, C4 plant has better robustness no matter the objective function is biomass or CO2 fixation. In addition, all the essential reactions in C3 model are also essential for C4, while there are some other reactions specifically essential for C4, which validated that the basic metabolism of C4 plant is similar to C3, but C4 is more complex. We also identified more correlated reaction sets in C4, and demonstrated C4 plants have better modularity with complex mechanism coordinates the reactions and pathways than that of C3 plants. Finally, the increase of both biomass and CO2 fixation with light intensity and CO2 concentration in C4 is faster than that in C3, which reflect more efficient use of light and CO2 in C4 plant. All results are consistent with the actual situation, which indicate that constraint-based modeling is a powerful method to study plant metabolism at systems level.