Coordination of Plant Primary Metabolism Studied with a Constraint-based Metabolic Model of C3 Mesophyll Cell

Abstract

Engineering plant primary metabolism is currently recognized as a major approach to gain improved productivity. Most of the current efforts in plant metabolic engineering focused on either individual enzymes or a few enzymes in a particular pathway without fully consider the potential interactions between metabolisms. More and more evidences suggested that engineering a particular pathway without consideration of the interacting pathways only generated limited success. Therefore, a long term goal of metabolic engineering is being able to engineer metabolism with consideration of the effects of external or internal perturbation on the whole plant primary metabolism. In this paper, we developed a constraint-based model of C3 Plant Primary Metabolism (C3PMM), which is generic for C3 plants such as rice, Arabidopsis, and soybean. The C3PMM was first combined with transcriptome data to demonstrate that there is substantial coordination of mesophyll primary metabolism at both transcriptome and metabolism levels in response to elevated CO2 concentration. Secondly, maximizing CO2 uptake is a plausible target function for metabolism of a typical C3 mesophyll cell. Finally, C3PMM predicted a decrease in nitrate assimilation flux coordinated with photorespiration, and increase in ammonium assimilation flux, when CO2 concentration increases. This suggested a potential mechanistic linkage between differences in the response of ecosystems differing in nitrogen source to elevated CO2. In conclusion, all the coordination of C3 plant primary metabolism at both transcriptome level and metabolism level, and the coordination between nitrate assimilation and photorespiration under elevated CO2 concentration, are beneficial for maximized CO2 uptake rate.