Proteins are modular functionalities regulating multiple cellular activities formed as monomers or multimers, ranging from prokaryotes to eukaryotes. In higher plants, as the consequence of adapting to arid and thermal conditions, and an example of convergence evolution, carbon fixation process has evolved to a multi-enzyme co-working fashion, named C4 photosynthesis. While how these enzymes interact with each other and whether they evolve in parallel to maintain the interaction in different plants remain elusive. To address this issue, here we report the global co-evolution relationship and local dynamics of co-varying sites shifts in key C4 enzymes. Protein co-evolution in plants is rather important for maintaining feasible functions. However, relevant research are not frequently reported, especially in residue resolution. To investigate the co-varying sites facilitating protein co-evolution, we develop a new pipeline to unravel the co-evolved sites in eight key photosynthetic enzymes and to investigate how they may affect the overall picture of carbon delivery during C4 photosynthesis.

Our results suggest that general co-evolution and protein-protein interaction exist in selected eight key photosynthetic enzymes, showing consistence with protein regulation, except for PEPC and PPCK. In addition, pockets are not necessary to appear to the interactive interface between PEPC and PPCK to perform protein regulation fuction. From an evolutionary perspective, our study provides a global view of C4 photosynthetic protein-co-evolution and its relationship between protein-protein interactions. This findings shed light on the precise localization of functional mutations which may tune the pairwise protein regulation in C4 photosynthesis.
 

Carbon delivery chain, C4 photosynthesis, protein co-evolution, co-varying sites, protein-protein regulation, protein-protein interaction, computational docking