Mechanistic Insights into Effector-Mediated Modulation of Rice Mitochondrial Proteins by Magnaporthe oryzae

Mitochondria are crucial for the plant and animal immunity. The effector protein MoCDIP4 reduces rice immunity by targeting the mitochondria-associated OsDjA9-OsDRP1E protein complex. The present study is focussed on how Magnaporthe oryzae, the fungus that causes rice blast disease, affects mitochondrial dynamics and inhibits innate immune responses in rice plants using molecular modelling, molecular dynamics simulations and free energy-based binding analysis. The protein structure prediction of the effector protein MoCDIP4 and the targets was carried out using artificial intelligence-based tool, AlphaFold. The MD simulation analysis of the effector protein showed significant changes in the secondary structure especially at its C-terminal. The protein-protein complex conformations for OsDjA9-OsDRP1E and OsDjA9-MoCDIP4 were predicted using ab initio molecular methods and energy minimised for enhanced sampling (accelerated) molecular dynamics (MD) simulations. We found that MoCDIP4 targets and binds to the same N-terminal "fork-like" binding site on OsDjA9 which is required for OsDjA9-OsDRP1E complex formation, thereby, resulting in accumulation of OsDRP1E in the mitochondria. Moreover, OsDjA9 was found to undergo large conformational globular folding when bound to OsDRP1E as shown by increased root-mean-square deviation (RMSD) values and overall structural compactness. The binding free energy was calculated by Molecular Mechanics with Generalised Born and Surface Area Solvation (MM/GBSA) model where the OsDjA9-OsDRP1E complexes were scored at - 83.79 kcal/mol and the OsDjA9-MoCDIP4 scored at - 49.24 kcal/mol. The study also highlighted the key residues involved in the interaction of the effector protein as well as from the mitochondria-associated OsDjA9-OsDRP1E protein complex which would pave the path for studying the plant-pathogen interaction.