The modification of proteins by malonylation plays an important regulatory role in multiple biological processes. Protein malonylation is the reversible addition of malonyl groups to lysine residues to regulate protein localization, enzyme activity, protein stability, and many other biochemical processes. However, little information was available on the malonylation of lysine in Eucommia ulmoides, an important traditional Chinese herb with multiple active substances. In this study, we analyzed the malonylation of lysine to determine the potential regulatory role of lysine malonylation in the growth and development of E. ulmoides using LC–MS/MS combined with immune-based purification. A total of 388 lysine malonylation sites distributed in 256 proteins were identified. A gene ontology (GO) analysis showed that the proteins in which lysine is malonylated are related to a wide range of cellular functions ranging from metabolic processes to responses to stimuli. A bioinformatic analysis showed that malonylated proteins are primarily distributed in the chloroplast (108 proteins, 42.19%), cytoplasm (90 proteins, 35.16%), and nucleus (27 proteins, 10.55%). They are primarily involved in energy metabolism, including photosynthesis, carbon metabolism, glycolysis, and the biosynthesis of secondary metabolites. Our research suggests that the malonylation of lysine is necessary for the life cycle of plants, which are primarily involved in the process of converting solar energy to biomass energy that is stored and converting the energy stored by plants into energy (ATP) available for direct use in E. ulmoides. To our knowledge, this is the first posttranslational malonylation modification of E. ulmoides proteins, which was conducted simultaneously to explore the mechanism of modification groups in protein functions, protein interactions, and biological metabolism, so as to provide a theoretical basis for the production and breeding of E. ulmoides.
