Global profiling of lysine-malonylated proteins in rice elucidates the immune-regulatory mechanisms of malonylation under herbivore or viral stresses.

Abstract

Lysine malonylation (K_mal), an evolutionarily conserved post-translational modification, serves as a critical regulator of cellular processes including transcriptional control, metabolic coordination, and enzyme activation. While K_mal sites have been mapped in rice (Oryza sativa L.) seeds, their dynamic regulation in rice responses to biotic stresses remains poorly characterized. Here, we reported a global profiling of lysine-malonylated proteins in rice leaf sheaths, and the changes in these proteins under herbivore (Nilaparvata lugens/Chilo suppressalis) or viral (rice stripe virus/rice black-streaked dwarf virus) stresses. Using affinity enrichment and proteomics, we identified 3,113 K_mal sites across 1,324 proteins in wild-type rice leaf sheaths, these data demonstrated that lysine-malonylated proteins are involved in diverse biological processes. K_mal levels were significantly upregulated following herbivore infestation or viral infection, with two herbivores inducing more pronounced changes than viruses infection, revealing stress-specific malonylation landscapes. K_mal preferentially targeted highly expressed proteins in energy metabolism (e.g., glycolysis and the tricarboxylic acid cycle) and photosynthesis, exhibiting an inverse correlation between hypermalonylation and protein abundance. Cleavage under targets and tagmentation analyses revealed K_mal-mediated chromatin remodeling through promoter occupancy at defense-related genes. In addition, the histone deacetylases OsHDA702-704, OsHDA711-713 were functionally characterized as key regulators mediating the erasure of specific malonylation marks in rice plants, with OsHDA711 knockout lines exhibiting enhanced resistance against both herbivore and virus infection. Our work establishes K_mal as a regulator in rice biotic immunity, uncovering novel insights into K_mal-mediated plant defense responses against herbivorous pests and viral pathogens. These findings identify potential genetic targets for developing rice varieties with broad-spectrum immunity to biotic stresses, enhancing crop resilience.