Transcriptomic Profiling of HepG2 Cells under PCCB Depletion Reveals Kpm-Mediated Metabolic Gene Regulation

Lysine alkylation and acylation serve as crucial links between cellular metabolism and a wide range of biological functions. However, hybrid modifications that combine features of both alkylation and acylation remain largely unexplored. Here, we report the discovery and in-depth characterization of lysine methylpropionylation (Kpm), a hybrid post-translational modification (PTM) defined by the propionylation of monomethyllysine residues. Mechanistically, we show that Kpm is metabolically regulated by propionyl-CoA homeostasis and is markedly upregulated upon depletion of the propionyl-CoA carboxylase beta subunit (PCCB). Genome-wide chromatin immunoprecipitation coupled with transcriptomic profiling revealed that Kpm exhibits distinct genomic distribution compared to canonical Kac and Kpr, with preferential enrichment at promoters of genes involved in metabolic pathways. To investigate the site-specific function of Kpm on non-histone proteins, we developed a genetic code expansion system to incorporate Kpm at defined sites. Using this system, we demonstrate that methylpropionylation of NSMCE3 at lysine 260 disrupts a critical electrostatic interaction with E284, thereby impairing its association with NSMCE4A and compromising DNA damage repair. Together, our findings establish Kpm as a dual-feature PTM that integrates metabolic cues with both chromatin regulation and non-histone protein function, offering a mechanistic framework for understanding metabolism-proteome crosstalk.