Ubiquitination proteomics-based analysis to identify the key regulators of intramuscular fat deposition in Large White pigs and Erhualian pigs.

Intramuscular fat (IMF) remarkably influences pork quality. However, the role of post-translational modifications, particularly ubiquitination, in IMF deposition remains unclear. We aimed to identify the key IMF-associated ubiquitinated proteins and pathways in the longissimus dorsi muscles from lean-type Large White and fat-type Erhualian pigs. Immunoblotting revealed a significant negative correlation between ubiquitination and IMF deposition in both breeds. High-throughput ubiquitination proteomics revealed 5280 ubiquitinated sites across 1036 proteins. Among these, 978 and 988 upregulated differentially expressed ubiquitination sites were detected in Large White and Erhualian pigs, respectively, with 80 proteins common to both breeds. Functional enrichment analysis revealed their association with skeletal muscle development, glycolytic metabolism, ubiquitin-mediated proteolysis, and mitochondrial function. Protein-protein interaction networks highlighted hubs centred on muscle-specific proteins, glycolytic enzymes, and proteasomal components. These findings provide novel insights into the ubiquitin-mediated regulatory mechanisms underlying IMF deposition in pigs and suggest potential targets for improving pork meat quality.