Multi-Omics and RNAi Reveal a Role for the Ubiquitin-Proteasome Pathway in Muscle Fiber Development of Common Carp (Cyprinus carpio)

To investigate the molecular mechanisms of muscle fiber development underlying locomotion differences between two common carp (Cyprinus carpio) strains cultured in a rice-fish symbiosis system, we conducted comparative transcriptomic and proteomic analyses of muscle tissues collected from indolent Congjiang (CJ) and active FFRC No. 2 (FR) strains cultured under identical paddy field conditions. RNA-seq revealed 3708 differentially expressed genes (DEGs), and proteomic analysis identified 108 differentially expressed proteins (DEPs). Functional enrichment and protein-protein interaction (PPI) network analyses highlighted key genes (psma3, ppargc1a, ube3a) and proteins (Myh, Ckmt2b, Suclg2) associated with proteasome activity, adipocytokine signaling, and ubiquitin-mediated protein degradation. Quantitative PCR (RT-qPCR) analysis of ubiquitin-proteasome pathway-related genes confirmed significantly higher expression levels in the muscle tissue of CJ compared with FR. After a 21-day interference experiment, ube3a knockdown increased average muscle fiber area and diameter and reduced muscle fiber density in juvenile CJ, indicating that ube3a knockdown might promote muscle development in common carp. Subsequent swimming performance measurements can be conducted to further explore the impact of ube3a on fish locomotion. These results provide molecular insights into fish locomotion capacity related to behavioral adaptation in agroecological systems.