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Peer-reviewedCC BY 4.0International Journal of Molecular Sciences

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

  • Yating Gong1
  • Mingkun Luo2
  • Xianbo Zhang3
  • Ning Qin3
  • Lanmei Wang1,2
  • Wenbin Zhu1,2
  • Jianjun Fu2
  • Zaijie Dong1,2
  1. 1Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
  2. 2Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
  3. 3Fisheries Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang 550025, China
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Abstract

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.

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Cite

BibTeXRIS
BibTeX
@article{gong2026multiomics,
  title = {{Multi-Omics and RNAi Reveal a Role for the Ubiquitin-Proteasome Pathway in Muscle Fiber Development of Common Carp (Cyprinus carpio)}},
  author = {Yating Gong and Mingkun Luo and Xianbo Zhang and Ning Qin and Lanmei Wang and Wenbin Zhu and Jianjun Fu and Zaijie Dong},
  journal = {International Journal of Molecular Sciences},
  year = {2026},
  month = oct,
  doi = {10.3390/ijms27219624},
  url = {https://www.mdpi.com/1422-0067/27/21/9624},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Multi-Omics and RNAi Reveal a Role for the Ubiquitin-Proteasome Pathway in Muscle Fiber Development of Common Carp (Cyprinus carpio)
AU  - Yating Gong
AU  - Mingkun Luo
AU  - Xianbo Zhang
AU  - Ning Qin
AU  - Lanmei Wang
AU  - Wenbin Zhu
AU  - Jianjun Fu
AU  - Zaijie Dong
PY  - 2026
DA  - 2026/10/27
JO  - International Journal of Molecular Sciences
DO  - 10.3390/ijms27219624
UR  - https://www.mdpi.com/1422-0067/27/21/9624
AB  - 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.
SN  - 1422-0067
ER  -