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Wang D, Hou L, Ji Y, Xie J, Zhao J, Zhu N, Yang X, Zhou J, Cui Y, Guo J, Feng X, Liu J. Ubiquitination-dependent degradation of nucleolin mediated by porcine circovirus type 3 capsid protein. J Virol 2023; 97:e0089423. [PMID: 38032196 PMCID: PMC10734473 DOI: 10.1128/jvi.00894-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Porcine circovirus type 3 (PCV3) is an emerging pathogen that causes multisystem disease in pigs and poses a severe threat to the swine industry. However, the mechanisms of how PCV3 uses host proteins to regulate its own life cycle are not well understood. In this study, we found that PCV3 capsid protein interacts with nucleolin and degrades it. Degradation of nucleolin by the PCV3 capsid protein requires recruitment of the enzyme RNF34, which is transported to the nucleolus from the cytoplasm in the presence of the PCV3 capsid protein. Nucleolin also decreases PCV3 replication by promoting the release of interferon β. These findings clarify the mechanism by which nucleolin modulates PCV3 replication in cells, thereby facilitating to provide an important strategy for preventing and controlling PCV3 infection.
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Affiliation(s)
- Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Ji
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jiali Xie
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jie Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ning Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xiaoyu Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jianwei Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongqiu Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jinshuo Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xufei Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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Wang W, Zhang Y, Liu D, Zhang H, Wang X, Zhou Y. PseAraUbi: predicting arabidopsis ubiquitination sites by incorporating the physico-chemical and structural features. PLANT MOLECULAR BIOLOGY 2022; 110:81-92. [PMID: 35773617 DOI: 10.1007/s11103-022-01288-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
We makes three kinds of important features from Arabidopsis thaliana: protein secondary structure based on the Chou-Fasman parameter, amino acids hydrophobicity and polarity information, and analyze their properties. Ubiquitination modification is an important post-translational modification of proteins, which participates in the regulation of many important life activities in cells. At present, ubiquitination proteomics research is mostly concentrated in animals and yeasts, while relatively few studies have been carried out in plants. It can be said that the calculation and prediction of Arabidopsis thaliana ubiquitination sites is still in its infancy. Based on this, we describe a calculation method, PseAraUbi (Prediction of Arabidopsis thaliana ubiquitination sites using pseudo amino acid composition), that can effectively detect ubiquitination sites on Arabidopsis thaliana using support vector machine learning classifiers. Based on protein sequence information, extract features from the Chou-Fasman parameter, amino acids hydrophobicity features, polarity information and selected for classification with the Boruta algorithm. PseAraUbi achieves promising performances with an AUC score of 0.953 with fivefold cross-validation on the training dataset, which are significantly better than that of the pioneer Arabidopsis thaliana ubiquitination sites method. We also proved the ability of our proposed method on independent test sets, thus gaining a competitive advantage. In addition, we also in-depth analyzed the physicochemical properties of amino acids in the region adjacent to the ubiquitination site. To facilitate the community, the source code, optimal feature subset, ubiquitination sites dataset in the Arbidopsis proteome are available at GitHub ( https://github.com/HNUBioinformatics/PseAraUbi.git ) for interest users.
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Affiliation(s)
- Wei Wang
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453000, China.
- Key Laboratory of Artificial Intelligence and Personalized Learning in Education of Henan Province, Xinxiang, China.
| | - Yu Zhang
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453000, China
| | - Dong Liu
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453000, China
| | - HongJun Zhang
- School of Computer Science and Technology, Anyang University, Anyang, 455000, China
| | - XianFang Wang
- College of Computer Science and Technology Engineering, Henan Institute of Technology, Xinxiang, 453000, China
| | - Yun Zhou
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453000, China.
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Sun M, Zhang X. Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture. Cell Biosci 2022; 12:126. [PMID: 35962460 PMCID: PMC9373315 DOI: 10.1186/s13578-022-00870-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Ubiquitination is a versatile post-translational modification (PTM), which regulates diverse fundamental features of protein substrates, including stability, activity, and localization. Unsurprisingly, dysregulation of the complex interaction between ubiquitination and deubiquitination leads to many pathologies, such as cancer and neurodegenerative diseases. The versatility of ubiquitination is a result of the complexity of ubiquitin (Ub) conjugates, ranging from a single Ub monomer to Ub polymers with different length and linkage types. To further understand the molecular mechanism of ubiquitination signaling, innovative strategies are needed to characterize the ubiquitination sites, the linkage type, and the length of Ub chain. With advances in chemical biology tools, computational methodologies, and mass spectrometry, protein ubiquitination sites and their Ub chain architecture have been extensively revealed. The obtained information on protein ubiquitination helps to crack the molecular mechanism of ubiquitination in numerous pathologies. In this review, we summarize the recent advances in protein ubiquitination analysis to gain updated knowledge in this field. In addition, the current and future challenges and barriers are also reviewed and discussed.
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Xie Y, Wang M, Xia M, Guo Y, Zu X, Zhong J. Ubiquitination regulation of aerobic glycolysis in cancer. Life Sci 2022; 292:120322. [PMID: 35031261 DOI: 10.1016/j.lfs.2022.120322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/18/2022]
Abstract
Aerobic glycolysis, or the Warburg effect, is regarded as a critical part of metabolic reprogramming and plays a crucial role in the occurrence and development of tumours. Ubiquitination and deubiquitination, essential post-translational modifications, have attracted increasing attention with regards to the regulation of metabolic reprogramming in cancer. However, the mechanism of ubiquitination in glycolysis remains unclear. In this review, we discuss the roles of ubiquitination and deubiquitination in regulating glycolysis, and their involvement in regulating important signalling pathways, enzymes, and transcription factors. Focusing on potential mechanisms may provide novel strategies for cancer treatment.
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Affiliation(s)
- Yao Xie
- Institute of Clinical Medicine, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China; Department of Clinical Laboratory, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China
| | - Mu Wang
- Clinical Research Institute, the NanHua Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China
| | - Min Xia
- Institute of Clinical Medicine, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China
| | - Yinping Guo
- Institute of Clinical Medicine, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China
| | - Xuyu Zu
- Institute of Clinical Medicine, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China; Cancer Research Institute, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China.
| | - Jing Zhong
- Institute of Clinical Medicine, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China; Cancer Research Institute, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, PR China.
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Wang X, Yan R, Wang Y. Computational identification of human ubiquitination sites using convolutional and recurrent neural networks. Mol Omics 2021; 17:948-955. [PMID: 34515266 DOI: 10.1039/d0mo00183j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Ubiquitination is a very important protein post-translational modification in humans, which is closely related to many human diseases such as cancers. Although some methods have been elegantly proposed to predict human ubiquitination sites, the accuracy of these methods is generally not very satisfactory. In order to improve the prediction accuracy of human ubiquitination sites, we propose a new ensemble method HUbipPred, which takes the binary encoding and physicochemical properties of amino acids as training features, and integrates two intensively trained convolutional neural networks and two recurrent neural networks to build the model. Finally, HUbiPred achieves AUC values of 0.852 and 0.844 in five-fold cross-validation and independent tests, respectively, which greatly improves the prediction accuracy compared to previous predictors. We also analyze the physicochemical properties of amino acids around ubiquitination sites, study the important roles of architectures (i.e., convolution, long short-term memory (LSTM) and fully connected hidden layers) in the networks for prediction performance, and also predict potential ubiquitination sites in humans using HUbiPred. The training and test datasets, predicted human ubiquitination sites, and source codes of HUbiPred are publicly available at https://github.com/amituofo-xf/HUbiPred.
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Affiliation(s)
- Xiaofeng Wang
- College of Mathematics and Computer Sciences, Shanxi Normal University, Linfen 041004, China.
| | - Renxiang Yan
- School of Biological Sciences and Engineering, Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou 350002, China.
| | - Yongji Wang
- College of Life Sciences, Shanxi Normal University, Linfen 041000, China
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Li L, Bai J, Fan H, Yan J, Li S, Jiang P. E2 ubiquitin-conjugating enzyme UBE2L6 promotes Senecavirus A proliferation by stabilizing the viral RNA polymerase. PLoS Pathog 2020; 16:e1008970. [PMID: 33104725 PMCID: PMC7588118 DOI: 10.1371/journal.ppat.1008970] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/08/2020] [Indexed: 12/29/2022] Open
Abstract
Senecavirus A (SVA), discovered in 2002, is an emerging pathogen of swine that has since been reported in numerous pork producing countries. To date, the mechanism of SVA replication remains poorly understood. In this study, utilizing iTRAQ analysis we found that UBE2L6, an E2 ubiquitin-conjugating enzyme, is up-regulated in SVA-infected BHK-21 cells, and that its overexpression promotes SVA replication. We determined that UBE2L6 interacts with, and ubiquitinates the RNA-dependent RNA polymerase of SVA, (the 3D protein) and this ubiquitination serves to inhibit the degradation of 3D. UBE2L6-mediated ubiquitination of 3D requires a cystine at residue 86 in UBE2L6, and lysines at residues 169 and 321 in 3D. Virus with mutations in 3D (rK169R and rK321R) exhibited significantly decreased replication compared to wild type SVA and the repaired viruses, rK169R(R) and rK321R(R). These data indicate that UBE2L6, the enzyme, targets the 3D polymerase, the substrate, during SVA infection to facilitate replication. Senecavirus A (SVA) is a newly emerging pathogen causing swine idiopathic vesicular disease and epidemic transient neonatal losses. Infections have been reported in many pork producing countries, yet the mechanism of SVA replication remains poorly understood. In this study, we found that UBE2L6, an E2 ubiquitin-conjugating enzyme, is up-regulated in SVA-infected BHK-21 cells. The viral RNA dependent RNA polymerase (RdRp) 3D is ubiquitinated by UBE2L6, and the lysines at residues 169 and 321 of 3D are the required ubiquitination sites. The level of replication of recombinant viruses harboring ubiquitination-deficient 3D was significantly decreased compared to parental SVA. Our data demonstrate that UBE2L6 ubiquitinates SVA 3D, thereby facilitating SVA infection. These results may make it possible to identify novel targets for disease treatment.
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Affiliation(s)
- Liang Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Juan Bai
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- * E-mail: (JB); (PJ)
| | - Hui Fan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Junfang Yan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shihai Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ping Jiang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- * E-mail: (JB); (PJ)
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