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Li X, Ke Q, Qu A, Wang J, Zhao J, Xu P, Zhou T. Effects of Gene Alternative Splicing Events on Resistance to Cryptocaryonosis of Large Yellow Croaker (Larimichthys crocea). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:741-753. [PMID: 38969905 DOI: 10.1007/s10126-024-10342-8] [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: 01/05/2024] [Accepted: 06/25/2024] [Indexed: 07/07/2024]
Abstract
Large yellow croaker (L. crocea) is a productive species in marine aquaculture with great economic value in China. However, the sustainable development of large yellow croaker is hampered by various diseases including cryptocaryonosis caused by Cryptocaryon irritans. The genetic regulation processes for cryptocaryonosis in large yellow croaker are still unclear. In this present study, we analyzed differential alternative splicing events between a C. irritans resistance strain (RS) and a commercial strain (CS). We identified 678 differential alternative splicing (DAS) events from 453 genes in RS and 719 DAS events from 500 genes in CS. A set of genes that are specifically alternatively spliced in RS was identified including mfap5, emp1, and trim33. Further pathway analysis revealed that the specifically alternative spliced genes in RS were involved in innate immune responses through the PRR pathway and the Toll and Imd pathway, suggesting their important roles in the genetic regulation processes for cryptocaryonosis in large yellow croaker. This study would be helpful for the studies of the pathogenesis of cryptocaryonosis and dissection of C. irritans resistance for L. crocea.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qiaozhen Ke
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Ang Qu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Jiaying Wang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ji Zhao
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Tao Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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He H, Cai T, Chen Q, Chen Z, Zhang B, Chen C, Wang Y, Liu Y, Wang Y, Luo Y, Huang S, Luo J, Guo X. TRIM44 Promotes Rabies Virus Replication by Autophagy-Dependent Mechanism. Int J Mol Sci 2024; 25:4616. [PMID: 38731834 PMCID: PMC11083291 DOI: 10.3390/ijms25094616] [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: 03/23/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Tripartite motif (TRIM) proteins are a multifunctional E3 ubiquitin ligase family that participates in various cellular processes. Recent studies have shown that TRIM proteins play important roles in regulating host-virus interactions through specific pathways, but their involvement in response to rabies virus (RABV) infection remains poorly understood. Here, we identified that several TRIM proteins are upregulated in mouse neuroblastoma cells (NA) after infection with the rabies virus using RNA-seq sequencing. Among them, TRIM44 was found to regulate RABV replication. This is supported by the observations that downregulation of TRIM44 inhibits RABV replication, while overexpression of TRIM44 promotes RABV replication. Mechanistically, TRIM44-induced RABV replication is brought about by activating autophagy, as inhibition of autophagy with 3-MA attenuates TRIM44-induced RABV replication. Additionally, we found that inhibition of autophagy with rapamycin reverses the TRIM44-knockdown-induced decrease in LC3B expression and autophagosome formation as well as RABV replication. The results suggest that TRIM44 promotes RABV replication by an autophagy-dependent mechanism. Our work identifies TRIM44 as a key host factor for RABV replication, and targeting TRIM44 expression may represent an effective therapeutic strategy.
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Affiliation(s)
- Hongling He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Ting Cai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Qiaozhu Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Zilian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Boyue Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Changyi Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Yueze Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Yan Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Yueming Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Yongwen Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130-3932, USA;
- Department of Hematology and Oncology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130-3932, USA
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130-3932, USA
| | - Jun Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
| | - Xiaofeng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510000, China; (H.H.); (T.C.); (Q.C.); (Z.C.); (B.Z.); (C.C.); (Y.W.); (Y.L.); (Y.W.); (Y.L.)
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Wu T, Chen X, Xu K, Dai C, Li X, Zhang YWQ, Li J, Gao M, Liu Y, Liu F, Zhang X, Wang B, Xia P, Li Z, Ma W, Yuan Y. LIM domain only 7 negatively controls nonalcoholic steatohepatitis in the setting of hyperlipidemia. Hepatology 2024; 79:149-166. [PMID: 37676481 PMCID: PMC10718224 DOI: 10.1097/hep.0000000000000585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND AND AIMS Hyperlipidemia has been extensively recognized as a high-risk factor for NASH; however, clinical susceptibility to NASH is highly heterogeneous. The key controller(s) of NASH susceptibility in patients with hyperlipidemia has not yet been elucidated. Here, we aimed to reveal the key regulators of NASH in patients with hyperlipidemia and to explore its role and underlying mechanisms. APPROACH AND RESULTS To identify the predominant suppressors of NASH in the setting of hyperlipidemia, we collected liver biopsy samples from patients with hyperlipidemia, with or without NASH, and performed RNA-sequencing analysis. Notably, decreased Lineage specific Interacting Motif domain only 7 (LMO7) expression robustly correlated with the occurrence and severity of NASH. Although overexpression of LMO7 effectively blocked hepatic lipid accumulation and inflammation, LMO7 deficiency in hepatocytes greatly exacerbated diet-induced NASH progression. Mechanistically, lysine 48 (K48)-linked ubiquitin-mediated proteasomal degradation of tripartite motif-containing 47 (TRIM47) and subsequent inactivation of the c-Jun N-terminal kinase (JNK)/p38 mitogen-activated protein kinase (MAPK) cascade are required for the protective function of LMO7 in NASH. CONCLUSIONS These findings provide proof-of-concept evidence supporting LMO7 as a robust suppressor of NASH in the context of hyperlipidemia, indicating that targeting the LMO7-TRIM47 axis is a promising therapeutic strategy for NASH.
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Affiliation(s)
- Tiangen Wu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Xi Chen
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Kequan Xu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Caixia Dai
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Xiaomian Li
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Yang-Wen-Qing Zhang
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Jinghua Li
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Meng Gao
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Yingyi Liu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Fusheng Liu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Xutao Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Bicheng Wang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Peng Xia
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Zhen Li
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Weijie Ma
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
| | - Yufeng Yuan
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan, Hubei, PR China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, PR China
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Aizaz M, Kiani YS, Nisar M, Shan S, Paracha RZ, Yang G. Genomic Analysis, Evolution and Characterization of E3 Ubiquitin Protein Ligase (TRIM) Gene Family in Common Carp ( Cyprinus carpio). Genes (Basel) 2023; 14:genes14030667. [PMID: 36980939 PMCID: PMC10048487 DOI: 10.3390/genes14030667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/03/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Tripartite motifs (TRIM) is a large family of E3 ubiquitin ligases that play an important role in ubiquitylation. TRIM proteins regulate a wide range of biological processes from cellular response to viral infection and are implicated in various pathologies, from Mendelian disease to cancer. Although the TRIM family has been identified and characterized in tetrapods, but the knowledge about common carp and other teleost species is limited. The genes and proteins in the TRIM family of common carp were analyzed for evolutionary relationships, characterization, and functional annotation. Phylogenetic analysis was used to elucidate the evolutionary relationship of TRIM protein among teleost and higher vertebrate species. The results show that the TRIM orthologs of highly distant vertebrates have conserved sequences and domain architectures. The pairwise distance was calculated among teleost species of TRIMs, and the result exhibits very few mismatches at aligned position thus, indicating that the members are not distant from each other. Furthermore, TRIM family of common carp clustered into six groups on the basis of phylogenetic analysis. Additionally, the analysis revealed conserved motifs and functional domains in the subfamily members. The difference in functional domains and motifs is attributed to the evolution of these groups from different ancestors, thus validating the accuracy of clusters in the phylogenetic tree. However, the intron-exon organization is not precisely similar, which suggests duplication of genes and complex alternative splicing. The percentage of secondary structural elements is comparable for members of the same group, but the tertiary conformation is varied and dominated by coiled-coil segments required for catalytic activity. Gene ontology analysis revealed that these proteins are mainly associated with the catalytic activity of ubiquitination, immune system, zinc ion binding, positive regulation of transcription, ligase activity, and cell cycle regulation. Moreover, the biological pathway analyses identified four KEGG and 22 Reactome pathways. The predicted pathways correspond to functional domains, and gene ontology which proposes that proteins with similar structures might perform the same functions.
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Affiliation(s)
- Muhammad Aizaz
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250061, China
| | - Yusra Sajid Kiani
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Maryum Nisar
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Shijuan Shan
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250061, China
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Guiwen Yang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250061, China
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Qian Y, Wang Z, Lin H, Lei T, Zhou Z, Huang W, Wu X, Zuo L, Wu J, Liu Y, Wang LF, Guan XH, Deng KY, Fu M, Xin HB. TRIM47 is a novel endothelial activation factor that aggravates lipopolysaccharide-induced acute lung injury in mice via K63-linked ubiquitination of TRAF2. Signal Transduct Target Ther 2022; 7:148. [PMID: 35513381 PMCID: PMC9072678 DOI: 10.1038/s41392-022-00953-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/01/2022] [Accepted: 03/06/2022] [Indexed: 12/18/2022] Open
Abstract
Endothelial activation plays an essential role in the pathogenesis of sepsis-induced acute lung injury, however, the detailed regulatory mechanisms remain largely unknown. Here, we reported that TRIM47, an E3 ubiquitin ligase of the tripartite motif-containing protein family, was highly expressed in vascular endothelial cells. TRIM47-deficient mice were effectively resistant to lipopolysaccharide (LPS)-induced acute lung injury and death by attenuating pulmonary inflammation. TRIM47 was upregulated during TNFα-induced endothelial activation in vitro. Knockdown of TRIM47 in endothelial cells inhibited the transcription of multiple pro-inflammatory cytokines, reduced monocyte adhesion and the expression of adhesion molecules, and suppressed the secretion of IL-1β and IL-6 in endothelial cells. By contrast, overexpression of TRIM47 promoted inflammatory response and monocyte adhesion upon TNFα stimulation. In addition, TRIM47 was able to activate the NF-κB and MAPK signaling pathways during endothelial activation. Furthermore, our experiments revealed that TRIM47 resulted in endothelial activation by promoting the K63-linked ubiquitination of TRAF2, a key component of the TNFα signaling pathway. Taken together, our studies demonstrated that TRIM47 as a novel activator of endothelial cells, promoted LPS-induced pulmonary inflammation and acute lung injury through potentiating the K63-linked ubiquitination of TRAF2, which in turn activates NF-κB and MAPK signaling pathways to trigger an inflammatory response in endothelial cells.
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Affiliation(s)
- Yisong Qian
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
- Department of Biomedical Science, School of Medicine, University of Missouri Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Ziwei Wang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Hongru Lin
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Tianhua Lei
- Department of Biomedical Science, School of Medicine, University of Missouri Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Zhou Zhou
- Department of Biomedical Science, School of Medicine, University of Missouri Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Weilu Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Xuehan Wu
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Li Zuo
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Jie Wu
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Yu Liu
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Ling-Fang Wang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Xiao-Hui Guan
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Ke-Yu Deng
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China
| | - Mingui Fu
- Department of Biomedical Science, School of Medicine, University of Missouri Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.
| | - Hong-Bo Xin
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, 1299 Xuefu Rd, Honggu District, 330031, Nanchang, China.
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Recurrent expansions of B30.2-associated immune receptor families in fish. Immunogenetics 2021; 74:129-147. [PMID: 34850255 DOI: 10.1007/s00251-021-01235-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022]
Abstract
B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.
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Upregulated Tripartite Motif 47 Could Facilitate Glioma Cell Proliferation and Metastasis as a Tumorigenesis Promoter. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5594973. [PMID: 33833824 PMCID: PMC8016597 DOI: 10.1155/2021/5594973] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/28/2021] [Accepted: 03/05/2021] [Indexed: 01/26/2023]
Abstract
Introduction Tripartite motif 47 (TRIM47) belongs to a category of the TRIM family. It takes part in cancer tumorigenesis, thus demonstrating important functions across numerous carcinomas. Unfortunately, it is still elusive towards TRIM47 expression, characteristic, and biological function in brain gliomas. Methods Public database analysis was applied to analyze TRIM47 expression, and quantitative real-time PCR (qRT-PCR) was applied to detect the expression of TRIM47 in 9 paired tissues of glioma. The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases were applied to evaluate the overall survival (OS). Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were applied to analyze differentially expressed gene (DEG) functions. In vitro experiments were performed to validate TRIM47-mediated effects on glioma cell proliferation, migration, and invasion. Results Compared to that in normal tissues, TRIM47 expression was greatly higher in glioma tissues, and its expression level was associated with different grades of glioma. Our data indicated that highly expressed TRIM47 displayed an association with the poor prognosis of glioma patients. Ablating TRIM47 obviously impeded glioma cell invasion and migration. Conclusion TRIM47 could modulate glioma cell proliferation, invasion, and migration. Highly expressed TRIM47 exhibited a correlation with poor prognosis. All data imply that TRIM47 is a probable biomarker for glioma and has the potentiality to become a newly generated target for glioma treatment.
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Modulation of the Tissue Expression Pattern of Zebrafish CRP-Like Molecules Suggests a Relevant Antiviral Role in Fish Skin. BIOLOGY 2021; 10:biology10020078. [PMID: 33498981 PMCID: PMC7912335 DOI: 10.3390/biology10020078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
Simple Summary The clinical use of the human short pentraxin C-reactive protein as a health biomarker is expanded worldwide. The acute increase of the serum levels of short pentraxins in response to bacterial infections is evolutionarily conserved, as are the main functions of pentraxins. Interestingly, fish orthologs have been found to increase similarly after bacterial and viral stimuli, thus becoming promising candidates for health biomarkers of both types of infection in this group of vertebrates. To preliminarily assess their adequacy for this application, zebrafish and a fish rhabdovirus were chosen as infection model systems for the analysis of the levels of gene expression of all short pentraxins in healthy and infected animals in a wide range of tissues. Because some significant increases were found in skin (a very suitable sampling source for testing purposes), further transcript analyses were carried out in this tissue. Due to the functional similarities between pentraxins and antibodies, it was also checked whether short pentraxins can compensate for the deficiencies in adaptive immunity by using mutant zebrafish lacking this system. In conclusion, the obtained results suggest that short pentraxins are highly reactant against viruses in skin and their overexpression seems to reflect a mechanism to compensate for the loss of adaptive immunity. Abstract Recent studies suggest that short pentraxins in fish might serve as biomarkers for not only bacterial infections, as in higher vertebrates including humans, but also for viral ones. These fish orthologs of mammalian short pentraxins are currently attracting interest because of their newly discovered antiviral activity. In the present work, the modulation of the gene expression of all zebrafish short pentraxins (CRP-like proteins, CRP1-7) was extensively analyzed by quantitative polymerase chain reaction. Initially, the tissue distribution of crp1-7 transcripts and how the transcripts varied in response to a bath infection with the spring viremia of carp virus, were determined. The expression of crp1-7 was widely distributed and generally increased after infection (mostly at 5 days post infection), except for crp1 (downregulated). Interestingly, several crp transcription levels significantly increased in skin. Further assays in mutant zebrafish of recombinant activation gene 1 (rag1) showed that all crps (except for crp2, downregulated) were already constitutively highly expressed in skin from rag1 knockouts and only increased moderately after viral infection. Similar results were obtained for most mx isoforms (a reporter gene of the interferon response), suggesting a general overcompensation of the innate immunity in the absence of the adaptive one.
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Huo S, Jiao H, Chen B, Kuang M, Li Q, Lu Y, Liu X. FTR67, a member of the fish-specific finTRIM family, triggers IFN pathway and against spring viremia of carp virus. FISH & SHELLFISH IMMUNOLOGY 2020; 103:1-8. [PMID: 32334126 DOI: 10.1016/j.fsi.2020.04.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Tripartite motif (TRIM) proteins have attracted particular research interest because of their multiple functions in the antiviral innate immune response. TRIM proteins perform different functions during virus infection, some play a role in inhibiting while others play a role in promoting. In this study, we described a species-specific TRIM gene named ftr67. Analysis of tissue distribution showed that ftr67 was mainly expressed in the gill and liver in five examined tissues of zebrafish. The phylogenic analysis showed that ftr67 was closest to the grass carp TRIM67. Overexpression of ftr67 resulted in a significantly decreased SVCV entry and impaired SVCV replication in FHM cells. Furthermore, overexpression of ftr67 could significantly induce the upregulation of molecular sensor RIG-I, IRF3/7, IFN and ISGs. In addition, RING domain of ftr67 was a required part essential for the antiviral effect. In summary, our results demonstrated that the important role of ftr67 in regulating SVCV infection, which offers a potential target for development of anti-SVCV therapies.
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Affiliation(s)
- Shitian Huo
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Houqi Jiao
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Bo Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Ming Kuang
- Institute of Systems Biomedicine, Department of Immunology, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Qing Li
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Yuanan Lu
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA
| | - Xueqin Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China.
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10
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Yao J, Li C, Shi L, Lu Y, Liu X. Zebrafish ubiquitin-specific peptidase 5 (USP5) activates interferon resistance to the virus by increase the expression of RIG-I. Gene 2020; 751:144761. [DOI: 10.1016/j.gene.2020.144761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/02/2020] [Accepted: 05/08/2020] [Indexed: 12/15/2022]
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11
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Integrated Transcriptomic and Proteomic Analysis of Red Blood Cells from Rainbow Trout Challenged with VHSV Point Towards Novel Immunomodulant Targets. Vaccines (Basel) 2019; 7:vaccines7030063. [PMID: 31324030 PMCID: PMC6789484 DOI: 10.3390/vaccines7030063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
Teleost red blood cells (RBCs) are nucleated and therefore can propagate cellular responses to exogenous stimuli. RBCs can mount an immune response against a variety of fish viruses, including the viral septicemia hemorrhagic virus (VHSV), which is one of the most prevalent fish viruses resulting in aquaculture losses. In this work, RBCs from blood and head kidney samples of rainbow trout challenged with VHSV were analyzed via transcriptomic and proteomic analyses. We detected an overrepresentation of differentially expressed genes (DEGs) related to the type I interferon response and signaling in RBCs from the head kidney and related to complement activation in RBCs from blood. Antigen processing and presentation of peptide antigen was overrepresented in RBCs from both tissues. DEGs shared by both tissues showed an opposite expression profile. In summary, this work has demonstrated that teleost RBCs can modulate the immune response during an in vivo viral infection, thus implicating RBCs as cell targets for the development of novel immunomodulants.
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12
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Langevin C, Levraud JP, Boudinot P. Fish antiviral tripartite motif (TRIM) proteins. FISH & SHELLFISH IMMUNOLOGY 2019; 86:724-733. [PMID: 30550990 DOI: 10.1016/j.fsi.2018.12.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Tripartite motif (TRIM) family or RBCC proteins comprises characteristic zinc-binding domains (a RING (R), a B-box type 1 (B1) and a B-box type 2 (B2)) and coiled-coil (CC) domain followed by a C-terminus variable domain. There are about 80 different TRIM proteins in human, but more than 200 in zebrafish with several large gene expansions (ftr >70 genes; btr >30 genes; trim35 > 30 genes). Repertoires of trim genes in fish are variable across fishes, but they have been remarkably diversified independently in a number of species. In mammals, TRIM proteins are involved in antiviral immunity through an astonishing diversity of mechanisms, from direct viral restriction to modulation of immune signaling and more recently autophagy. In fish, the antiviral role of TRIM proteins remains poorly understood. In zebrafish, fish specific TRIMs so called fintrims show a signature of positive selection in the C terminus SPRY domain, reminding features of mammalian antiviral trims such as TRIM5. Expression studies show that a number of trim genes, including many fintrims, can be induced during viral infections, and may play a role in antiviral defence. Some of them trigger antiviral activity in vitro against DNA and RNA viruses, such as FTR83 that also up-regulates the expression of type I IFN in zebrafish larvae. The tissue distribution of TRIM expression suggests that they may be involved in the regionalization of antiviral immunity, providing a particular protection to sensitive areas exposed to invading pathogens.
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Affiliation(s)
- Christelle Langevin
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, Jouy-en-Josas, France.
| | - Jean-Pierre Levraud
- Institut Pasteur, Macrophages et Développement de l'Immunité, Paris, France; Centre National de la Recherche Scientifique, UMR3738, Paris, France
| | - Pierre Boudinot
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, Jouy-en-Josas, France.
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13
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Chaves-Pozo E, Bandín I, Olveira JG, Esteve-Codina A, Gómez-Garrido J, Dabad M, Alioto T, Ángeles Esteban M, Cuesta A. European sea bass brain DLB-1 cell line is susceptible to nodavirus: A transcriptomic study. FISH & SHELLFISH IMMUNOLOGY 2019; 86:14-24. [PMID: 30428392 DOI: 10.1016/j.fsi.2018.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/15/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Viral diseases are responsible for high rates of mortality and subsequent economic losses in modern aquaculture. The nervous necrosis virus (NNV) produces viral encephalopathy and retinopathy (VER), which affects the fish central nervous system. It is considered one of the most serious viral diseases in marine aquaculture, the European sea bass (Dicentrarchus labrax) being amongst the most susceptible. We have evaluated the European sea bass brain derived cell line (DLB-1) susceptibility to NNV genotypes and evaluated its transcriptomic profile. DLB-1 cells supported NNV gene transcription and replication since strains belonging to the four NNV genotypes produce cytopathic effects. Afterwards, DLB-1 cells were infected with an RGNNV strain, the one which showed the highest replication, for 12 and 72 h and an RNA-seq analysis was performed to identify potential genes involved in the host-NNV interactions. Differential expression analysis showed the up-regulation of many genes related to immunity, heat-shock proteins or apoptosis but not to proteasome or autophagy processes. These data suggest that the immune response, mainly the interferon (IFN) pathway, is not powerful enough to abrogate the infection, and cells finally suffer stress and die by apoptosis liberating infective particles. GO enrichment also revealed, for the first time, the down-regulation of terms related to brain/neuron biology indicating molecular mechanisms causing the pathogenic effect of NNV. This study opens the way to understand key elements in sea bass brain and NNV interactions.
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Affiliation(s)
- Elena Chaves-Pozo
- Centro Oceanográfico de Murcia, Instituto Español de Oceanografía (IEO), Carretera de la Azohía s/n, Puerto de Mazarrón, 30860 Murcia, Spain
| | - Isabel Bandín
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, Spain
| | - José G Olveira
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M Ángeles Esteban
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - Alberto Cuesta
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain.
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14
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Chen B, Huo S, Liu W, Wang F, Lu Y, Xu Z, Liu X. Fish-specific finTRIM FTR36 triggers IFN pathway and mediates inhibition of viral replication. FISH & SHELLFISH IMMUNOLOGY 2019; 84:876-884. [PMID: 30366094 DOI: 10.1016/j.fsi.2018.10.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/15/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
The tripartite motif (TRIM) family involves many cellular processes, including fundamental functions in antiviral immunity. Antiviral activities of TRIMs are reported in a variety of patterns, and one of the most significant channels is related to the activation of the type-I interferon (IFN) pathway. In this study, we described a fintrim (ftr) gene named ftr36, which is mainly expressed in the gills, skin, and intestines. This study shows that ftr36 encodes a protein affording a potent antiviral effect. In vitro, overexpression of FTR36 mediated an upregulated pattern of recognition receptor retinoic acid-inducible gene I (RIG-I), interferon regulatory factor 3/7(IRF3/7), IFN, and IFN-stimulated genes (ISGs) expression. Thereby, FTR36 expression could afford host defense against the spring viremia of carp virus (SVCV) and the giant salamander iridovirus (GSIV). With the deletion of the RING domain or B30.2 domain separately, the antiviral ability of FTR36 was abolished partially and almost lost its ability to activate the IFN-pathway. These findings indicate that both RING and B30.2 domains are indispensable for the antiviral activity of FTR36. Altogether, this study described a finTRIM FTR36, which can activate IFN-pathways and stimulate ISGs to provide host defense against viral infections.
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Affiliation(s)
- Bo Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Shitian Huo
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Wanmeng Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Fang Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Yuanan Lu
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Zhen Xu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China
| | - Xueqin Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China; Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, China.
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