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Jang JH, Kim H, Kim HR, Cho JH. Rainbow trout DUBA inhibits type I interferon signaling by deubiquitinating TRAF3. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109581. [PMID: 38670412 DOI: 10.1016/j.fsi.2024.109581] [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: 02/13/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024]
Abstract
Deubiquitinating enzyme A (DUBA), a member of the ovarian tumor (OTU) subfamily of deubiquitinases (DUBs), is recognized for its negative regulatory role in type I interferon (IFN) expression downstream of Toll-like receptor 3 (TLR3). However, its involvement in the TLR3 signaling pathway in fish remains largely unexplored. In this study, we investigated the regulatory role of DUBA (OmDUBA) in the TLR3 response in rainbow trout (Oncorhynchus mykiss). OmDUBA features a conserved OTU domain, and its expression increased in RTH-149 cells following stimulation with the TLR3 agonist poly(I:C). Gain- and loss-of-function experiments demonstrated that OmDUBA attenuated the activation of TANK-binding kinase 1 (TBK1), resulting in a subsequent reduction in type I IFN expression and IFN-stimulated response element (ISRE) activation in poly(I:C)-stimulated cells. OmDUBA interacted with TRAF3, a crucial mediator in TLR3-mediated type I IFN production. Under poly(I:C) stimulation, there was an augmentation in the K63-linked polyubiquitination of TRAF3, a process significantly inhibited upon OmDUBA overexpression. These findings suggest that OmDUBA may function similarly to its mammalian counterparts in downregulating the poly(I:C)-induced type I IFN response in rainbow trout by removing the K63-linked ubiquitin chain on TRAF3. Our study provides novel insights into the role of fish DUBA in antiviral immunity.
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Affiliation(s)
- Ju Hye Jang
- Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, South Korea
| | - Hyun Kim
- Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, South Korea
| | - Ha Rang Kim
- Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju, 52828, South Korea
| | - Ju Hyun Cho
- Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, South Korea; Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju, 52828, South Korea; Division of Life Science, Gyeongsang National University, Jinju, 52828, South Korea.
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Warren CJ, Barbachano-Guerrero A, Bauer VL, Stabell AC, Dirasantha O, Yang Q, Sawyer SL. Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.13.566830. [PMID: 38014262 PMCID: PMC10680607 DOI: 10.1101/2023.11.13.566830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Simian immunodeficiency viruses (SIVs) comprise a large group of primate lentiviruses that endemically infect African monkeys. HIV-1 spilled over to humans from this viral reservoir, but the spillover did not occur directly from monkeys to humans. Instead, a key event was the introduction of SIVs into great apes, which then set the stage for infection of humans. Here, we investigate the role of the lentiviral entry receptor, CD4, in this key and fateful event in the history of SIV/HIV emergence. First, we reconstructed and tested ancient forms of CD4 at two important nodes in ape speciation, both prior to the infection of chimpanzees and gorillas with these viruses. These ancestral CD4s fully supported entry of diverse SIV isolates related to the viruses that made this initial jump to apes. In stark contrast, modern chimpanzee and gorilla CD4 orthologs are more resistant to these viruses. To investigate how this resistance in CD4 was gained, we acquired CD4 gene sequences from 32 gorilla individuals of two species, and identified alleles that encode 8 unique CD4 protein variants. Functional testing of these identified variant-specific differences in susceptibility to virus entry. By engineering single point mutations from resistant gorilla CD4 variants into the permissive human CD4 receptor, we demonstrate that acquired substitutions in gorilla CD4 did convey resistance to virus entry. We provide a population genetic analysis to support the theory that selection is acting in favor of more and more resistant CD4 alleles in ape species harboring SIV endemically (gorillas and chimpanzees), but not in other ape species that lack SIV infections (bonobos and orangutans). Taken together, our results show that SIV has placed intense selective pressure on ape CD4, acting to propagate SIV-resistant alleles in chimpanzee and gorilla populations.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Vanessa L. Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Alex C. Stabell
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Obaiah Dirasantha
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Qing Yang
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
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Jang JH, Jung IY, Kim H, Cho JH. Rainbow trout USP4 downregulates LPS-induced inflammation by removing the K63-linked ubiquitin chain on TAK1. FISH & SHELLFISH IMMUNOLOGY 2022; 131:1019-1026. [PMID: 36372204 DOI: 10.1016/j.fsi.2022.11.005] [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: 09/19/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Ubiquitin-specific protease 4 (USP4) is pivotal in negatively regulating the Toll-like receptor (TLR) signaling-mediated innate immune response. Although USP4 has been well studied in mammals, its role in TLR signaling pathways in fish remains largely unknown. In this study, we investigated the role of USP4 (OmUSP4) in regulating TLR response in rainbow trout Oncorhynchus mykiss. OmUSP4 contained the characteristic domains conserved in other USP4s: domain in USP (DUSP), ubiquitin-like (UBL), and the bi-part catalytic domain known as USP. OmUSP4 expression was increased in RTH-149 cells by stimulation with fish-pathogenic bacteria and bacterial ligands. Gain- and loss-of-function experiments revealed that OmUSP4 mitigated the activation of MAPKs and NF-κB, as well as the expression of pro-inflammatory cytokines in LPS-stimulated cells. OmUSP4 interacted with TAK1, a critical mediator in TLR-mediated NF-κB signaling pathways. LPS stimulation increased the K63-linked polyubiquitination of TAK1, which was significantly suppressed when OmUSP4 was compelled to be overexpressed. These results imply that OmUSP4 might function like mammals to downregulate LPS-induced inflammation in rainbow trout by removing the K63-linked ubiquitin chain on TAK1.
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Affiliation(s)
- Ju Hye Jang
- Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, South Korea
| | - In Young Jung
- Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju, 52828, South Korea
| | - Hyun Kim
- Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, South Korea
| | - Ju Hyun Cho
- Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52828, South Korea; Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju, 52828, South Korea; Division of Life Science, Gyeongsang National University, Jinju, 52828, South Korea.
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Zhang Q, Jia Q, Gao W, Zhang W. The Role of Deubiquitinases in Virus Replication and Host Innate Immune Response. Front Microbiol 2022; 13:839624. [PMID: 35283827 PMCID: PMC8908266 DOI: 10.3389/fmicb.2022.839624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
As a critical post-translational modification, ubiquitination is known to affect almost all the cellular processes including immunity, signaling pathways, cell death, cancer development, and viral infection by controlling protein stability. Deubiquitinases (DUBs) cleave ubiquitin from proteins and reverse the process of ubiquitination. Thus, DUBs play an important role in the deubiquitination process and serve as therapeutic targets for various diseases. DUBs are found in eukaryotes, bacteria, and viruses and influence various biological processes. Here, we summarize recent findings on the function of DUBs in modulating viral infection, the mechanism by which viral DUBs regulate host innate immune response, and highlight those DUBs that have recently been discovered as antiviral therapeutic targets.
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Affiliation(s)
- Qinglin Zhang
- College of Life Sciences of Jilin University, Changchun, China
| | - Qizhen Jia
- College of Life Sciences of Jilin University, Changchun, China
| | - Wenying Gao
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Wenyan Zhang
- Center for Pathogen Biology and Infectious Diseases, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
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Zhang Y, Huang L, Gao X, Qin Q, Huang X, Huang Y. Grouper USP12 exerts antiviral activity against nodavirus infection. FISH & SHELLFISH IMMUNOLOGY 2022; 121:332-341. [PMID: 35032679 DOI: 10.1016/j.fsi.2022.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
The ubiquitin-specific proteases (USPs) have attracted particular attention due to their multiple functions in different biological processes. USP12, a member of the USP family, has been demonstrated to exert critical roles in diverse cellular processes, including cell death, cancer and antiviral immunity. Here, we cloned a USP12 homolog from orange spotted grouper (Epinephelus coioides, E. coioides), and its roles in fish RNA virus replication were investigated. EcUSP12 contained a 1119-bp open reading frame (ORF) encoding a 372-amino acid polypeptide, which shared 100.00% and 91.32% identity with USP12 homolog of Etheostoma cragini and Homo sapiens, respectively. Sequence analysis indicated that EcUSP12 contained a conserved peptidase-C19G domain (aa 40-369). qPCR analysis showed that EcUSP12 transcript was most abundant in head kidney and spleen of grouper E. coioides. The expression of EcUSP12 was significantly upregulated in grouper spleen (GS) cells in response to red-spotted grouper nervous necrosis virus (RGNNV) infection. Subcellular localization analysis showed that EcUSP12 was evenly distributed throughout the cytoplasm, and mainly co-localized with endoplasmic reticulum (ER). Interestingly, during RGNNV infection, the endogenous distribution of EcUSP12 was obviously altered, and mostly overlapped with viral coat protein (CP). Co-Immunoprecipitation (Co-IP) assay indicated that EcUSP12 interacted with viral CP. In addition, overexpression of EcUSP12 significantly inhibited the replication of RGNNV in vitro, as evidenced by the decrease in viral gene transcription and protein synthesis during infection. Consistently, knockdown of EcUSP12 by small interfering RNA (siRNA) promoted the replication of RGNNV. Furthermore, EcUSP12 overexpression also increased the transcription level of inflammatory factors and interferon-related genes, including tumor necrosis factor α (TNF-α), interleukin (IL)-1β, IL-6, IL-8, interferon regulatory factor 3 (IRF3), and IRF7. Taken together, our results demonstrated that EcUSP12, as a positive regulator of IFN signaling, interacted with viral CP to inhibit virus infection.
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Affiliation(s)
- Ya Zhang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liwei Huang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaolin Gao
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qiwei Qin
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, 519082, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
| | - Xiaohong Huang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Youhua Huang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Qian G, Zhu L, Huang C, Liu Y, Ren Y, Ding Y, Qian W, Xu Q, Zheng H, Lv H. Ubiquitin specific protease 5 negatively regulates the IFNs-mediated antiviral activity via targeting SMURF1. Int Immunopharmacol 2020; 87:106763. [PMID: 32683298 DOI: 10.1016/j.intimp.2020.106763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/03/2020] [Accepted: 06/28/2020] [Indexed: 02/06/2023]
Abstract
Type I interferons are broadly used for antiviral therapy in clinical. However, the IFNs-mediated antiviral efficacy is commonly restricted by negative regulators. Here, we show that the ubiquitin-specific protease 5 (USP5) inhibits the IFNs-induced p-STAT1 activation (phosphorylation at tyrosine site of STAT1) and its downstream antiviral genes expression. We clarify that USP5 physically interacts with SMURF1 (Smad ubiquitination regulating factor 1) and IFNs signaling regulates the interaction and turnover of both proteins. USP5 enhances the stability and turnover of SMURF1 via decreasing its polyubiquitin expression level, which caused STAT1 to decrease. Importantly, USP5 is also involved in the SMURF1-mediated antiviral response, and its small-molecule inhibitor PYR41 remarkably enhances the IFNs antiviral efficacy. These findings reveal a previously unrecognized function of the USP5 and USP5-SMURF1 axis in regulating the IFNs-mediated antiviral activity.
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Affiliation(s)
- Guanghui Qian
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu Province 215025, China
| | - Liyan Zhu
- Medical College of Soochow University, Suzhou 215123, China
| | - Chengcheng Huang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu Province 215025, China
| | - Ying Liu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu Province 215025, China
| | - Ying Ren
- Medical College of Soochow University, Suzhou 215123, China
| | - Yueyue Ding
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu Province 215025, China
| | - Weiguo Qian
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu Province 215025, China
| | - Qiuqin Xu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu Province 215025, China
| | - Hui Zheng
- Medical College of Soochow University, Suzhou 215123, China.
| | - Haitao Lv
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu Province 215025, China.
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