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Wang Y, Xu X, Zhang A, Yang S, Li H. Role of alternative splicing in fish immunity. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109601. [PMID: 38701992 DOI: 10.1016/j.fsi.2024.109601] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Alternative splicing serves as a pivotal source of complexity in the transcriptome and proteome, selectively connecting various coding elements to generate a diverse array of mRNAs. This process encodes multiple proteins with either similar or distinct functions, contributing significantly to the intricacies of cellular processes. The role of alternative splicing in mammalian immunity has been well studied. Remarkably, the immune system of fish shares substantial similarities with that of humans, and alternative splicing also emerges as a key player in the immune processes of fish. In this review, we offer an overview of alternative splicing and its associated functions in the immune processes of fish, and summarize the research progress on alternative splicing in the fish immunity. Furthermore, we review the impact of alternative splicing on the fish immune system's response to external stimuli. Finally, we present our perspectives on future directions in this field. Our aim is to provide valuable insights for the future investigations into the role of alternative splicing in immunity.
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Affiliation(s)
- Yunchao Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinyi Xu
- Hunan Fisheries Science Institute, Changsha, 410153, China
| | - Ailong Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266003, China.
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2
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Jang H, Kim S, Kim DY, Han JH, Park HH. TRAF1 from a Structural Perspective. Biomolecules 2024; 14:510. [PMID: 38785916 PMCID: PMC11117997 DOI: 10.3390/biom14050510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/13/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Tumor necrosis factor receptor-associated factor (TRAF) proteins play pivotal roles in a multitude of cellular signaling pathways, encompassing immune response, cell fate determination, development, and thrombosis. Their involvement in these processes hinges largely on their ability to interact directly with diverse receptors via the TRAF domain. Given the limited binding interface, understanding how specific TRAF domains engage with various receptors and how structurally similar binding interfaces of TRAF family members adapt their distinct binding partners has been the subject of extensive structural investigations over several decades. This review presents an in-depth exploration of the current insights into the structural and molecular diversity exhibited by the TRAF domain and TRAF-binding motifs across a range of receptors, with a specific focus on TRAF1.
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Affiliation(s)
| | | | | | | | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea; (H.J.); (S.K.); (D.Y.K.); (J.H.H.)
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3
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Bandyopadhyay S, Gurjar D, Saha B, Bodhale N. Decoding the contextual duality of CD40 functions. Hum Immunol 2023; 84:590-599. [PMID: 37596136 DOI: 10.1016/j.humimm.2023.08.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/13/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
Previously, we established that as a function of its mode of interaction with its ligand or cellular conditions such as membrane lipids, preexisting signaling intermediates activation status, a transmembrane receptor, as represented here with CD40, can induce counteractive cellular responses. Using CD40-binding peptides, recombinant mutated CD40-ligands, and an agonistic antibody, we have established the functional duality of CD40. CD40 builds up two constitutionally different signalosomes on lipid raft and non-raft membrane domains initiating two different signaling pathways. Although this initial signaling may be modified by the pre-existing signaling conditions downstream and may be subjected to feed-forward or negative signaling effects, the initial CD40-CD40L interaction plays a crucial role in the functional outcome of CD40. Herein, we have reviewed the influence of interaction between the CD40-CD40L evoking the functional duality of CD40 contingent upon different physiological states of the cells.
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Affiliation(s)
| | - Dhiraj Gurjar
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Neelam Bodhale
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
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4
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Wang R, Han P, Liu X, Wang X. Genome-wide identification of TNF receptor-associated factors in Japanese flounder (Paralichthys olivaceus) and functional analysis of resistance to temperature and Edwardsiella tarda stress. FISH & SHELLFISH IMMUNOLOGY 2023; 138:108862. [PMID: 37263548 DOI: 10.1016/j.fsi.2023.108862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/16/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023]
Abstract
Tumor necrosis factor receptor-associated factors (TRAFs), as the signaling mediators of the tumor necrosis factor (TNFR) superfamily, toll-like receptors (TLR) and interleukin-1 receptor (IL-1R) superfamily, can activate downstream signal transduction pathways and play an important role in the body's immune process. In this study, six TRAF genes, namely PoTRAF2a, PoTRAF2b, PoTRAF3, PoTRAF4, PoTRAF6 and PoTRAF7, were identified and annotated in Japanese flounder by using bioinformatics methods. Phylogenetic analysis confirmed that TRAF genes can be divided into seven groups. Analysis of motif composition and gene structure demonstrated that all PoTRAF members were evolutionarily conserved. The expression patterns of PoTRAF genes were then further investigated in six different developmental stages and eleven tissues of healthy fish, and it was found that there were spatial and tissue specificities among the members. To investigate the immune response of Japanese flounder to abiotic and biotic stresses, we further analyzed the expression profile of PoTRAFs after temperature stress and pathogen challenge. The result showed that PoTRAF3 and PoTRAF4 were observably differentially expressed under temperature stress, indicating that they were involved in the immune response after temperature stress. The expression of PoTRAF2a, PoTRAF2b and PoTRAF4 was significantly different after E. tarda infection, suggesting that they might have antibacterial effects. These results would help to clarify the molecular roles of PoTRAF genes in the regulation of immune and inflammatory responses in Japanese flounder.
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Affiliation(s)
- Ruoxin Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Ping Han
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China.
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China.
| | - Xubo Wang
- Key Laboratory of Aquacultural Biotechnology (Ningbo University), Ministry of Education, Ningbo, Zhejiang, China; National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, China; Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, China.
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5
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Aten S, Du Y, Taylor O, Dye C, Collins K, Thomas M, Kiyoshi C, Zhou M. Chronic Stress Impairs the Structure and Function of Astrocyte Networks in an Animal Model of Depression. Neurochem Res 2023; 48:1191-1210. [PMID: 35796915 PMCID: PMC9823156 DOI: 10.1007/s11064-022-03663-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/18/2022] [Indexed: 01/11/2023]
Abstract
Now astrocytes appear to be the key contributors to the pathophysiology of major depression. Evidence in rodents shows that chronic stress is associated with a decreased expression of astrocytic GFAP-immunoreactivity within the cortex in addition to changes in the complexity and length of astrocyte processes. Furthermore, postmortem brains of individuals with depression have revealed a decrease in astrocyte density. Notably, astrocytes are extensively coupled to one another through gap junctions to form a network, or syncytium, and we have previously demonstrated that syncytial isopotentiality is a mechanism by which astrocytes function as an efficient system with respect to brain homeostasis. Interestingly, the question of how astrocyte network function changes following chronic stress is yet to be elucidated. Here, we sought to examine the effects of chronic stress on network-level astrocyte (dys)function. Using a transgenic aldh1l1-eGFP astrocyte reporter mouse, a six-week unpredictable chronic mild stress (UCMS) paradigm as a rodent model of major depression, and immunohistochemical approaches, we show that the morphology of individual astrocytes is altered by chronic stress exposure. Additionally, in astrocyte syncytial isopotentiality measurement, we found that UCMS impairs the syncytial coupling strength of astrocytes within the hippocampus and prefrontal cortex-two brain regions that have been implicated in the regulation of mood. Together, these findings reveal that chronic stress leads to astrocyte atrophy and impaired gap junction coupling, raising the prospect that both individual and network-level astrocyte functionality are important in the etiology of major depression and other neuropsychiatric disorders.
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Affiliation(s)
- Sydney Aten
- Department of Neuroscience, Ohio State University Wexner Medical Center, Graves Hall, Rm 4066C, 333 W. 10th Ave, Columbus, OH, 43210, USA
- Department of Neurology, Division of Sleep Medicine, and Program in Neuroscience, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Yixing Du
- Department of Neuroscience, Ohio State University Wexner Medical Center, Graves Hall, Rm 4066C, 333 W. 10th Ave, Columbus, OH, 43210, USA
| | - Olivia Taylor
- Department of Neuroscience, Ohio State University Wexner Medical Center, Graves Hall, Rm 4066C, 333 W. 10th Ave, Columbus, OH, 43210, USA
| | - Courtney Dye
- Department of Neuroscience, Ohio State University Wexner Medical Center, Graves Hall, Rm 4066C, 333 W. 10th Ave, Columbus, OH, 43210, USA
| | - Kelsey Collins
- Department of Neuroscience, Ohio State University Wexner Medical Center, Graves Hall, Rm 4066C, 333 W. 10th Ave, Columbus, OH, 43210, USA
| | - Matthew Thomas
- Department of Neuroscience, Ohio State University Wexner Medical Center, Graves Hall, Rm 4066C, 333 W. 10th Ave, Columbus, OH, 43210, USA
| | - Conrad Kiyoshi
- Department of Neuroscience, Ohio State University Wexner Medical Center, Graves Hall, Rm 4066C, 333 W. 10th Ave, Columbus, OH, 43210, USA
- Northern Marianas College, Saipan, MP, USA
| | - Min Zhou
- Department of Neuroscience, Ohio State University Wexner Medical Center, Graves Hall, Rm 4066C, 333 W. 10th Ave, Columbus, OH, 43210, USA.
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6
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Kim CM, Jang H, Hong E, Lee JH, Park HH. Structure of fish TRAF4 and its implication in TRAF4-mediated immune cell and platelet signaling. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108462. [PMID: 36455779 DOI: 10.1016/j.fsi.2022.108462] [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: 08/02/2022] [Revised: 11/20/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Due to an increasing interest in immunity and signal transduction in teleost fish, important key signaling molecules associated with the immune response, including TRAF molecules, have been recently cloned and characterized. To better understand the role of TRAF4 in fish immune signaling and compare it with the human system, our study cloned the TRAF4 gene from the Antarctic yellowbelly rockcod Notothenia coriiceps (ncTRAF4) and purified the protein. Here, we report the first crystal structure of teleost fish TRAF4. Based on biochemical characterization, our findings elucidated the mechanisms through which signaling molecules gain cold adaptivity. Additionally, we identified a platelet receptor GPIbβ homolog in N. coriiceps (ncGPIbβ) and found that the "RRFERLFKEARRTS" region of this homolog directly binds to ncTRAF4, indicating that ncTRAF4 also recognizes the "RLXA" motif for receptor interactions and further TARF4-mediated cellular signaling. Collectively, our findings provide novel insights into the mechanisms of TRAF4-mediated immune cell and platelet signaling in fish and the structural flexibility-mediated cold adaptiveness of signaling molecules.
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Affiliation(s)
- Chang Min Kim
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyunseok Jang
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.
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Negative Regulatory Role of the Spring Viremia of Carp Virus Matrix Protein in the Host Interferon Response by Targeting the MAVS/TRAF3 Signaling Axis. J Virol 2022; 96:e0079122. [PMID: 35913215 PMCID: PMC9400495 DOI: 10.1128/jvi.00791-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Spring viremia of carp virus (SVCV) is a severe infectious pathogen that causes high rates of mortality in cyprinids and other fish species. Despite numerous investigations of SVCV infection, the underlying molecular mechanisms remain poorly understood. In this study, we found that the SVCV matrix protein (SVCV-M) played an inhibitory role in the host interferon (IFN) response by targeting the MAVS/TRAF3 signaling axis, thereby uncovering a previously unrecognized mechanism of SVCV escape from host innate antiviral immunity. Mechanistically, SVCV-M was located at the mitochondria independent of MAVS, which allowed SVCV-M to build an arena for competition with the MAVS platform. A microscale thermophoresis assay showed that SVCV-M had a high affinity for TRAF3, as indicated by a lower equilibrium dissociation constant (KD) value than that of MAVS with TRAF3. Therefore, the association of MAVS with TRAF3 was competitively impaired by SVCV-M in a dose-dependent manner. Accordingly, SVCV-M showed a potent ability to inhibit the K63-linked polyubiquitination of TRAF3. This inhibition was accompanied by the impairment of the IFN response, as shown by the marked decline in IFN-φ1-promoter (pro) luciferase reporter activity. By constructing truncated TRAF3 and SVCV-M proteins, the RING finger, zinc finger, and coiled-coil domains of TRAF3 and the hydrophobic-pocket-like structure formed by the α2-, α3-, and α4-helices of SVCV-M may be the major target and antagonistic modules responsible for the protein-protein interaction between the TRAF3 and SVCV-M proteins. These findings highlighted the intervention of SVCV-M in host innate immunity, thereby providing new insights into the extensive participation of viral matrix proteins in multiple biological activities. IMPORTANCE The matrix protein of SVCV (SVCV-M) is an indispensable structural element for nucleocapsid condensation and virion formation during viral morphogenesis, and it connects the core nucleocapsid particle to the outer membrane within the mature virus. Previous studies have emphasized the architectural role of SVCV-M in viral construction; however, the potential nonstructural functions of SVCV-M in viral replication and virus-host interactions remain poorly understood. In this study, we identified the inhibitory role of the SVCV-M protein in host IFN production by competitively recruiting TRAF3 from the MAVS signaling complex and impairing TRAF3 activation via inhibition of K63-linked polyubiquitination. This finding provided new insights into the regulatory role of SVCV-M in host innate immunity, which highlighted the broader functionality of rhabdovirus matrix protein apart from being a structural protein. This study also revealed a previously unrecognized mechanism underlying SVCV immune evasion by inhibiting the IFN response by targeting the MAVS/TRAF3 signaling axis.
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Sun M, Wu S, Zhang X, Zhang L, Kang S, Qin Q, Wei J. Grouper TRAF5 exerts negative regulation on antiviral immune response against iridovirus. FISH & SHELLFISH IMMUNOLOGY 2021; 115:7-13. [PMID: 34062236 DOI: 10.1016/j.fsi.2021.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Tumor necrosis factor receptor-associated factor 5 (TRAF5) is an intracellular protein that binds to the cytoplasmic portion of tumor necrosis factor receptors and mediates the activation of downstream nuclear factor-kappa B (NF-κB), interferon regulatory factor 3, and mitogen activated protein kinase signaling pathways. Compared with other TRAF proteins, TRAF5 is largely unknown in teleosts. In the present study, a TRAF5 homologue (HgTRAF5) from the hybrid grouper (Epinephelus fuscoguttatus♂ × Epinephelus lanceolatus♀) was cloned and characterized. The open reading frame of HgTRAF5 consists of 1743 nucleotides encoding a 581 amino acid protein with a predicted molecular mass of 64.90 kDa. Similar to its mammalian counterpart, HgTRAF5 contains an N-terminal RING finger domain, a zinc finger domain, and a C-terminal TRAF domain, including a coiled-coil domain and a MATH domain. HgTRAF5 shares 99.83% identity with giant grouper (Epinephelus lanceolatus) TRAF5. Quantitative real-time PCR analysis indicated that HgTRAF5 mRNA was broadly expressed in all examined tissues. The expression of HgTRAF5 increased after Singapore grouper iridovirus (SGIV) infection in grouper spleen (GS) cells. Intracellular localization analysis demonstrated that the full-length HgTRAF5 protein mainly distributed in the cytoplasm. HgTRAF5 overexpression also promoted SGIV replication during viral infection in vitro. HgTRAF5 significantly promoted the activities of interferon-β, interferon-sensitive response element, and NF-κB. Taken together, these results are important for a better understanding of the function of TRAF5 in fish and reveal its involvement in the host response to immune challenge by SGIV.
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Affiliation(s)
- Mengshi Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Siting Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Xin Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Luhao Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Shaozhu Kang
- Guangdong Laboratory for Lingnan Modern Agriculture, Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Qiwei Qin
- Guangdong Laboratory for Lingnan Modern Agriculture, Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, PR China.
| | - Jingguang Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China.
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Yu X, James S, Felce JH, Kellermayer B, Johnston DA, Chan HTC, Penfold CA, Kim J, Inzhelevskaya T, Mockridge CI, Watanabe Y, Crispin M, French RR, Duriez PJ, Douglas LR, Glennie MJ, Cragg MS. TNF receptor agonists induce distinct receptor clusters to mediate differential agonistic activity. Commun Biol 2021; 4:772. [PMID: 34162985 PMCID: PMC8222242 DOI: 10.1038/s42003-021-02309-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/04/2021] [Indexed: 02/05/2023] Open
Abstract
Monoclonal antibodies (mAb) and natural ligands targeting costimulatory tumor necrosis factor receptors (TNFR) exhibit a wide range of agonistic activities and antitumor responses. The mechanisms underlying these differential agonistic activities remain poorly understood. Here, we employ a panel of experimental and clinically-relevant molecules targeting human CD40, 4-1BB and OX40 to examine this issue. Confocal and STORM microscopy reveal that strongly agonistic reagents induce clusters characterized by small area and high receptor density. Using antibody pairs differing only in isotype we show that hIgG2 confers significantly more receptor clustering than hIgG1 across all three receptors, explaining its greater agonistic activity, with receptor clustering shielding the receptor-agonist complex from further molecular access. Nevertheless, discrete receptor clustering patterns are observed with different hIgG2 mAb, with a unique rod-shaped assembly observed with the most agonistic mAb. These findings dispel the notion that larger receptor clusters elicit greater agonism, and instead point to receptor density and subsequent super-structure as key determinants.
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Affiliation(s)
- Xiaojie Yu
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK.
| | - Sonya James
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | | | | | - David A Johnston
- Biomedical Imaging Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - H T Claude Chan
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Christine A Penfold
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Jinny Kim
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Tatyana Inzhelevskaya
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - C Ian Mockridge
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Yasunori Watanabe
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Ruth R French
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Patrick J Duriez
- CRUK Protein Core Facility, University of Southampton Faculty of Medicine, Southampton, UK
| | - Leon R Douglas
- CRUK Protein Core Facility, University of Southampton Faculty of Medicine, Southampton, UK
| | - Martin J Glennie
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Mark S Cragg
- Antibody and Vaccine Group, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK.
- Institute for Life Sciences, University of Southampton, Southampton, UK.
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10
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Park HH. Structural feature of TRAFs, their related human diseases and therapeutic intervention. Arch Pharm Res 2021; 44:475-486. [PMID: 33970438 DOI: 10.1007/s12272-021-01330-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
Several studies have been conducted over the years to unravel the structural information on the receptors that bind to tumor necrosis factor receptor-associated factor (TRAF) and the driving forces for the TRAF/receptor complex. In addition, studies have also been performed to highlight the influence of TRAF malfunctioning and mutations on the development of human disease. However, a holistic study that systematically summarizes the available information and the existing clinical trends towards development of the TRAF-targeting drugs has not been conducted to date. Herein, I reviewed existing research that focused on the structural information of various receptors recognized by the different members of the TRAF family. I also reviewed studies on the different human diseases that occur due to TRAF malfunctioning or mutations as well as the clinical trials undertaken to treat TRAF-associated diseases.
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Affiliation(s)
- Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea. .,Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.
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11
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Lei Y, Cao X, Xu W, Yang B, Xu Y, Zhou W, Dong S, Wu Q, Rahman K, Tyagi R, Zhao S, Chen X, Cao G. Rv3722c Promotes Mycobacterium tuberculosis Survival in Macrophages by Interacting With TRAF3. Front Cell Infect Microbiol 2021; 11:627798. [PMID: 33718275 PMCID: PMC7947218 DOI: 10.3389/fcimb.2021.627798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/19/2021] [Indexed: 01/08/2023] Open
Abstract
Mycobacterium tuberculosis (M.tb) secretes numerous proteins to interfere with host immune response for its long-term survival. As one of the top abundant M.tb secreted proteins, Rv3722c was found to be essential for bacilli growth. However, it remains elusive how this protein interferes with the host immune response and regulates M.tb survival. Here, we confirmed that Rv3722c interacted with host TRAF3 to promote M.tb replication in macrophages. Knock-down of TRAF3 attenuated the effect of Rv3722c on the intracellular M.tb survival. The interaction between Rv3722c and TRAF3 hampered MAPK and NF-κB pathways, resulting in a significant increase of IFN-β expression and decrease of IL-1β, IL-6, IL-12p40, and TNF-α expression. Our study revealed that Rv3722c interacted with TRAF3 and interrupted its downstream pathways to promote M.tb survival in macrophages. These findings facilitate further understanding of the mechanism of M.tb secreted proteins in regulating the host cell immune response and promoting its intracellular survival.
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Affiliation(s)
- Yingying Lei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yangyang Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shuang Dong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qijun Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Khaista Rahman
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rohit Tyagi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Bio-Medical Center, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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12
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Kim CM, Jang H, Ha HJ, Kim GE, Park HH. Structural and biochemical characterization of TRAF5 from Notothenia coriiceps and its implications in fish immune cell signaling. FISH & SHELLFISH IMMUNOLOGY 2020; 102:56-63. [PMID: 32283248 DOI: 10.1016/j.fsi.2020.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/08/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Conserved immune cell signaling in fish was recently highlighted by the identification of various immune cell signaling molecules. Tumor necrosis factor (TNF) receptor-associated factor (TRAF) proteins are critical adaptor molecules in immune cell signaling and contain E3 ubiquitin ligase activity. Here, we report the first crystal structure of the TRAF5 TRAF domain from the black rockcod (Notothenia coriiceps; ncTRAF5). Our structure revealed both similarities and differences with mammalian TRAF5. Structural and biochemical analyses indicated that ncTRAF5 forms a functional trimer unit in solution, with a structural flexibility that might be critical for imparting resistance to cold temperature-induced stress. We also found conserved surface residues on ncTRAF5 that might be critical binding hot spots for interaction with various receptors.
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Affiliation(s)
- Chang Min Kim
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyunseok Jang
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Gi Eob Kim
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.
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13
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Kim CM, Park HH. Comparison of Target Recognition by TRAF1 and TRAF2. Int J Mol Sci 2020; 21:ijms21082895. [PMID: 32326186 PMCID: PMC7215387 DOI: 10.3390/ijms21082895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/10/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022] Open
Abstract
Although TRAF1 and TRAF2 share common receptors and have extremely conserved amino acid residues, recent studies have shown that key differences in receptor binding preferences with different affinities exist, which might be important for their different functions in TRAF-mediated signal transduction. To better understand TRAF1 and TRAF2 signaling, we analyzed and compared their receptor binding-affinities. Our study revealed that TRADD, TANK, and caspase-2 bind to both TRAF1 and TRAF2 with different affinities in vitro. Sequence and structural analyses revealed that S454 on TRAF2 (corresponding to A369 of TRAF1) is critical for the binding of TRADD, and F347 on TRAF1 (corresponding to L432 of TRAF2) is a critical determinant for high affinity binding of TANK and caspase-2.
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14
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Thioredoxin 2 Negatively Regulates Innate Immunity to RNA Viruses by Disrupting the Assembly of the Virus-Induced Signaling Adaptor Complex. J Virol 2020; 94:JVI.01756-19. [PMID: 31915282 DOI: 10.1128/jvi.01756-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/18/2019] [Indexed: 12/24/2022] Open
Abstract
The virus-induced signaling adaptor (VISA) complex plays a critical role in the innate immune response to RNA viruses. However, the mechanism of VISA complex formation remains unclear. Here, we demonstrate that thioredoxin 2 (TRX2) interacts with VISA at mitochondria both in vivo and in vitro Knockdown and knockout of TRX2 enhanced the formation of the VISA-associated complex, as well as virus-triggered activation of interferon regulatory factor 3 (IRF3) and transcription of the interferon beta 1 (IFNB1) gene. TRX2 inhibits the formation of VISA aggregates by repressing reactive oxygen species (ROS) production, thereby disrupting the assembly of the VISA complex. Furthermore, our data suggest that the C93 residue of TRX2 is essential for inhibition of VISA aggregation, whereas the C283 residue of VISA is required for VISA aggregation. Collectively, these findings uncover a novel mechanism of TRX2 that negatively regulates VISA complex formation.IMPORTANCE The VISA-associated complex plays pivotal roles in inducing type I interferons (IFNs) and eliciting the innate antiviral response. Many host proteins are identified as VISA-associated-complex proteins, but how VISA complex formation is regulated by host proteins remains enigmatic. We identified the TRX2 protein as an important regulator of VISA complex formation. Knockout of TRX2 increases virus- or poly(I·C)-triggered induction of type I IFNs at the VISA level. Mechanistically, TRX2 inhibits the production of ROS at its C93 site, which impairs VISA aggregates at its C283 site, and subsequently impedes the assembly of the VISA complex. Our findings suggest that TRX2 plays an important role in the regulation of VISA complex assembly.
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15
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Park HH. Structure of TRAF Family: Current Understanding of Receptor Recognition. Front Immunol 2018; 9:1999. [PMID: 30214450 PMCID: PMC6125299 DOI: 10.3389/fimmu.2018.01999] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/14/2018] [Indexed: 12/20/2022] Open
Abstract
Tumor necrosis factor receptor–associated factor (TRAF) proteins are key signaling molecules that function in various cellular signaling events including immune response, cell death and survival, development, and thrombosis. Their roles in cellular signaling are mediated mostly by direct interactions with various receptors via the TRAF domain. To determine how specific TRAF domains can interact with various receptors with a limited binding interface and how similar binding interfaces of TRAF family members can recognize their specific binding partners, extensive structural studies on TRAF family proteins have been conducted for several decades. In this review, we discuss the current understanding of the structural and molecular diversity of the TRAF domain and TRAF-binding motifs in many receptors according to available structural information.
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Affiliation(s)
- Hyun H Park
- College of Pharmacy, Chung-Ang University, Seoul, South Korea
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16
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Lv H, Dong W, Guo K, Jin M, Li X, Li C, Zhang Y. Tumor Necrosis Factor Receptor-Associated Factor 5 Interacts with the NS3 Protein and Promotes Classical Swine Fever Virus Replication. Viruses 2018; 10:v10060305. [PMID: 29874812 PMCID: PMC6024839 DOI: 10.3390/v10060305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 12/21/2022] Open
Abstract
Classical swine fever, caused by classical swine fever virus (CSFV), is a highly contagious and high-mortality viral disease, causing huge economic losses in the swine industry worldwide. CSFV non-structural protein 3 (NS3), a multifunctional protein, plays crucial roles in viral replication. However, how NS3 exactly exerts these functions is currently unknown. Here, we identified tumor necrosis factor receptor-associated factor 5 (TRAF5) as a novel binding partner of the NS3 protein via yeast two-hybrid, co-immunoprecipitation and glutathione S-transferase pull-down assays. Furthermore, we observed that TRAF5 promoted CSFV replication in porcine alveolar macrophages (PAMs). Additionally, CSFV infection or NS3 expression upregulated TRAF5 expression, implying that CSFV may exploit TRAF5 via NS3 for better growth. Moreover, CSFV infection and TRAF5 expression activated p38 mitogen activated protein kinase (MAPK) activity, and inhibition of p38 MAPK activation by the SB203580 inhibitor suppressed CSFV replication. Notably, TRAF5 overexpression did not promote CSFV replication following inhibition of p38 MAPK activation. Our findings reveal that TRAF5 promotes CSFV replication via p38 MAPK activation. This work provides a novel insight into the role of TRAF5 in CSFV replication capacity.
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Affiliation(s)
- Huifang Lv
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- College of Pharmaceutical Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China.
| | - Wang Dong
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China.
| | - Kangkang Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
| | - Mingxing Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
| | - Xiaomeng Li
- Ningbo Entry-Exit Inspection and Quarantine Bureau, Ningbo 315000, China.
| | - Cunfa Li
- College of Pharmaceutical Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China.
| | - Yanming Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
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17
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Wei X, Qian W, Sizhu S, Li Y, Guo K, Jin M, Zhou H. Negative Regulation of Interferon-β Production by Alternative Splicing of Tumor Necrosis Factor Receptor-Associated Factor 3 in Ducks. Front Immunol 2018; 9:409. [PMID: 29599773 PMCID: PMC5863512 DOI: 10.3389/fimmu.2018.00409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/14/2018] [Indexed: 02/06/2023] Open
Abstract
Tumor necrosis factor receptor-associated factor 3 (TRAF3), an intracellular signal transducer, is identified as an important component of Toll-like receptors and RIG-I-like receptors induced type I interferon (IFN) signaling pathways. Previous studies have clarified TRAF3 function in mammals, but little is known about the role of TRAF3 in ducks. Here, we cloned and characterized the full-length duck TRAF3 (duTRAF3) gene and an alternatively spliced isoform of duTRAF3 (duTRAF3-S) lacking the fragment encoding amino acids 217–319, from duck embryo fibroblasts (DEFs). We found that duTRAF3 and duTRAF3-S played different roles in regulating IFN-β production in DEFs. duTRAF3 through its TRAF domain interacted with duMAVS or duTRIF, leading to the production of IFN-β. However, duTRAF3-S, containing the TRAF domain, was unable to bind duMAVS or duTRIF due to the intramolecular binding between the N- and C-terminal of duTRAF3-S that blocked the function of its TRAF domain. Further analysis identified that duTRAF3-S competed with duTRAF3 itself for binding to duTRAF3, perturbing duTRAF3 self-association, which impaired the assembly of duTRAF3-duMAVS/duTRIF complex, ultimately resulted in a reduced production of IFN-β. These findings suggest that duTRAF3 is an important regulator of duck innate immune signaling and reveal a novel mechanism for the negative regulation of IFN-β production via changing the formation of the homo-oligomerization of wild molecules, implying a novel regulatory role of truncated proteins.
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Affiliation(s)
- Xiaoqin Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Department of Animal Science, XiZang Agriculture and Animal Husbandry College, Linzhi, China
| | - Wei Qian
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Suolang Sizhu
- Department of Animal Science, XiZang Agriculture and Animal Husbandry College, Linzhi, China
| | - Yongtao Li
- College of Animal Husbandry & Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Kelei Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Hongbo Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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18
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Fang R, Jiang Q, Zhou X, Wang C, Guan Y, Tao J, Xi J, Feng JM, Jiang Z. MAVS activates TBK1 and IKKε through TRAFs in NEMO dependent and independent manner. PLoS Pathog 2017; 13:e1006720. [PMID: 29125880 PMCID: PMC5699845 DOI: 10.1371/journal.ppat.1006720] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 11/22/2017] [Accepted: 10/30/2017] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial antiviral-signaling protein (MAVS) transmits signals from RIG-I-like receptors after RNA virus infections. However, the mechanism by which MAVS activates downstream components, such as TBK1 and IKKα/β, is unclear, although previous work suggests the involvement of NEMO or TBK1-binding proteins TANK, NAP1, and SINTBAD. Here, we report that MAVS-mediated innate immune activation is dependent on TRAFs, partially on NEMO, but not on TBK1-binding proteins. MAVS recruited TBK1/IKKε by TRAFs that were pre-associated with TBK1/IKKε via direct interaction between the coiled-coil domain of TRAFs and the SDD domain of TBK1/IKKε. TRAF2-/-3-/-5-/-6-/- cells completely lost RNA virus responses. TRAFs' E3 ligase activity was required for NEMO activation by synthesizing ubiquitin chains that bound to NEMO for NF-κB and TBK1/IKKε activation. NEMO-activated IKKα/β were important for TBK1/IKKε activation through IKKα/β-mediated TBK1/IKKε phosphorylation. Moreover, individual TRAFs differently mediated TBK1/IKKε activation and thus fine-tuned antiviral immunity under physiological conditions.
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Affiliation(s)
- Run Fang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Qifei Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Xiang Zhou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Chenguang Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yukun Guan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Jianli Tao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Jianzhong Xi
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ji-Ming Feng
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Zhengfan Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- * E-mail:
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19
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Molecular basis for unique specificity of human TRAF4 for platelets GPIbβ and GPVI. Proc Natl Acad Sci U S A 2017; 114:11422-11427. [PMID: 29073066 DOI: 10.1073/pnas.1708688114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tumor necrosis factor (TNF)-receptor associated factor 4 (TRAF4), an adaptor protein with E3-ligase activity, is involved in embryogenesis, cancer initiation and progression, and platelet receptor (GPIb-IX-V complex and GPVI)-mediated signaling for reactive oxygen species (ROS) production that initiates thrombosis at arterial shears. Disruption of platelet receptors and the TRAF4 interaction is a potential target for therapeutic intervention by antithrombotic drugs. Here, we report a crystal structure of TRAF4 (amino acid residues 290∼470) in complex with a peptide from the GPIbβ receptor (amino acid residues 177∼181). The GPIbβ peptide binds to a unique shallow surface composed of two hydrophobic pockets on TRAF4. Further studies revealed the TRAF4-binding motif Arg-Leu-X-Ala. The TRAF4-binding motif was present not only in platelet receptors but also in the TGF-β receptor. The current structure will provide a template for furthering our understanding of the receptor-binding specificity of TRAF4, TRAF4-mediated signaling, and related diseases.
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20
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Hajek M, Sewell A, Kaech S, Burtness B, Yarbrough WG, Issaeva N. TRAF3/CYLD mutations identify a distinct subset of human papillomavirus-associated head and neck squamous cell carcinoma. Cancer 2017; 123:1778-1790. [PMID: 28295222 PMCID: PMC5419871 DOI: 10.1002/cncr.30570] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/18/2016] [Accepted: 12/21/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND The incidence of human papillomavirus (HPV)‐associated (HPV‐positive) head and neck squamous cell carcinoma (HNSCC) of the oropharynx has dramatically increased over the last decade and continues to rise. Newly diagnosed HPV‐positive HNSCCs in the United States currently outnumber any other HPV‐associated cancers, including cervical cancer. Despite introduction of the HPV vaccine, the epidemic of HPV‐positive HNSCC is expected to continue for approximately 60 years. Compared with patients who have tobacco‐associated HNSCC, those who have HPV‐positive HNSCC have better overall survival and response to treatment. Current treatment, including chemotherapy and radiation therapy, is associated with lifelong morbidity, and there are limited treatments and no curative options for patients who develop recurrent metastatic disease. Therapeutic de‐escalation (decreased radiation dose) is being tested through clinical trials; however, those studies select patients based solely on tumor and patient smoking characteristics. Mechanisms of HPV‐driven carcinogenesis in HNSCC are not well understood, which limits new therapeutic strategies and hinders the appropriate selection of patients for de‐escalation therapy. METHODS The authors analyzed HNSCC data from The Cancer Genome Atlas to identify molecular characteristics that correlate with outcomes and integration status of the HPV genome. RESULTS The current investigations identified a subset of HPV‐positive HNSCCs with mutations in the genes TRAF3 (tumor necrosis factor receptor‐associated factor 3) and CYLD (cylindromatosis lysine 63 deubiquitinase). Defects in TRAF3 and CYLD correlated with the activation of transcriptional factor nuclear factor κB, episomal HPV status of tumors, and improved patient survival. CONCLUSIONS Defects in TRAF3/CYLD were accompanied with the activation of nuclear factor κB signaling and maintenance of episomal HPV in tumors, suggesting that these mutations may support an alternative mechanism of HPV tumorigenesis in head and neck tumors. Cancer 2017;123:1778–1790. © 2017 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. Human papillomavirus‐associated head and neck cancer tends to respond better to treatment compared with tobacco‐associated tumors; however, patients suffer severe and long‐lasting side effects. Somatic mutations in the genes TRAF3 and CYLD identified in The Cancer Genome Atlas data set are correlated with the activation of nuclear factor‐κB, define a distinct etiologic subset of head and neck cancers, and will be useful as biomarkers for predicting improved prognosis and selecting patients with human papillomavirus‐positive head and neck cancer who may be successfully treated with de‐escalating therapy. See also pages 1695‐98.
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Affiliation(s)
- Michael Hajek
- Division of Otolaryngology, Department of Surgery, Yale University, New Haven, Connecticut
| | - Andrew Sewell
- Division of Otolaryngology, Department of Surgery, Yale University, New Haven, Connecticut
| | - Susan Kaech
- Department of Immunobiology, Yale University, New Haven, Connecticut
| | - Barbara Burtness
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Wendell G Yarbrough
- Division of Otolaryngology, Department of Surgery, Yale University, New Haven, Connecticut.,Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut.,Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - Natalia Issaeva
- Division of Otolaryngology, Department of Surgery, Yale University, New Haven, Connecticut.,Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
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21
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Kim CM, Jeong J, Son Y, Choi J, Kim S, Park HH. Molecular basis for TANK recognition by TRAF1 revealed by the crystal structure of TRAF1/TANK complex. FEBS Lett 2017; 591:810-821. [DOI: 10.1002/1873-3468.12584] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/07/2016] [Accepted: 01/30/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Chang Min Kim
- Department of Chemistry and Biochemistry Graduate School of Biochemistry Yeungnam University Gyeongsan South Korea
| | - Jae‐Hee Jeong
- Pohang Accelerator Laboratory Pohang University of Science and Technology South Korea
| | - Young‐Jin Son
- New Drug Development Center Daegu‐Gyungpook Medical Innovation Foundation South Korea
| | - Jun‐Hyuk Choi
- Department of Metrology for Quality of Life Center for Bioanalysis Korea Research Institute of Standards and Science Daejeon South Korea
| | - Sunghwan Kim
- New Drug Development Center Daegu‐Gyungpook Medical Innovation Foundation South Korea
| | - Hyun Ho Park
- Department of Chemistry and Biochemistry Graduate School of Biochemistry Yeungnam University Gyeongsan South Korea
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22
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Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R. TRAF3 signaling: Competitive binding and evolvability of adaptive viral molecular mimicry. Biochim Biophys Acta Gen Subj 2016; 1860:2646-55. [PMID: 27208423 PMCID: PMC7117012 DOI: 10.1016/j.bbagen.2016.05.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/18/2016] [Accepted: 05/08/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND The tumor necrosis factor receptor (TNFR) associated factor 3 (TRAF3) is a key node in innate and adaptive immune signaling pathways. TRAF3 negatively regulates the activation of the canonical and non-canonical NF-κB pathways and is one of the key proteins in antiviral immunity. SCOPE OF REVIEW Here we provide a structural overview of TRAF3 signaling in terms of its competitive binding and consequences to the cellular network. For completion, we also include molecular mimicry of TRAF3 physiological partners by some viral proteins. MAJOR CONCLUSIONS By out-competing host partners, viral proteins aim to subvert TRAF3 antiviral action. Mechanistically, dynamic, competitive binding by the organism's own proteins and same-site adaptive pathogen mimicry follow the same conformational selection principles. GENERAL SIGNIFICANCE Our premise is that irrespective of the eliciting event - physiological or acquired pathogenic trait - pathway activation (or suppression) may embrace similar conformational principles. However, even though here we largely focus on competitive binding at a shared site, similar to physiological signaling other pathogen subversion mechanisms can also be at play. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- Emine Guven-Maiorov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702,USA.
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey.
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey; Department of Computer Engineering, Koc University, Istanbul, Turkey.
| | - Carter VanWaes
- Clinical Genomic Unit, Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorders, NIH, Bethesda, MD 20892, USA.
| | - Zhong Chen
- Clinical Genomic Unit, Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorders, NIH, Bethesda, MD 20892, USA.
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702,USA.
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702,USA; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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23
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Foight GW, Keating AE. Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5. Protein Sci 2016; 25:1273-89. [PMID: 26779844 PMCID: PMC4918428 DOI: 10.1002/pro.2881] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 12/17/2022]
Abstract
Tumor necrosis factor receptor-associated factors (TRAFs) constitute a family of adapter proteins that act in numerous signaling pathways important in human biology and disease. The MATH domain of TRAF proteins binds peptides found in the cytoplasmic domains of signaling receptors, thereby connecting extracellular signals to downstream effectors. Beyond several very general motifs, the peptide binding preferences of TRAFs have not been extensively characterized, and differences between the binding preferences of TRAF paralogs are poorly understood. Here we report a screening system that we established to explore TRAF peptide-binding specificity using deep mutational scanning of TRAF-peptide ligands. We displayed single- and double-mutant peptide libraries based on the TRAF-binding sites of CD40 or TANK on the surface of Escherichia coli and screened them for binding to TRAF2, TRAF3, and TRAF5. Enrichment analysis of the library sequencing results showed differences in the permitted substitution patterns in the TANK versus CD40 backgrounds. The three TRAF proteins also demonstrated different preferences for binding to members of the CD40 library, and three peptides from that library that were analyzed individually showed striking differences in affinity for the three TRAFs. These results illustrate a previously unappreciated level of binding specificity between these close paralogs and demonstrate that established motifs are overly simplistic. The results from this work begin to outline differences between TRAF family members, and the experimental approach established herein will enable future efforts to investigate and redesign TRAF peptide-binding specificity.
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Affiliation(s)
- Glenna Wink Foight
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
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Kim CM, Choi JY, Bhat EA, Jeong JH, Son YJ, Kim S, Park HH. Crystal structure of TRAF1 TRAF domain and its implications in the TRAF1-mediated intracellular signaling pathway. Sci Rep 2016; 6:25526. [PMID: 27151821 PMCID: PMC4858697 DOI: 10.1038/srep25526] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/14/2016] [Indexed: 01/08/2023] Open
Abstract
TNF-receptor associated factor (TRAF) proteins are key adaptor molecules containing E3 ubiquitin ligase activity that play a critical role in immune cell signaling. TRAF1 is a unique family of TRAF lacking the N-terminal RING finger domain. TRAF1 is an important scaffold protein that participates in TNFR2 signaling in T cells as a negative or positive regulator via direct interaction with TRAF2, which has recently been identified as a pro-apoptotic regulator in neuronal cell death. Here, we report the first crystal structure of the TRAF1 TRAF domain containing both the TRAF-N coiled-coil domain and the TRAF-C domain. Our structure reveals both similarities and differences with other TRAF family members, which may be functionally relevant to TRAFs. We also found that the TRAF-N coiled-coil domain of TRAF1 is critical for the trimer formation and stability of the protein. Finally, we found that conserved surface residues on the TRAF1 TRAF domain that might be binding hot spots that are critical for interaction with signaling molecules.
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Affiliation(s)
- Chang Min Kim
- Department of Biochemistry, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Jae Young Choi
- Department of Biochemistry, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Eijaz Ahmed Bhat
- Department of Biochemistry, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 790-784, South Korea
| | - Young-Jin Son
- New Drug Development Center, Daegu-Gyungpook Medical Innovation Foundation, Daegu, 701-310, South Korea
| | - Sunghwan Kim
- New Drug Development Center, Daegu-Gyungpook Medical Innovation Foundation, Daegu, 701-310, South Korea
| | - Hyun Ho Park
- Department of Biochemistry, Yeungnam University, Gyeongsan, 712-749, South Korea
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Shi Z, Zhang Z, Zhang Z, Wang Y, Li C, Wang X, He F, Sun L, Jiao S, Shi W, Zhou Z. Structural Insights into mitochondrial antiviral signaling protein (MAVS)-tumor necrosis factor receptor-associated factor 6 (TRAF6) signaling. J Biol Chem 2015; 290:26811-20. [PMID: 26385923 DOI: 10.1074/jbc.m115.666578] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Indexed: 12/25/2022] Open
Abstract
In response to viral infection, cytosolic retinoic acid-inducible gene I-like receptors sense viral RNA and promote oligomerization of mitochondrial antiviral signaling protein (MAVS), which then recruits tumor necrosis factor receptor-associated factor (TRAF) family proteins, including TRAF6, to activate an antiviral response. Currently, the interaction between MAVS and TRAF6 is only partially understood, and atomic details are lacking. Here, we demonstrated that MAVS directly interacts with TRAF6 through its potential TRAF6-binding motif 2 (T6BM2; amino acids 455-460). Further, we solved the crystal structure of MAVS T6BM2 in complex with the TRAF6 TRAF_C domain at 2.95 Å resolution. T6BM2 of MAVS binds to the canonical adaptor-binding groove of the TRAF_C domain. Structure-directed mutational analyses in vitro and in cells revealed that MAVS binding to TRAF6 via T6BM2 instead of T6BM1 is essential but not sufficient for an optimal antiviral response. Particularly, a MAVS mutant Y460E retained its TRAF6-binding ability as predicted but showed significantly impaired signaling activity, highlighting the functional importance of this tyrosine. Moreover, these observations were further confirmed in MAVS(-/-) mouse embryonic fibroblast cells. Collectively, our work provides a structural basis for understanding the MAVS-TRAF6 antiviral response.
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Affiliation(s)
- Zhubing Shi
- From the School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 200092, China, the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
| | - Zhen Zhang
- the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
| | - Zhenzhen Zhang
- the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
| | - Yanyan Wang
- the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
| | - Chuanchuan Li
- the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
| | - Xin Wang
- the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
| | - Feng He
- the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
| | - Lina Sun
- Qingdao Binhai University, Qingdao, Shandong 266555, China
| | - Shi Jiao
- the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
| | - Weiyang Shi
- From the School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai 200092, China,
| | - Zhaocai Zhou
- the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, State Key Laboratory of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, and
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Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R. A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway. Biophys J 2015; 109:1214-26. [PMID: 26276688 PMCID: PMC4576153 DOI: 10.1016/j.bpj.2015.06.048] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 02/07/2023] Open
Abstract
Even though the Toll-like receptor (TLR) pathway is integral to inflammatory defense mechanisms, its excessive signaling may be devastating. Cells have acquired a cascade of strategies to regulate TLR signaling by targeting protein-protein interactions, or ubiquitin chains, but the details of the inhibition mechanisms are still unclear. Here, we provide the structural basis for the regulation of TLR signaling by constructing architectures of protein-protein interactions. Structural data suggest that 1) Toll/IL-1R (TIR) domain-containing regulators (BCAP, SIGIRR, and ST2) interfere with TIR domain signalosome formation; 2) major deubiquitinases such as A20, CYLD, and DUBA prevent association of TRAF6 and TRAF3 with their partners, in addition to removing K63-linked ubiquitin chains that serve as a docking platform for downstream effectors; 3) alternative downstream pathways of TLRs also restrict signaling by competing to bind common partners through shared binding sites. We also performed in silico mutagenesis analysis to characterize the effects of oncogenic mutations on the negative regulators and to observe the cellular outcome (whether there is/is not inflammation). Missense mutations that fall on interfaces and nonsense/frameshift mutations that result in truncated negative regulators disrupt the interactions with the targets, thereby enabling constitutive activation of the nuclear factor-kappa B, and contributing to chronic inflammation, autoimmune diseases, and oncogenesis.
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Affiliation(s)
- Emine Guven-Maiorov
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey.
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey; Department of Computer Engineering, Koc University, Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R. The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway. Sci Rep 2015; 5:13128. [PMID: 26293885 PMCID: PMC4544004 DOI: 10.1038/srep13128] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/17/2015] [Indexed: 12/22/2022] Open
Abstract
Activated Toll-like receptors (TLRs) cluster in lipid rafts and induce pro- and anti-tumor responses. The organization of the assembly is critical to the understanding of how these key receptors control major signaling pathways in the cell. Although several models for individual interactions were proposed, the entire TIR-domain signalosome architecture has not been worked out, possibly due to its complexity. We employ a powerful algorithm, crystal structures and experimental data to model the TLR4 and its cluster. The architecture that we obtain with 8 MyD88 molecules provides the structural basis for the MyD88-templated myddosome helical assembly and receptor clustering; it also provides clues to pro- and anti-inflammatory signaling pathways branching at the signalosome level to Mal/MyD88 and TRAM/TRIF pro- and anti-inflammatory pathways. The assembly of MyD88 death domain (DD) with TRAF3 (anti-viral/anti-inflammatory) and TRAF6 (pro-inflammatory) suggest that TRAF3/TRAF6 binding sites on MyD88 DD partially overlap, as do IRAK4 and FADD. Significantly, the organization illuminates mechanisms of oncogenic mutations, demonstrates that almost all TLR4 parallel pathways are competitive and clarifies decisions at pathway branching points. The architectures are compatible with the currently-available experimental data and provide compelling insights into signaling in cancer and inflammation pathways.
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Affiliation(s)
- Emine Guven-Maiorov
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
- Department of Computer Engineering, Koc University, Istanbul, Turkey
| | - Carter VanWaes
- Clinical Genomic Unit, Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Zhong Chen
- Clinical Genomic Unit, Head and Neck Surgery Branch, National Institute on Deafness and Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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28
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Yoon JH, Cho YJ, Park HH. Structure of the TRAF4 TRAF domain with a coiled-coil domain and its implications for the TRAF4 signalling pathway. ACTA ACUST UNITED AC 2013; 70:2-10. [DOI: 10.1107/s139900471302333x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/19/2013] [Indexed: 01/10/2023]
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29
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TRAF4 is a novel phosphoinositide-binding protein modulating tight junctions and favoring cell migration. PLoS Biol 2013; 11:e1001726. [PMID: 24311986 PMCID: PMC3848981 DOI: 10.1371/journal.pbio.1001726] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 10/23/2013] [Indexed: 12/26/2022] Open
Abstract
The cancer-associated TRAF4 protein has a TRAF domain that is a bona fide phosphoinositide-binding domain and involved in the modulation of tight junctions and cell migration. Tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4) is frequently overexpressed in carcinomas, suggesting a specific role in cancer. Although TRAF4 protein is predominantly found at tight junctions (TJs) in normal mammary epithelial cells (MECs), it accumulates in the cytoplasm of malignant MECs. How TRAF4 is recruited and functions at TJs is unclear. Here we show that TRAF4 possesses a novel phosphoinositide (PIP)-binding domain crucial for its recruitment to TJs. Of interest, this property is shared by the other members of the TRAF protein family. Indeed, the TRAF domain of all TRAF proteins (TRAF1 to TRAF6) is a bona fide PIP-binding domain. Molecular and structural analyses revealed that the TRAF domain of TRAF4 exists as a trimer that binds up to three lipids using basic residues exposed at its surface. Cellular studies indicated that TRAF4 acts as a negative regulator of TJ and increases cell migration. These functions are dependent from its ability to interact with PIPs. Our results suggest that TRAF4 overexpression might contribute to breast cancer progression by destabilizing TJs and favoring cell migration. Tumor necrosis factor (TNF) receptor-associated factor 4, also known as TRAF4, is an unusual member of the TRAF protein family. While TRAFs are primarily known as regulators of inflammation, antiviral responses, and apoptosis, research on TRAF4 has identified its involvement in development and cancer. Importantly TRAF4 overexpression has been associated with a poor prognosis in breast cancers. TRAF4 has multiple subcellular localizations: to the plasma membrane in tight junctions (TJs), cytoplasmic and nuclear. The recruitment mechanisms and the functional impact of these distinct localizations are not completely understood. Here we investigate how TRAF4 is recruited to TJs and its involvement in cell–cell contacts in mammary epithelial cells (MECs). We show that the TRAF domain of all TRAFs contains a lipid binding module, and that TRAF4 uses this domain to form a trimeric complex that associates with phosphoinositides at the plasma membrane. Moreover this interaction is necessary for its recruitment to TJs. Additionally, we show that through its interaction with lipids TRAF4 delays TJ assembly and increases cell migration. We propose that TRAF4 has an important function in cancer progression by destabilizing TJs and favoring cell migration.
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30
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Yoon JH, Park HH. Preliminary X-ray crystallographic studies of the TRAF domain of human TRAF4. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1026-8. [PMID: 23989155 PMCID: PMC3758155 DOI: 10.1107/s1744309113021192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022]
Abstract
TNF receptor-associated factor (TRAF) proteins were initially identified as tumour necrosis factor receptor (TNFR)-interacting proteins that perform critical functions in the regulation of inflammation, antiviral responses and apoptosis. Although TRAF4 is a canonical TRAF protein, it contains a unique domain boundary and functions differently in the cell. In this study, the human TRAF4 TRAF domain, corresponding to amino acids 290-470, was overexpressed in Escherichia coli using engineered C-terminal His tags. The TRAF4 TRAF domain was then purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 2.3 Å from a crystal belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.9, b = 87.9, c = 117.3 Å, α = β = γ = 90°.
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Affiliation(s)
- Jong Hwan Yoon
- School of Biotechnology and Graduate School of Biochemistry, Yeungnam University, Gyeungsan, Republic of Korea
| | - Hyun Ho Park
- School of Biotechnology and Graduate School of Biochemistry, Yeungnam University, Gyeungsan, Republic of Korea
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31
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Niu F, Ru H, Ding W, Ouyang S, Liu ZJ. Structural biology study of human TNF receptor associated factor 4 TRAF domain. Protein Cell 2013; 4:687-94. [PMID: 23982741 DOI: 10.1007/s13238-013-3068-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/05/2013] [Indexed: 01/02/2023] Open
Abstract
TRAF4 is a unique member of TRAF family, which is essential for innate immune response, nervous system and other systems. In addition to be an adaptor protein, TRAF4 was identified as a regulator protein in recent studies. We have determined the crystal structure of TRAF domain of TRAF4 (residues 292-466) at 2.60 Å resolution by X-ray crystallography method. The trimericly assembled TRAF4 resembles a mushroom shape, containing a super helical "stalk" which is made of three right-handed intertwined α helixes and a C-terminal "cap", which is divided at residue L302 as a boundary. Similar to other TRAFs, both intermolecular hydrophobic interaction in super helical "stalk" and hydrogen bonds in "cap" regions contribute directly to the formation of TRAF4 trimer. However, differing from other TRAFs, there is an additional flexible loop (residues 421-426), which contains a previously identified phosphorylated site S426 exposing on the surface. This S426 was reported to be phosphorylated by IKKα which is the pre-requisite for TRAF4-NOD2 complex formation and thus to inhibit NOD2-induced NF-κB activation. Therefore, the crystal structure of TRAF4-TRAF is valuable for understanding its molecular basis for its special function and provides structural information for further studies.
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Affiliation(s)
- Fengfeng Niu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng Ru
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, 650500, China
| | - Wei Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Songying Ouyang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, 650500, China.
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32
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Bernfur K, Larsson O, Larsson C, Gustavsson N. Relative abundance of integral plasma membrane proteins in Arabidopsis leaf and root tissue determined by metabolic labeling and mass spectrometry. PLoS One 2013; 8:e71206. [PMID: 23990937 PMCID: PMC3747180 DOI: 10.1371/journal.pone.0071206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/03/2013] [Indexed: 12/21/2022] Open
Abstract
Metabolic labeling of proteins with a stable isotope (15N) in intact Arabidopsis plants was used for accurate determination by mass spectrometry of differences in protein abundance between plasma membranes isolated from leaves and roots. In total, 703 proteins were identified, of which 188 were predicted to be integral membrane proteins. Major classes were transporters, receptors, proteins involved in membrane trafficking and cell wall-related proteins. Forty-one of the integral proteins, including nine of the 13 isoforms of the PIP (plasma membrane intrinsic protein) aquaporin subfamily, could be identified by peptides unique to these proteins, which made it possible to determine their relative abundance in leaf and root tissue. In addition, peptides shared between isoforms gave information on the proportions of these isoforms. A comparison between our data for protein levels and corresponding data for mRNA levels in the widely used database Genevestigator showed an agreement for only about two thirds of the proteins. By contrast, localization data available in the literature for 21 of the 41 proteins show a much better agreement with our data, in particular data based on immunostaining of proteins and GUS-staining of promoter activity. Thus, although mRNA levels may provide a useful approximation for protein levels, detection and quantification of isoform-specific peptides by proteomics should generate the most reliable data for the proteome.
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Affiliation(s)
- Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
- * E-mail:
| | - Olaf Larsson
- Mutation Analysis Facility, Clinical Research Centre, Novum, Huddinge University Hospital, Stockholm, Sweden
| | - Christer Larsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
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Yoon JH, Park HH. Preliminary X-ray crystallographic studies of the short form of the human TRAF4 TRAF domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:916-9. [PMID: 23908043 PMCID: PMC3729174 DOI: 10.1107/s1744309113019179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 07/10/2013] [Indexed: 11/11/2022]
Abstract
TNF (tumour necrosis factor) receptor-associated factor 4 (TRAF4) is a unique TRAF protein that participates in morphogenetic and developmental function and cell migration. TRAF-family proteins contain a TRAF domain for target interaction. In this study, the short form of the human TRAF4 TRAF domain, corresponding to amino acids 290-462, was overexpressed in Escherichia coli using engineered C-terminal His tags. The short form of the TRAF4 TRAF domain was purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 4.2 Å from a crystal belonging to the hexagonal space group P3₂, with unit-cell parameters a = b = 147.17, c = 202.69 Å.
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Affiliation(s)
- Jong Hwan Yoon
- School of Biotechnology and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Hyun Ho Park
- School of Biotechnology and Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
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34
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Abstract
The tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of intracellular proteins were originally identified as signaling adaptors that bind directly to the cytoplasmic regions of receptors of the TNF-R superfamily. The past decade has witnessed rapid expansion of receptor families identified to employ TRAFs for signaling. These include Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs), T cell receptor, IL-1 receptor family, IL-17 receptors, IFN receptors and TGFβ receptors. In addition to their role as adaptor proteins, most TRAFs also act as E3 ubiquitin ligases to activate downstream signaling events. TRAF-dependent signaling pathways typically lead to the activation of nuclear factor-κBs (NF-κBs), mitogen-activated protein kinases (MAPKs), or interferon-regulatory factors (IRFs). Compelling evidence obtained from germ-line and cell-specific TRAF-deficient mice demonstrates that each TRAF plays indispensable and non-redundant physiological roles, regulating innate and adaptive immunity, embryonic development, tissue homeostasis, stress response, and bone metabolism. Notably, mounting evidence implicates TRAFs in the pathogenesis of human diseases such as cancers and autoimmune diseases, which has sparked new appreciation and interest in TRAF research. This review presents an overview of the current knowledge of TRAFs, with an emphasis on recent findings concerning TRAF molecules in signaling and in human diseases.
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Affiliation(s)
- Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, 604 Allison Road, Nelson Labs Room B336, Piscataway, New Jersey 08854.
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35
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Sasaki O, Yoshizumi T, Kuboyama M, Ishihara T, Suzuki E, Kawabata SI, Koshiba T. A structural perspective of the MAVS-regulatory mechanism on the mitochondrial outer membrane using bioluminescence resonance energy transfer. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1833:1017-27. [PMID: 23337771 DOI: 10.1016/j.bbamcr.2013.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 02/07/2023]
Abstract
In most eukaryotic cells, mitochondria have various essential roles for proper cell function, such as energy production, and in mammals mitochondria also act as a platform for antiviral innate immunity. Mitochondrial-mediated antiviral immunity depends on the activation of the cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) signaling pathway, and on the participation of mitochondrial antiviral signaling (MAVS), which is localized on the mitochondrial outer membrane. After RNA virus infection, RLRs translocate to the mitochondrial surface to interact with MAVS, and the adaptor protein undergoes a conformational change that is essential for downstream signaling, although its structural features are poorly understood. Here we examined the MAVS-regulatory mechanism on the mitochondrial outer membrane using bioluminescence resonance energy transfer (BRET) in live cells. Using a combination of BRET and functional analysis, we found that the activated MAVS conformation is a highly ordered oligomer, at least more than three molecules per complex unit on the membrane. Hepatitis C virus NS3/4A protease and mitofusin 2, which are known MAVS inhibitors, interfere with MAVS homotypic oligomerization in a distinct manner, each differentially altering the active conformation of MAVS. Our results reveal structural features underlying the precise regulation of MAVS signaling on the mitochondrial outer membrane, and may provide insight into other signaling systems involving organelles.
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Affiliation(s)
- Osamu Sasaki
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
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36
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Abstract
Synthetic biology, cancer signaling, and metabolism all made the list of breakthroughs in basic signal transduction research or the translational application of signaling knowledge.
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Affiliation(s)
- Michael B. Yaffe
- Chief Scientific Editor of Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005, USA
- Professor, David H. Koch Institute for Integrative Cancer Research, The Broad Institute, and the Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nancy R. Gough
- Editor of Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005, USA
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