1
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Singer A, Ramos A, Keating AE. Elaboration of the Homer1 Recognition Landscape Reveals Incomplete Divergence of Paralogous EVH1 Domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576863. [PMID: 38645240 PMCID: PMC11030225 DOI: 10.1101/2024.01.23.576863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Short sequences that mediate interactions with modular binding domains are ubiquitous throughout eukaryotic proteomes. Networks of Short Linear Motifs (SLiMs) and their corresponding binding domains orchestrate many cellular processes, and the low mutational barrier to evolving novel interactions provides a way for biological systems to rapidly sample selectable phenotypes. Mapping SLiM binding specificity and the rules that govern SLiM evolution is fundamental to uncovering the pathways regulated by these networks and developing the tools to manipulate them. We used high-throughput screening of the human proteome to identify sequences that bind to the Enabled/VASP homology 1 (EVH1) domain of the postsynaptic density scaffolding protein Homer1. In doing so, we expanded current understanding of the determinants of Homer EVH1 binding preferences and defined a new motif that can facilitate the discovery of additional Homer-mediated interactions. Interestingly, the Homer1 EVH1 domain preferentially binds to sequences containing an N-terminally overlapping motif that is bound by the paralogous family of Ena/VASP actin polymerases, and many of these sequences can bind to EVH1 domains from both protein families. We provide evidence from orthologous EVH1 domains in pre-metazoan organisms that the overlap in human Ena/VASP and Homer binding preferences corresponds to an incomplete divergence from a common Ena/VASP ancestor. Given this overlap in binding profiles, promiscuous sequences that can be recognized by both families either achieve specificity through extrinsic regulatory strategies or may provide functional benefits via multi-specificity. This may explain why these paralogs incompletely diverged despite the accessibility of further diverged isoforms.
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Affiliation(s)
- Avinoam Singer
- MIT Department of Biology, Cambridge, Massachusetts, USA
| | | | - Amy E. Keating
- MIT Department of Biology, Cambridge, Massachusetts, USA
- MIT Department of Biological Engineering, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts, USA
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2
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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3
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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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4
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The Roles of TRAF3 in Immune Responses. DISEASE MARKERS 2023; 2023:7787803. [PMID: 36845015 PMCID: PMC9949957 DOI: 10.1155/2023/7787803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/18/2023]
Abstract
Seven tumor necrosis factor receptor- (TNFR-) associated factors (TRAFs) have been found in mammals, which are primarily involved in the signal translation of the TNFR superfamily, the Toll-like receptor (TLR) family, and the retinoic acid-inducible gene I- (RIG-I-) like receptor (RLR) family. TRAF3 is one of the most diverse members of the TRAF family. It can positively regulate type I interferon production while negatively regulating signaling pathways of classical nuclear factor-κB, nonclassical nuclear factor-κB, and mitogen-activated protein kinase (MAPK). This review summarizes the roles of TRAF3 signaling and the related immune receptors (e.g., TLRs) in several preclinical and clinical diseases and focuses on the roles of TRAF3 in immune responses, the regulatory mechanisms, and its role in disease.
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5
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Halpin JC, Whitney D, Rigoldi F, Sivaraman V, Singer A, Keating AE. Molecular determinants of TRAF6 binding specificity suggest that native interaction partners are not optimized for affinity. Protein Sci 2022; 31:e4429. [PMID: 36305766 PMCID: PMC9597381 DOI: 10.1002/pro.4429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/14/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022]
Abstract
TRAF6 is an adaptor protein involved in signaling pathways that are essential for development and the immune system. It participates in many protein-protein interactions, some of which are mediated by the C-terminal MATH domain, which binds to short peptide segments containing the motif PxExx[FYWHDE], where x is any amino acid. Blocking MATH domain interactions is associated with favorable effects in various disease models. To better define TRAF6 MATH domain binding preferences, we screened a combinatorial library using bacterial cell-surface peptide display. We identified 236 of the best TRAF6-interacting peptides and a set of 1,200 peptides that match the sequence PxE but do not bind TRAF6 MATH. The peptides that were most enriched in the screen bound TRAF6 tighter than previously measured native peptides. To better understand the structural basis for TRAF6 interaction preferences, we built all-atom structural models of the MATH domain in complex with high-affinity binders and nonbinders identified in the screen. We identified favorable interactions for motif features in binders as well as negative design elements distributed across the motif that can disfavor or preclude binding. Searching the human proteome revealed that the most biologically relevant TRAF6 motif matches occupy a different sequence space from the best hits discovered in combinatorial library screening, suggesting that native interactions are not optimized for affinity. Our experimentally determined binding preferences and structural models support the design of peptide-based interaction inhibitors with higher affinities than endogenous TRAF6 ligands.
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Affiliation(s)
| | | | | | | | | | - Amy E. Keating
- MIT Department of BiologyCambridgeMassachusettsUSA
- MIT Department of Biological EngineeringCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMassachusettsUSA
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Han M, Liu Y, Jin C, Wang X, Song W, Zhang Q. Genome-wide identification, characterization and expression profiling of TRAF family genes in Sebastes schlegelii. FISH & SHELLFISH IMMUNOLOGY 2022; 127:203-210. [PMID: 35724846 DOI: 10.1016/j.fsi.2022.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Tumor necrosis factor receptor-associated factors (TRAFs) are signaling mediators for Toll-like receptor (TLR) and tumor necrosis factor (TNFR) superfamily that play important roles in organism immune response. However, reports on systematic identification of TRAF gene family in teleost fish and the function of TRAFs in innate immunity of black rockfish (Sebastes schlegelii) are lacked. In our study, eight TRAF genes were identified and characterized, namely, SsTRAF2a, SsTRAF2a-like, SsTRAF2b, SsTRAF3, SsTRAF4, SsTRAF5, SsTRAF6 and SsTRAF7 in S. schegelii. Furthermore, we analyzed their sequences, conserved domains, gene structures, motif compositions, phylogeny, tissue expression patterns in healthy and Vibro. anguillarum challenged individuals. All the SsTRAFs contained typical conserved domain, including C-terminal MATH domain and N-terminal RING finger domain. Analyses of gene structures and motifs showed the distribution of exon-intron and conserved motifs in S. schegelii and serval other teleost fish. We also analyzed the expression file of SsTRAFs in five immune-relate organs, liver, spleen, kidney, gill and intestine in healthy and bacterial challenged fish. The results indicated that all SsTRAF member were widely involved in immune response after pathogenic bacteria infection. In summary, the analyses of TRAFs in S. schegelii will be helpful to better understand the diverse roles of TRAF genes in the innate immune response to bacterial challenge.
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Affiliation(s)
- Miao Han
- MOE Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Yuxiang Liu
- MOE Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Chaofan Jin
- MOE Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Xuangang Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Weihao Song
- MOE Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Quanqi Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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7
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Hwang T, Parker SS, Hill SM, Grant RA, Ilunga MW, Sivaraman V, Mouneimne G, Keating AE. Native proline-rich motifs exploit sequence context to target actin-remodeling Ena/VASP protein ENAH. eLife 2022; 11:70680. [PMID: 35076015 PMCID: PMC8789275 DOI: 10.7554/elife.70680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022] Open
Abstract
The human proteome is replete with short linear motifs (SLiMs) of four to six residues that are critical for protein-protein interactions, yet the importance of the sequence surrounding such motifs is underexplored. We devised a proteomic screen to examine the influence of SLiM sequence context on protein-protein interactions. Focusing on the EVH1 domain of human ENAH, an actin regulator that is highly expressed in invasive cancers, we screened 36-residue proteome-derived peptides and discovered new interaction partners of ENAH and diverse mechanisms by which context influences binding. A pocket on the ENAH EVH1 domain that has diverged from other Ena/VASP paralogs recognizes extended SLiMs and favors motif-flanking proline residues. Many high-affinity ENAH binders that contain two proline-rich SLiMs use a noncanonical site on the EVH1 domain for binding and display a thermodynamic signature consistent with the two-motif chain engaging a single domain. We also found that photoreceptor cilium actin regulator (PCARE) uses an extended 23-residue region to obtain a higher affinity than any known ENAH EVH1-binding motif. Our screen provides a way to uncover the effects of proteomic context on motif-mediated binding, revealing diverse mechanisms of control over EVH1 interactions and establishing that SLiMs can’t be fully understood outside of their native context.
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Affiliation(s)
- Theresa Hwang
- Department of Biology, Massachusetts Institute of Technology
| | - Sara S Parker
- Department of Cellular & Molecular Medicine, University of Arizona
| | - Samantha M Hill
- Department of Cellular & Molecular Medicine, University of Arizona
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology
| | - Meucci W Ilunga
- Department of Biology, Massachusetts Institute of Technology
| | | | | | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
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8
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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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9
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Zhou W, Lin D, Zhong Z, Ye Q. Roles of TRAFs in Ischemia-Reperfusion Injury. Front Cell Dev Biol 2020; 8:586487. [PMID: 33224951 PMCID: PMC7674171 DOI: 10.3389/fcell.2020.586487] [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: 07/23/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
Tumor necrosis factor receptor-associated factor (TRAF) proteins are a family of signaling molecules that function downstream of multiple receptor signaling pathways, and they play a pivotal role in the regulation of intracellular biological progresses. These TRAF-dependent signaling pathways and physiological functions have been involved in the occurrence and progression of ischemia-reperfusion injury (IRI), which is a common pathophysiological process that occurs in a wide variety of clinical events, including ischemic shock, organ transplantation, and thrombolytic therapy, resulting in a poor prognosis and high mortality. IRI occurs in multiple organs, including liver, kidney, heart, lung, brain, intestine, and retina. In recent years, mounting compelling evidence has confirmed that the genetic alterations of TRAFs can cause subversive phenotype changes during IRI of those organs. In this review, based on current knowledge, we summarized and analyzed the regulatory effect of TRAFs on the IRI of various organs, providing clear direction and a firm theoretical basis for the development of treatment strategies to manipulate TRAF proteins or TRAF-dependent signaling pathways in IRI-related diseases.
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Affiliation(s)
- Wei Zhou
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Engineering Research Center of Natural Polymer-based Medical Materials in Hubei Province, Wuhan, China
| | - Danni Lin
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Engineering Research Center of Natural Polymer-based Medical Materials in Hubei Province, Wuhan, China.,The First Affiliated Hospital, Zhejiang University School of Medicine, Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Zibiao Zhong
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Engineering Research Center of Natural Polymer-based Medical Materials in Hubei Province, Wuhan, China
| | - Qifa Ye
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Engineering Research Center of Natural Polymer-based Medical Materials in Hubei Province, Wuhan, China.,The Third Xiangya Hospital of Central South University, Research Center of National Health Ministry on Transplantation Medicine Engineering and Technology, Changsha, China
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10
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Liu T, Wu Y, Han Y, Liu Q, Chen S, Zhao H. Genome-wide characterization of TNF receptor-associated factors in the Chinese soft-shelled turtle Pelodiscus sinensis and their expression profiling in response to Aeromonas hydrophila challenge. FISH & SHELLFISH IMMUNOLOGY 2020; 101:88-98. [PMID: 32229294 DOI: 10.1016/j.fsi.2020.03.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 06/10/2023]
Abstract
Tumor necrosis factor receptor (TNFR)-associated factors (TRAFs) are a family of crucial signaling molecules that mediate the signal transduction of various immune signaling pathways. Extensive studies have demonstrated that TRAFs play vital roles in regulating cellular immune responses. However, the biological functions and expression profiling of TRAFs in Chinese soft-shelled turtle (Pelodiscus sinensis) remain unclear. In this study, the genes of the PsTRAF family at the genome-wide level were identified in P. sinensis, revealing six PsTRAF members that contained the conserved TRAF domain in the C-terminal regions. Molecular evolutionary analysis showed that PsTRAFs shared close evolutionary relationships and similar protein crystal structures with the TRAF homologs from other turtles, indicating the evolutionary conservation of PsTRAFs. Further expression analysis revealed the tissue-specific expression of PsTRAF genes. Obvious variations in the expression of PsTRAF genes were observed in the spleen in response to Aeromonas hydrophila infection. Three PsTRAF genes, PsTRAF2, PsTRAF3, and PsTRAF6, were significantly upregulated at the mRNA and protein levels post-infection, indicating their potential function in the immune response. Moreover, the protein-protein associations of PsTRAFs with several signaling receptors were predicted in P. sinensis. These results provide a basis for the investigation of the functional roles of PsTRAFs in immune defense against bacterial infection.
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Affiliation(s)
- Tengfei Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Yongjie Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Yawen Han
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Qingyang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Shulin Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Huiying Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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11
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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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12
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Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biol 2019; 20:223. [PMID: 31679514 PMCID: PMC6827219 DOI: 10.1186/s13059-019-1845-6] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 11/10/2022] Open
Abstract
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB ( https://www.mavedb.org ), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.
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Affiliation(s)
- Daniel Esposito
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jochen Weile
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Frederick P Roth
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
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13
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Das S, Sutoh Y, Cancro MP, Rast JP, Han Q, Bommakanti G, Cooper MD, Hirano M. Ancient BCMA-like Genes Herald B Cell Regulation in Lampreys. THE JOURNAL OF IMMUNOLOGY 2019; 203:2909-2916. [PMID: 31666307 DOI: 10.4049/jimmunol.1900026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 09/25/2019] [Indexed: 11/19/2022]
Abstract
The TNF superfamily ligands BAFF and APRIL interact with three receptors, BAFFR, BCMA, and TACI, to play discrete and crucial roles in regulating B cell selection and homeostasis in mammals. The interactions between these ligands and receptors are both specific and redundant: BAFFR binds BAFF, whereas BCMA and TACI bind to either BAFF or APRIL. In a previous phylogenetic inquiry, we identified and characterized a BAFF-like gene in lampreys, which, with hagfish, are the only extant jawless vertebrates, both of which have B-like and T-like lymphocytes. To gain insight into lymphocyte regulation in jawless vertebrates, in this study we identified two BCMA-like genes in lampreys, BCMAL1 and BCMAL2, which were found to be preferentially expressed by B-like lymphocytes. In vitro analyses indicated that the lamprey BAFF-like protein can bind to a BCMA-like receptor Ig fusion protein and to both BCMAL1- and BCMAL2-transfected cells. Discriminating regulatory roles for the two BCMA-like molecules are suggested by their differential expression before and after activation of the B-like lymphocytes in lampreys. Our composite results imply that BAFF-based mechanisms for B cell regulation evolved before the divergence of jawed and jawless vertebrates.
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Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322; .,Emory Vaccine Center, Emory University, Atlanta, GA 30317; and
| | - Yoichi Sutoh
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322.,Emory Vaccine Center, Emory University, Atlanta, GA 30317; and
| | - Michael P Cancro
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jonathan P Rast
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322.,Emory Vaccine Center, Emory University, Atlanta, GA 30317; and
| | - Qifeng Han
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322.,Emory Vaccine Center, Emory University, Atlanta, GA 30317; and
| | - Gayathri Bommakanti
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322.,Emory Vaccine Center, Emory University, Atlanta, GA 30317; and
| | - Max D Cooper
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322.,Emory Vaccine Center, Emory University, Atlanta, GA 30317; and
| | - Masayuki Hirano
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322; .,Emory Vaccine Center, Emory University, Atlanta, GA 30317; and
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14
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Xia H, Li Y, Wang Z, Chen W, Cheng J, Yu D, Lu Y. Expression and functional analysis of tumor necrosis factor receptor (TNFR)-associated factor 5 from Nile tilapia, Oreochromis niloticus. FISH & SHELLFISH IMMUNOLOGY 2019; 93:781-788. [PMID: 31326588 DOI: 10.1016/j.fsi.2019.07.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Nile tilapia (Oreochromis niloticus) is a pivotal economic fish that has been plagued by Streptococcus infections. Tumor necrosis factor receptor-associated factor 5 (TRAF5) is a crucial adaptor molecule, which can trigger downstream signaling cascades involved in immune pathway. In this study, Nile tilapia TRAF5 coding sequence (named OnTRAF5) was obtained, which contained typical functional domains, such as RING, zinc finger, coiled-coil and MATH domain. Different from other TRAF molecules, OnTRAF5 had shown relatively low identify with its homolog, and it was clustered into other teleost TRAF5 proteins. qRT-PCR was used to analysis the expression level of OnTRAF5 in gill, skin, muscle, head kidney, heart, intestine, thymus, liver, spleen and brain, In healthy Nile tilapia, the expression level of OnTRAF5 in intestine, gill and spleen were significantly higher than other tissues. While under Streptococcus agalactiae infection, the expression level of OnTRAF5 was improved significantly in all detected organs. Additionally, over-expression WT OnTRAF5 activated NF-κB, deletion of RING or zinc finger caused the activity impaired. In conclusion, OnTRAF5 participate in anti-bacteria immune response and is crucial for the signaling transduction.
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Affiliation(s)
- Hongli Xia
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, 518120, China; Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China
| | - Yuan Li
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Zhiwen Wang
- College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Wenjie Chen
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, 518120, China; Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430000, China
| | - Jun Cheng
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, 518120, China; Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China
| | - Dapeng Yu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, 518120, China; Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China
| | - Yishan Lu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, 518120, China; Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China; College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China.
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15
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Yang M, Han R, Ni LY, Luo XC, Li AX, Dan XM, Li YW. Molecular characteristics and functional study of tumor necrosis factor receptor-associated factor 2 from the orange-spotted grouper (Epinephelus coioides). FISH & SHELLFISH IMMUNOLOGY 2019; 84:726-732. [PMID: 30393173 DOI: 10.1016/j.fsi.2018.10.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/09/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
In mammals, tumor necrosis factor receptor-associated factor 2 (TRAF2) is a crucial intracellular adaptor protein, which performs a vital role in numerous signaling pathways that activate NF-κB, MAPKs, and IRFs. In the present study, three TRAF2 sequences were identified from the orange-spotted grouper (Epinephelus coioides), and named EcTRAF2-1, EcTRAF2-2, and EcTRAF2-3. These sequences contained conserved structure features that were similar to those of mammals. EcTRAF2-1 shared relatively low sequence identity with the other two EcTRAF2s. In healthy E. coioides, EcTRAF2s were widely expressed in all tissues tested, but with distinct expression profiles. After infection with Cryptocaryon irritans, EcTRAF2s was markedly upregulated in the gill and head kidney at most time points, implying that EcTRAF2s may be involved in host defense against C. irritans infection. In HEK293T cells, EcTRAF2s were scattered in the cytoplasm. EcTRAF2-1 and EcTRAF2-2 increased the activity of NF-κB, while EcTRAF2-3 reduced NF-κB activation mediated by EcTRAF2-1 implying that EcTRAF2-3 might be a negative regulator of EcTRAF2-1.
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Affiliation(s)
- Man Yang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China
| | - Rui Han
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China
| | - Lu-Yun Ni
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China
| | - Xiao-Chun Luo
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - An-Xing Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Lab for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong Province, PR China
| | - Xue-Ming Dan
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China.
| | - Yan-Wei Li
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China, Agricultural University, Guangzhou, 510642, China.
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16
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Zapata JM, Perez-Chacon G, Carr-Baena P, Martinez-Forero I, Azpilikueta A, Otano I, Melero I. CD137 (4-1BB) Signalosome: Complexity Is a Matter of TRAFs. Front Immunol 2018; 9:2618. [PMID: 30524423 PMCID: PMC6262405 DOI: 10.3389/fimmu.2018.02618] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/24/2018] [Indexed: 12/11/2022] Open
Abstract
CD137 (4-1BB, Tnsfr9) is a member of the TNF-receptor (TNFR) superfamily without known intrinsic enzymatic activity in its cytoplasmic domain. Hence, akin to other members of the TNFR family, it relies on the TNFR-Associated-Factor (TRAF) family of adaptor proteins to build the CD137 signalosome for transducing signals into the cell. Thus, upon CD137 activation by binding of CD137L trimers or by crosslinking with agonist monoclonal antibodies, TRAF1, TRAF2, and TRAF3 are readily recruited to the cytoplasmic domain of CD137, likely as homo- and/or heterotrimers with different configurations, initiating the construction of the CD137 signalosome. The formation of TRAF2-RING dimers between TRAF2 molecules from contiguous trimers would help to establish a multimeric structure of TRAF-trimers that is probably essential for CD137 signaling. In addition, available studies have identified a large number of proteins that are recruited to CD137:TRAF complexes including ubiquitin ligases and proteases, kinases, and modulatory proteins. Working in a coordinated fashion, these CD137-signalosomes will ultimately promote CD137-mediated T cell proliferation and survival and will endow T cells with stronger effector functions. Current evidence allows to envision the molecular events that might take place in the early stages of CD137-signalosome formation, underscoring the key roles of TRAFs and of K63 and K48-ubiquitination of target proteins in the signaling process. Understanding the composition and fine regulation of CD137-signalosomes assembly and disassembly will be key to improve the therapeutic activities of chimeric antigen receptors (CARs) encompassing the CD137 cytoplasmic domain and a new generation of CD137 agonists for the treatment of cancer.
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Affiliation(s)
- Juan M Zapata
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain.,Instituto de Investigación Hospital Universitario La Paz, Madrid, Spain
| | - Gema Perez-Chacon
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain.,Instituto de Investigación Hospital Universitario La Paz, Madrid, Spain
| | - Pablo Carr-Baena
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Ivan Martinez-Forero
- Departamento de Inmunologia and Inmunoterapia, Centro de Investigación Medica Aplicada, Universidad de Navarra, Pamplona, Spain
| | - Arantza Azpilikueta
- Departamento de Inmunologia and Inmunoterapia, Centro de Investigación Medica Aplicada, Universidad de Navarra, Pamplona, Spain
| | - Itziar Otano
- Departamento de Inmunologia and Inmunoterapia, Centro de Investigación Medica Aplicada, Universidad de Navarra, Pamplona, Spain
| | - Ignacio Melero
- Departamento de Inmunologia and Inmunoterapia, Centro de Investigación Medica Aplicada, Universidad de Navarra, Pamplona, Spain.,MSD, London, United Kingdom.,Departamento de Inmunologia e Inmunoterapia, Clinica Universitaria, Universidad de Navarra, Pamplona, Spain.,Instituto de Investigacion Sanitaria de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
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17
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Hu W, Wu W, Sun S, Liu Z, Li A, Gao L, Liu X, Liu D, Deng H, Zhao B, Liu B, Pang Q. Identification and characterization of a TNF receptor-associated factor in Dugesia japonica. Gene 2018; 681:52-61. [PMID: 30267808 DOI: 10.1016/j.gene.2018.09.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/03/2018] [Accepted: 09/21/2018] [Indexed: 12/25/2022]
Abstract
The tumor necrosis factor (TNF) superfamily consists of a wide variety of inflammatory cytokine, including cell-bound and secreted proteins. These TNFs function through binding and activation of the TNF receptors for modulating TNF-associated intracellular signals. A set of mammalian TNF receptor-associated factors (TRAFs) that have emerged as the major signal transducers for the TNF receptor superfamily, play an important role in both adaptive and innate immunity. However, the existence of TRAFs and their biological functions in planarian are still unknown. In this study, a new member of TRAFs, DjTRAF2, was identified in planarian Dugesia japonica. Phylogenetic analysis revealed that DjTRAF2 could be a new member of the invertebrate TRAF2 family. Sequence analysis showed that the open reading frame of DjTRAF2 had 1353 bp in length and encoded a putative protein of 450 amino acids with a predicted molecular mass of ~51.8 kDa and an isoelectric point of 7.052. Whole-mount in situ hybridization showed that DjTRAF2 was predominantly expressed in adult and regenerative pharynx, which is an important immune organ of planarian. Quantitative real-time PCR revealed that the transcriptional level of DjTRAF2 was significantly up-regulated after induced by pathogen-associated molecular patterns (polyinosinic-polycytidylic acid, lipopolysaccharide, peptidoglycan and β-glucan), suggesting that DjTRAF2 is involved in the immune response against pathogen invasion. Collectively, these results demonstrated that DjTRAF2 might play important roles in the innate immunity of planarian.
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Affiliation(s)
- Wenjing Hu
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Weiwei Wu
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Shimin Sun
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Zuojun Liu
- Shenzhen University of Health Science Center, Shenzhen, Guangdong 518060, China
| | - Ao Li
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Lili Gao
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Xi Liu
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Dongwu Liu
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Hongkuan Deng
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Bosheng Zhao
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China.
| | - Baohua Liu
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Shenzhen University of Health Science Center, Shenzhen, Guangdong 518060, China.
| | - Qiuxiang Pang
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China; Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences, Shandong University of Technology, Zibo, Shandong 255049, China.
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18
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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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19
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Lalani AI, Zhu S, Gokhale S, Jin J, Xie P. TRAF molecules in inflammation and inflammatory diseases. ACTA ACUST UNITED AC 2017. [PMID: 29527458 DOI: 10.1007/s40495-017-0117-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Purpose of Review This review presents an overview of the current knowledge of TRAF molecules in inflammation with an emphasis on available human evidence and direct in vivo evidence of mouse models that demonstrate the contribution of TRAF molecules in the pathogenesis of inflammatory diseases. Recent Findings The tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of cytoplasmic proteins was initially identified as signaling adaptors that bind directly to the intracellular domains of receptors of the TNF-R superfamily. It is now appreciated that TRAF molecules are widely employed in signaling by a variety of adaptive and innate immune receptors as well as cytokine receptors. 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). Most of these signaling pathways have been linked to inflammation, and therefore TRAF molecules were expected to regulate inflammation and inflammatory responses since their discovery in 1990s. However, direct in vivo evidence of TRAFs in inflammation and especially in inflammatory diseases had been lacking for many years, partly due to the difficulty imposed by early lethality of TRAF2-/-, TRAF3-/-, and TRAF6-/- mice. With the creation of conditional knockout and lineage-specific transgenic mice of different TRAF molecules, our understanding about TRAFs in inflammation and inflammatory responses has rapidly advanced during the past decade. Summary Increasing evidence indicates that TRAF molecules are versatile and indispensable regulators of inflammation and inflammatory responses and that aberrant expression or function of TRAFs contributes to the pathogenesis of inflammatory diseases.
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Affiliation(s)
- Almin I Lalani
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Sining Zhu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Samantha Gokhale
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Juan Jin
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Department of Pharmacology, Anhui Medical University, Meishan Road 81st, Shushan District, Hefei, Anhui province, China
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Member, Rutgers Cancer Institute of New Jersey
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20
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Araghi RR, Ryan JA, Letai A, Keating AE. Rapid Optimization of Mcl-1 Inhibitors using Stapled Peptide Libraries Including Non-Natural Side Chains. ACS Chem Biol 2016; 11:1238-44. [PMID: 26854535 PMCID: PMC4874891 DOI: 10.1021/acschembio.5b01002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpha helices form a critical part of the binding interface for many protein-protein interactions, and chemically stabilized synthetic helical peptides can be effective inhibitors of such helix-mediated complexes. In particular, hydrocarbon stapling of peptides to generate constrained helices can improve binding affinity and other peptide properties, but determining the best stapled peptide variant often requires laborious trial and error. Here, we describe the rapid discovery and optimization of a stapled-helix peptide that binds to Mcl-1, an antiapoptotic protein that is overexpressed in many chemoresistant cancers. To accelerate discovery, we developed a peptide library synthesis and screening scheme capable of identifying subtle affinity differences among Mcl-1-binding stapled peptides. We used our method to sample combinations of non-natural amino-acid substitutions that we introduced into Mcl-1 inhibitors in the context of a fixed helix-stabilizing hydrocarbon staple that increased peptide helical content and reduced proteolysis. Peptides discovered in our screen contained surprising substitutions at sites that are conserved in natural binding partners. Library-identified peptide M3d is the most potent molecule yet tested for selectively triggering mitochondrial permeabilization in Mcl-1 dependent cell lines. Our library approach for optimizing helical peptide inhibitors can be readily applied to the study of other biomedically important targets.
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Affiliation(s)
- Raheleh Rezaei Araghi
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave. Cambridge MA 02139, United States
| | - Jeremy A. Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave. Cambridge MA 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave. Cambridge MA 02139, United States
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