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      InTRIMsic immunity: Positive and negative regulation of immune signaling by tripartite motif proteins

      review-article
      a , * , a , b , c , d , b , c , e
      Cytokine & Growth Factor Reviews
      Elsevier Ltd.
      5′ppp-RNA, 5′-triphosphate RNA, AIM2, Absent in melanoma 2, ASC, apoptosis-associated speck-like protein containing a CARD, CARD, caspase activation and recruitment domain, CLR, C-type lectin receptor, DC, dendritic cell, DDX41, DEAD-box protein 41, dsRNA, double-stranded RNA, GART, gene encoding phosphoribosylglycinamide formyltransferase, IFITM, interferon-induced transmembrane protein, IFN, interferon, IFNαR, IFNα receptor, IKK, IκB kinase, IL, interleukin, iNOS, inducible nitric oxide synthetase, IRF, IFN regulatory factor, ISG, interferon-stimulated gene, ISG15, IFN-stimulated gene 15, JAK, Janus kinase, MAVS, mitochondrial antiviral signaling, MDA5, melanoma differentiation-associated protein 5, MEF, mouse embryonic fibroblast, MHC, major histocompatibility complex, MΦ, macrophage, MYD88, myeloid differentiation primary response gene 88, NEDD8, neural precursor cell expressed developmentally down-regulated 8, NEMO, NFκB essential modulator, NFκB, nuclear factor κB, NK, natural killer cell, NLR, NOD-like receptor, NS1, influenza virus non structural 1, OAS, 3–5 oligo adenylate synthetase, PAMP, pathogen-associated molecular pattern, PBMC, peripheral blood mononuclear cell, PHD, plant homeo domain, PI3KC2β, phosphatidylinositol 3 kinase C2β, PIN1, prolyl isomerase 1, PRR, pattern recognition receptor (PRR), RBCC, RING-BBox-coiled coil (= tripartite motif), RIG-I, retinoic acid inducible I, RING, really interesting new gene, RLR, RIG-I-like receptor, ROS, reactive oxygen species, SeV, Sendai virus, STAT, stimulator and activator of transcription, STING, stimulator of interferon genes, SUMO, small ubiquitin-like modifier, TAB, TGFβ-activated kinase binding protein, TAK, TGFβ-activated kinase, TBK1, TANK-binding kinase, TCR, T cell receptor, TLR, toll-like receptor, TNF, tumor necrosis factor, TRAF, TNF receptor associated factor, TRIF, TIR-domain-containing adapter-inducing IFN, TRIM, tripartite motif protein, TUB, TRIM-ubiquitin body, Ub, ubiquitin, E3 ligase, TRIMmunity, Ubiquitin, TRIM protein, Interferon

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          Abstract

          During the immune response, striking the right balance between positive and negative regulation is critical to effectively mount an anti-microbial defense while preventing detrimental effects from exacerbated immune activation. Intra-cellular immune signaling is tightly regulated by various post-translational modifications, which allow for this dynamic response. One of the post-translational modifiers critical for immune control is ubiquitin, which can be covalently conjugated to lysines in target molecules, thereby altering their functional properties. This is achieved in a process involving E3 ligases which determine ubiquitination target specificity.

          One of the most prominent E3 ligase families is that of the tripartite motif (TRIM) proteins, which counts over 70 members in humans. Over the last years, various studies have contributed to the notion that many members of this protein family are important immune regulators. Recent studies into the mechanisms by which some of the TRIMs regulate the innate immune system have uncovered important immune regulatory roles of both covalently attached, as well as unanchored poly-ubiquitin chains. This review highlights TRIM evolution, recent findings in TRIM-mediated immune regulation, and provides an outlook to current research hurdles and future directions.

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          Most cited references81

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          Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions.

          Ubiquitin acts as a versatile cellular signal that controls a wide range of biological processes including protein degradation, DNA repair, endocytosis, autophagy, transcription, immunity, and inflammation. The specificity of ubiquitin signaling is achieved by alternative conjugation signals (monoubiquitin and ubiquitin chains) and interactions with ubiquitin-binding proteins (known as ubiquitin receptors) that decode ubiquitinated target signals into biochemical cascades in the cell. Herein, we review the current knowledge pertaining to the structural and functional features of ubiquitin-binding proteins and the mechanisms by which they recognize various types of ubiquitin topologies. The combinatorial use of diverse ubiquitin-binding domains (UBDs) in full-length proteins, selective recognition of chains with distinct linkages and length, and posttranslational modifications of ubiquitin receptors or multivalent interactions within protein complexes illustrate a few mechanisms by which a circuitry of signaling networks can be rewired by ubiquitin-binding proteins to control cellular functions in vivo.
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            Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity.

            RIG-I detects invading viral RNA and activates the transcription factors NF-kappaB and IRF3 through the mitochondrial protein MAVS. Here we show that RNA bearing 5'-triphosphate strongly activates the RIG-I-IRF3 signaling cascade in a reconstituted system composed of RIG-I, mitochondria, and cytosol. Activation of RIG-I requires not only RNA but also polyubiquitin chains linked through lysine 63 (K63) of ubiquitin. RIG-I binds specifically to K63-polyubiquitin chains through its tandem CARD domains in a manner that depends on RNA and ATP. Mutations in the CARD domains that abrogate ubiquitin binding also impair RIG-I activation. Remarkably, unanchored K63-ubiquitin chains, which are not conjugated to any target protein, potently activate RIG-I. These ubiquitin chains function as an endogenous ligand of RIG-I in human cells. Our results delineate the mechanism of RIG-I activation, identify CARD domains as a ubiquitin sensor, and demonstrate that unanchored K63-polyubiquitin chains are signaling molecules in antiviral innate immunity. Copyright 2010 Elsevier Inc. All rights reserved.
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              Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5.

              MDA5, a viral double-stranded RNA (dsRNA) receptor, shares sequence similarity and signaling pathways with RIG-I yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. Revealing the molecular basis for the functional divergence, we report here the crystal structure of MDA5 bound to dsRNA, which shows how, using the same domain architecture, MDA5 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. We further show that MDA5 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement, and that the signaling domain (tandem CARD), which decorates the outside of the core MDA5 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. These data support a model in which MDA5 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. Copyright © 2013 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                Journal
                Cytokine Growth Factor Rev
                Cytokine Growth Factor Rev
                Cytokine & Growth Factor Reviews
                Elsevier Ltd.
                1359-6101
                1879-0305
                13 August 2014
                October 2014
                13 August 2014
                : 25
                : 5
                : 563-576
                Affiliations
                [a ]Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
                [b ]Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
                [c ]Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
                [d ]Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
                [e ]University of Texas Medical Branch, Department of Microbiology and Immunology, 301 University Avenue, Galveston, TX 77555, USA
                Author notes
                [* ]Corresponding author at: Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria. Tel.: +43 1 427754614. Gijs.Versteeg@ 123456univie.ac.at
                Article
                S1359-6101(14)00084-7
                10.1016/j.cytogfr.2014.08.001
                7173094
                25172371
                9a6785e3-7391-429b-b51b-24d9ea941839
                Copyright © 2014 Elsevier Ltd. All rights reserved.

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

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                Molecular biology
                5′ppp-rna, 5′-triphosphate rna,aim2, absent in melanoma 2,asc, apoptosis-associated speck-like protein containing a card,card, caspase activation and recruitment domain,clr, c-type lectin receptor,dc, dendritic cell,ddx41, dead-box protein 41,dsrna, double-stranded rna,gart, gene encoding phosphoribosylglycinamide formyltransferase,ifitm, interferon-induced transmembrane protein,ifn, interferon,ifnαr, ifnα receptor,ikk, iκb kinase,il, interleukin,inos, inducible nitric oxide synthetase,irf, ifn regulatory factor,isg, interferon-stimulated gene,isg15, ifn-stimulated gene 15,jak, janus kinase,mavs, mitochondrial antiviral signaling,mda5, melanoma differentiation-associated protein 5,mef, mouse embryonic fibroblast,mhc, major histocompatibility complex,mφ, macrophage,myd88, myeloid differentiation primary response gene 88,nedd8, neural precursor cell expressed developmentally down-regulated 8,nemo, nfκb essential modulator,nfκb, nuclear factor κb,nk, natural killer cell,nlr, nod-like receptor,ns1, influenza virus non structural 1,oas, 3–5 oligo adenylate synthetase,pamp, pathogen-associated molecular pattern,pbmc, peripheral blood mononuclear cell,phd, plant homeo domain,pi3kc2β, phosphatidylinositol 3 kinase c2β,pin1, prolyl isomerase 1,prr, pattern recognition receptor (prr),rbcc, ring-bbox-coiled coil (= tripartite motif),rig-i, retinoic acid inducible i,ring, really interesting new gene,rlr, rig-i-like receptor,ros, reactive oxygen species,sev, sendai virus,stat, stimulator and activator of transcription,sting, stimulator of interferon genes,sumo, small ubiquitin-like modifier,tab, tgfβ-activated kinase binding protein,tak, tgfβ-activated kinase,tbk1, tank-binding kinase,tcr, t cell receptor,tlr, toll-like receptor,tnf, tumor necrosis factor,traf, tnf receptor associated factor,trif, tir-domain-containing adapter-inducing ifn,trim, tripartite motif protein,tub, trim-ubiquitin body,ub, ubiquitin,e3 ligase,trimmunity,ubiquitin,trim protein,interferon
                Molecular biology
                5′ppp-rna, 5′-triphosphate rna, aim2, absent in melanoma 2, asc, apoptosis-associated speck-like protein containing a card, card, caspase activation and recruitment domain, clr, c-type lectin receptor, dc, dendritic cell, ddx41, dead-box protein 41, dsrna, double-stranded rna, gart, gene encoding phosphoribosylglycinamide formyltransferase, ifitm, interferon-induced transmembrane protein, ifn, interferon, ifnαr, ifnα receptor, ikk, iκb kinase, il, interleukin, inos, inducible nitric oxide synthetase, irf, ifn regulatory factor, isg, interferon-stimulated gene, isg15, ifn-stimulated gene 15, jak, janus kinase, mavs, mitochondrial antiviral signaling, mda5, melanoma differentiation-associated protein 5, mef, mouse embryonic fibroblast, mhc, major histocompatibility complex, mφ, macrophage, myd88, myeloid differentiation primary response gene 88, nedd8, neural precursor cell expressed developmentally down-regulated 8, nemo, nfκb essential modulator, nfκb, nuclear factor κb, nk, natural killer cell, nlr, nod-like receptor, ns1, influenza virus non structural 1, oas, 3–5 oligo adenylate synthetase, pamp, pathogen-associated molecular pattern, pbmc, peripheral blood mononuclear cell, phd, plant homeo domain, pi3kc2β, phosphatidylinositol 3 kinase c2β, pin1, prolyl isomerase 1, prr, pattern recognition receptor (prr), rbcc, ring-bbox-coiled coil (= tripartite motif), rig-i, retinoic acid inducible i, ring, really interesting new gene, rlr, rig-i-like receptor, ros, reactive oxygen species, sev, sendai virus, stat, stimulator and activator of transcription, sting, stimulator of interferon genes, sumo, small ubiquitin-like modifier, tab, tgfβ-activated kinase binding protein, tak, tgfβ-activated kinase, tbk1, tank-binding kinase, tcr, t cell receptor, tlr, toll-like receptor, tnf, tumor necrosis factor, traf, tnf receptor associated factor, trif, tir-domain-containing adapter-inducing ifn, trim, tripartite motif protein, tub, trim-ubiquitin body, ub, ubiquitin, e3 ligase, trimmunity, ubiquitin, trim protein, interferon

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