51
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Abstract
Detection of double-stranded RNAs (dsRNAs) is a central mechanism of innate immune defense in many organisms. We here discuss several families of dsRNA-binding proteins involved in mammalian antiviral innate immunity. These include RIG-I-like receptors, protein kinase R, oligoadenylate synthases, adenosine deaminases acting on RNA, RNA interference systems, and other proteins containing dsRNA-binding domains and helicase domains. Studies suggest that their functions are highly interdependent and that their interdependence could offer keys to understanding the complex regulatory mechanisms for cellular dsRNA homeostasis and antiviral immunity. This review aims to highlight their interconnectivity, as well as their commonalities and differences in their dsRNA recognition mechanisms.
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Affiliation(s)
- Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
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52
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Yu Q, Qu K, Modis Y. Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis. Mol Cell 2018; 72:999-1012.e6. [PMID: 30449722 PMCID: PMC6310684 DOI: 10.1016/j.molcel.2018.10.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/09/2018] [Accepted: 10/09/2018] [Indexed: 12/24/2022]
Abstract
Double-stranded RNA (dsRNA) is a potent proinflammatory signature of viral infection. Long cytosolic dsRNA is recognized by MDA5. The cooperative assembly of MDA5 into helical filaments on dsRNA nucleates the assembly of a multiprotein type I interferon signaling platform. Here, we determined cryoelectron microscopy (cryo-EM) structures of MDA5-dsRNA filaments with different helical twists and bound nucleotide analogs at resolutions sufficient to build and refine atomic models. The structures identify the filament-forming interfaces, which encode the dsRNA binding cooperativity and length specificity of MDA5. The predominantly hydrophobic interface contacts confer flexibility, reflected in the variable helical twist within filaments. Mutation of filament-forming residues can result in loss or gain of signaling activity. Each MDA5 molecule spans 14 or 15 RNA base pairs, depending on the twist. Variations in twist also correlate with variations in the occupancy and type of nucleotide in the active site, providing insights on how ATP hydrolysis contributes to MDA5-dsRNA recognition. Cryo-EM structures of MDA5-dsRNA filaments determined for three catalytic states Filament forming interfaces are flexible and predominantly hydrophobic Mutation of filament-forming residues can cause loss or gain of IFN-β signaling ATPase cycle is coupled to changes in filament twist and size of the RNA footprint
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Affiliation(s)
- Qin Yu
- Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Kun Qu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Yorgo Modis
- Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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53
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Kumar S, Jain S. Immune signalling by supramolecular assemblies. Immunology 2018; 155:435-445. [PMID: 30144032 DOI: 10.1111/imm.12995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
Formation of supramolecular assemblies appears to be a general mechanism in immune signalling pathways. These supramolecular assemblies appear to form through a nucleated polymerization mechanism. This review examines selected immune signalling pathways that involve supramolecular assemblies, describes the concepts of protein polymerization, and discusses how those concepts of protein polymerization implicate new elegant ways for signal amplification, setting threshold and noise reduction in these pathways.
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Affiliation(s)
- Santosh Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Shweta Jain
- Department of Neurology and Graduate Programs in Neuroscience and Biomedical Sciences, University of California at San Francisco, San Francisco, CA, USA
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54
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Dias Junior AG, Sampaio NG, Rehwinkel J. A Balancing Act: MDA5 in Antiviral Immunity and Autoinflammation. Trends Microbiol 2018; 27:75-85. [PMID: 30201512 PMCID: PMC6319154 DOI: 10.1016/j.tim.2018.08.007] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/28/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022]
Abstract
Induction of interferons during viral infection is mediated by cellular proteins that recognise viral nucleic acids. MDA5 is one such sensor of virus presence and is activated by RNA. MDA5 is required for immunity against several classes of viruses, including picornaviruses. Recent work showed that mutations in the IFIH1 gene, encoding MDA5, lead to interferon-driven autoinflammatory diseases. Together with observations made in cancer cells, this suggests that MDA5 detects cellular RNAs in addition to viral RNAs. It is therefore important to understand the properties of the RNAs which activate MDA5. New data indicate that RNA length and secondary structure are features sensed by MDA5. We review these developments and discuss how MDA5 strikes a balance between antiviral immunity and autoinflammation. MDA5 is a pattern-recognition receptor for RNA and induces a type I interferon response. MDA5 is activated in a variety of clinically relevant settings. This includes infection with ssRNA, dsRNA, and dsDNA viruses; several autoimmune and autoinflammatory diseases, such as type 1 diabetes and Aicardi–Goutières syndrome; and some forms of cancer treatment. Synthetic, viral, and cellular RNAs can all activate MDA5. The latter may include transcripts from endogenous retroelements such as Alu repeats. Length and secondary structure are important features that determine whether an RNA molecule is detected by MDA5. Indeed, long, base-paired RNA molecules potently activate MDA5 in the test tube.
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Affiliation(s)
- Antonio Gregorio Dias Junior
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK. https://twitter.com/GregorioDias1
| | - Natalia G Sampaio
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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55
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Wu Y, Zhao W, Liu Y, Tan X, Li X, Zou Q, Xiao Z, Xu H, Wang Y, Yang X. Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response. EMBO J 2018; 37:embj.201899017. [PMID: 30158112 PMCID: PMC6276880 DOI: 10.15252/embj.201899017] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/02/2018] [Accepted: 08/07/2018] [Indexed: 01/03/2023] Open
Abstract
Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG‐I was responsible for such tumor‐inhibitory effect. Interestingly, repression of HNRNPC resulted in accumulation of endogenous double‐stranded RNA (dsRNA), the binding ligand of RIG‐I. These up‐regulated dsRNA species were highly enriched by Alu sequences and mostly originated from pre‐mRNA introns that harbor the known HNRNPC binding sites. Such source of dsRNA is different than the recently well‐characterized endogenous retroviruses that encode dsRNA. In summary, essentialness of HNRNPC in the breast cancer cells was attributed to its function in controlling the endogenous dsRNA and the down‐stream interferon response. This is a novel extension from the previous understandings about HNRNPC in binding with introns and regulating RNA splicing.
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Affiliation(s)
- Yusheng Wu
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenwei Zhao
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Liu
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Xiangtian Tan
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin Li
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Qin Zou
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Zhengtao Xiao
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Hui Xu
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuting Wang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Xuerui Yang
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China .,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
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56
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Yong HY, Luo D. RIG-I-Like Receptors as Novel Targets for Pan-Antivirals and Vaccine Adjuvants Against Emerging and Re-Emerging Viral Infections. Front Immunol 2018; 9:1379. [PMID: 29973930 PMCID: PMC6019452 DOI: 10.3389/fimmu.2018.01379] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022] Open
Abstract
Emerging and re-emerging viruses pose a significant public health challenge around the world, among which RNA viruses are the cause of many major outbreaks of infectious diseases. As one of the early lines of defense in the human immune system, RIG-I-like receptors (RLRs) play an important role as sentinels to thwart the progression of virus infection. The activation of RLRs leads to an antiviral state in the host cells, which triggers the adaptive arm of immunity and ultimately the clearance of viral infections. Hence, RLRs are promising targets for the development of pan-antivirals and vaccine adjuvants. Here, we discuss the opportunities and challenges of developing RLR agonists into antiviral therapeutic agents and vaccine adjuvants against a broad range of viruses.
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Affiliation(s)
- Hui Yee Yong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
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57
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Abstract
Pattern recognition receptors (PRRs) survey intra- and extracellular spaces for pathogen-associated molecular patterns (PAMPs) within microbial products of infection. Recognition and binding to cognate PAMP ligand by specific PRRs initiates signaling cascades that culminate in a coordinated intracellular innate immune response designed to control infection. In particular, our immune system has evolved specialized PRRs to discriminate viral nucleic acid from host. These are critical sensors of viral RNA to trigger innate immunity in the vertebrate host. Different families of PRRs of virus infection have been defined and reveal a diversity of PAMP specificity for wide viral pathogen coverage to recognize and extinguish virus infection. In this review, we discuss recent insights in pathogen recognition by the RIG-I-like receptors, related RNA helicases, Toll-like receptors, and other RNA sensor PRRs, to present emerging themes in innate immune signaling during virus infection.
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Affiliation(s)
- Kwan T Chow
- Center for Innate Immunity and Immune Disease and Department of Immunology, University of Washington, Seattle, Washington 98109, USA; , ,
| | - Michael Gale
- Center for Innate Immunity and Immune Disease and Department of Immunology, University of Washington, Seattle, Washington 98109, USA; , ,
| | - Yueh-Ming Loo
- Center for Innate Immunity and Immune Disease and Department of Immunology, University of Washington, Seattle, Washington 98109, USA; , ,
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58
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Poynter SJ, DeWitte-Orr SJ. Understanding Viral dsRNA-Mediated Innate Immune Responses at the Cellular Level Using a Rainbow Trout Model. Front Immunol 2018; 9:829. [PMID: 29740439 PMCID: PMC5924774 DOI: 10.3389/fimmu.2018.00829] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/05/2018] [Indexed: 12/20/2022] Open
Abstract
Viruses across genome types produce long dsRNA molecules during replication [viral (v-) dsRNA]. dsRNA is a potent signaling molecule and inducer of type I interferon (IFN), leading to the production of interferon-stimulated genes (ISGs), and a protective antiviral state within the cell. Research on dsRNA-induced immune responses has relied heavily on a commercially available, and biologically irrelevant dsRNA, polyinosinic:polycytidylic acid (poly I:C). Alternatively, dsRNA can be produced by in vitro transcription (ivt-) dsRNA, with a defined sequence and length. We hypothesized that ivt-dsRNA, containing legitimate viral sequence and length, would be a more appropriate proxy for v-dsRNA, compared with poly I:C. This is the first study to investigate the effects of v-dsRNA on the innate antiviral response and to compare v-dsRNA to ivt-dsRNA-induced responses in fish cells, specifically rainbow trout. Previously, class A scavenger receptors (SR-As) were found to be surface receptors for poly I:C in rainbow trout cells. In this study, ivt-dsRNA binding was blocked by poly I:C and v-dsRNA, as well as SR-A competitive ligands, suggesting all three dsRNA molecules are recognized by SR-As. Downstream innate antiviral effects were determined by measuring IFN and ISG transcript levels using qRT-PCR and antiviral assays. Similar to what has been shown previously with ivt-dsRNA, v-dsRNA was able to induce IFN and ISG transcript production between 3 and 24 h, and its effects were length dependent (i.e., longer v-dsRNA produced a stronger response). Interestingly, when v-dsRNA and ivt-dsRNA were length and sequence matched both molecules induced statistically similar IFN and ISG transcript levels, which resulted in similar antiviral states against two aquatic viruses. To pursue sequence effects further, three ivt-dsRNA molecules of the same length but different sequences (including host and viral sequences) were tested for their ability to induce IFN/ISG transcripts and an antiviral state. All three induced responses similarly. This study is the first of its kind to look at the effects v-dsRNA in fish cells as well as to compare ivt-dsRNA to v-dsRNA, and suggests that ivt-dsRNA may be a good surrogate for v-dsRNA in the study of dsRNA-induced responses and potential future antiviral therapies.
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Affiliation(s)
- Sarah J. Poynter
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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59
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Zhu Q, Tan P, Li Y, Lin M, Li C, Mao J, Cui J, Zhao W, Wang HY, Wang RF. DHX29 functions as an RNA co-sensor for MDA5-mediated EMCV-specific antiviral immunity. PLoS Pathog 2018; 14:e1006886. [PMID: 29462185 PMCID: PMC5834211 DOI: 10.1371/journal.ppat.1006886] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 03/02/2018] [Accepted: 01/18/2018] [Indexed: 12/13/2022] Open
Abstract
Melanoma differentiation-associated gene-5 (MDA5) recognizes distinct subsets of viruses including Encephalomyocarditis virus (EMCV) of picornavirus family, but the molecular mechanisms underlying the specificity of the viral recognition of MDA5 in immune cells remain obscure. DHX29 is an RNA helicase required for the translation of 5’ structured mRNA of host and many picornaviruses (such as EMCV). We identify that DXH29 as a key RNA co-sensor, plays a significant role for specific recognition and triggering anti-EMCV immunity. We have observed that DHX29 regulates MDA5-, but not RIG-I-, mediated type I interferon signaling by preferentially interacting with structured RNAs and specifically with MDA5 for enhancing MDA5-dsRNA binding affinity. Overall, our results identify a critical role for DHX29 in innate immune response and provide molecular insights into the mechanisms by which DHX29 recognizes 5’ structured EMCV RNA and interacts with MDA5 for potent type I interferon signaling and antiviral immunity. Cytosolic sensor melanoma differentiation-associated gene-5 (MDA5) specifically detects long-duplex RNAs in the genome of double-stranded (ds)RNA viruses such as Encephalomyocarditis virus (EMCV) whereas retinoic acid-inducible gene-I (RIG-I) preferentially recognizes vesicular stomatitis virus (VSV) to trigger signaling cascades that lead to production of interferons and cytokines. However, weak RNA binding capacity of MDA5 significantly attenuates the antiviral response. Here, we reveal that DHX29 as a co-sensor of MDA5 ensures the specific and efficient MDA5-RNA interactions leading to a complete MDA5-mediated antiviral signaling. Depletion of DHX29 substantially reduces the activity of MDA5 whereas activity of RIG-I remains intact. These findings provide a mechanism for DHX29 coactivation of MDA5 and a biological context for MDA5-RNA filaments in antiviral response.
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Affiliation(s)
- Qingyuan Zhu
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States of America
| | - Peng Tan
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States of America
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, United States of America
| | - Yinyin Li
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States of America
| | - Meng Lin
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States of America
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chaoran Li
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States of America
- Xiangya Hospital, Central South University, Changsha, China
| | - Jingrong Mao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States of America
- Xiangya Hospital, Central South University, Changsha, China
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Zhao
- Key Laboratory for Stem Cells and Tissue Engineering of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Helen Y. Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States of America
| | - Rong-Fu Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX, United States of America
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, United States of America
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, United States of America
- * E-mail:
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60
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Raghuraman P, Sudandiradoss C. R516Q mutation in Melanoma differentiation-associated protein 5 (MDA5) and its pathogenic role towards rare Singleton-Merten syndrome; a signature associated molecular dynamics study. J Biomol Struct Dyn 2018; 37:750-765. [DOI: 10.1080/07391102.2018.1439770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- P. Raghuraman
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
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61
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Buers I, Rice GI, Crow YJ, Rutsch F. MDA5-Associated Neuroinflammation and the Singleton-Merten Syndrome: Two Faces of the Same Type I Interferonopathy Spectrum. J Interferon Cytokine Res 2018; 37:214-219. [PMID: 28475458 DOI: 10.1089/jir.2017.0004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In 1973, Singleton and Merten described a new syndrome in 2 female probands with aortic and cardiac valve calcifications, early loss of secondary dentition, and widened medullary cavities of the phalanges. In 1984, Aicardi and Goutières defined a phenotype resembling congenital viral infection with basal ganglia calcification and increased protein content in the cerebrospinal fluid. Between 2006 and 2012, mutations in 6 different genes were described to be associated with Aicardi-Goutières syndrome, specifically-TREX1, RNASEH2A, RNASEH2B, RNASEH2C, ADAR, and SAMHD1. More recently, mutations in IFIH1 were reported in a variety of neuroimmunological phenotypes, including Aicardi-Goutières syndrome, while a specific Arg822Gln mutation in IFIH1 was described in 3 discrete families with Singleton-Merten syndrome (SMS). IFIH1 encodes for melanoma differentiation-associated gene 5 (MDA5), and all mutations identified to date have been associated with an enhanced interferon response in affected individuals. In this study, we present a male child demonstrating recurrent febrile episodes, spasticity, and basal ganglia calcification suggestive of Aicardi-Goutières syndrome, who carries the same Arg822Gln mutation in IFIH1 previously associated with SMS. We conclude that both diseases are part of the interferonopathy grouping and that the Arg822Gln mutation in IFIH1 can cause a spectrum of disease, including neurological involvement.
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Affiliation(s)
- Insa Buers
- 1 Department of General Pediatrics, Muenster University Children's Hospital , Muenster, Germany
| | - Gillian I Rice
- 2 Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester , Manchester, United Kingdom
| | - Yanick J Crow
- 2 Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester , Manchester, United Kingdom .,3 Laboratory of Neurogenetics and Neuroinflammation , INSERM UMR 1163, Paris, France .,4 Paris Descartes-Sorbonne Paris Cité University , Institute Imagine, Paris, France
| | - Frank Rutsch
- 1 Department of General Pediatrics, Muenster University Children's Hospital , Muenster, Germany
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62
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Ahmad S, Mu X, Yang F, Greenwald E, Park JW, Jacob E, Zhang CZ, Hur S. Breaching Self-Tolerance to Alu Duplex RNA Underlies MDA5-Mediated Inflammation. Cell 2018; 172:797-810.e13. [PMID: 29395326 DOI: 10.1016/j.cell.2017.12.016] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 10/09/2017] [Accepted: 12/08/2017] [Indexed: 01/23/2023]
Abstract
Aberrant activation of innate immune receptors can cause a spectrum of immune disorders, such as Aicardi-Goutières syndrome (AGS). One such receptor is MDA5, a viral dsRNA sensor that induces antiviral immune response. Using a newly developed RNase-protection/RNA-seq approach, we demonstrate here that constitutive activation of MDA5 in AGS results from the loss of tolerance to cellular dsRNAs formed by Alu retroelements. While wild-type MDA5 cannot efficiently recognize Alu-dsRNAs because of its limited filament formation on imperfect duplexes, AGS variants of MDA5 display reduced sensitivity to duplex structural irregularities, assembling signaling-competent filaments on Alu-dsRNAs. Moreover, we identified an unexpected role of an RNA-rich cellular environment in suppressing aberrant MDA5 oligomerization, highlighting context dependence of self versus non-self discrimination. Overall, our work demonstrates that the increased efficiency of MDA5 in recognizing dsRNA comes at a cost of self-recognition and implicates a unique role of Alu-dsRNAs as virus-like elements that shape the primate immune system.
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Affiliation(s)
- Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xin Mu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Fei Yang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Emily Greenwald
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ji Woo Park
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Biology Department in Morrissey College of Arts and Sciences, Boston College, Chestnut Hill, MA, USA
| | - Etai Jacob
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cheng-Zhong Zhang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biomedical Informatics, Harvard Medical School, MA 02115, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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63
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Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis. Genome Biol 2017; 18:166. [PMID: 28874170 PMCID: PMC5585977 DOI: 10.1186/s13059-017-1301-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023] Open
Abstract
Background Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most is unknown. Editing causing protein recoding is the essential function of ADAR2, but an essential role for recoding by ADAR1 has not been demonstrated. ADAR1 has been proposed to have editing-dependent and editing-independent functions. The relative contribution of these in vivo has not been clearly defined. A critical function of ADAR1 is editing of endogenous RNA to prevent activation of the dsRNA sensor MDA5 (Ifih1). Outside of this, how ADAR1 editing contributes to normal development and homeostasis is uncertain. Results We describe the consequences of ADAR1 editing deficiency on murine homeostasis. Adar1E861A/E861AIfih1-/- mice are strikingly normal, including their lifespan. There is a mild, non-pathogenic innate immune activation signature in the Adar1E861A/E861AIfih1-/- mice. Assessing A-to-I editing across adult tissues demonstrates that outside of the brain, ADAR1 performs the majority of editing and that ADAR2 cannot compensate in its absence. Direct comparison of the Adar1-/- and Adar1E861A/E861A alleles demonstrates a high degree of concordance on both Ifih1+/+ and Ifih1-/- backgrounds, suggesting no substantial contribution from ADAR1 editing-independent functions. Conclusions These analyses demonstrate that the lifetime absence of ADAR1-editing is well tolerated in the absence of MDA5. We conclude that protein recoding arising from ADAR1-mediated editing is not essential for organismal homeostasis. Additionally, the phenotypes associated with loss of ADAR1 are the result of RNA editing and MDA5-dependent functions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1301-4) contains supplementary material, which is available to authorized users.
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RNAs Containing Modified Nucleotides Fail To Trigger RIG-I Conformational Changes for Innate Immune Signaling. mBio 2016; 7:mBio.00833-16. [PMID: 27651356 PMCID: PMC5030355 DOI: 10.1128/mbio.00833-16] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Invading pathogen nucleic acids are recognized and bound by cytoplasmic (retinoic acid-inducible gene I [RIG-I]-like) and membrane-bound (Toll-like) pattern recognition receptors to activate innate immune signaling. Modified nucleotides, when present in RNA molecules, diminish the magnitude of these signaling responses. However, mechanisms explaining the blunted signaling have not been elucidated. In this study, we used several independent biological assays, including inhibition of virus replication, RIG-I:RNA binding assays, and limited trypsin digestion of RIG-I:RNA complexes, to begin to understand how RNAs containing modified nucleotides avoid or suppress innate immune signaling. The experiments were based on a model innate immune activating RNA molecule, the polyU/UC RNA domain of hepatitis C virus, which was transcribed in vitro with canonical nucleotides or with one of eight modified nucleotides. The approach revealed signature assay responses associated with individual modified nucleotides or classes of modified nucleotides. For example, while both N-6-methyladenosine (m6A) and pseudouridine nucleotides correlate with diminished signaling, RNA containing m6A modifications bound RIG-I poorly, while RNA containing pseudouridine bound RIG-I with high affinity but failed to trigger the canonical RIG-I conformational changes associated with robust signaling. These data advance understanding of RNA-mediated innate immune signaling, with additional relevance for applying nucleotide modifications to RNA therapeutics. The innate immune system provides the first response to virus infections and must distinguish between host and pathogen nucleic acids to mount a protective immune response without activating autoimmune responses. While the presence of nucleotide modifications in RNA is known to correlate with diminished innate immune signaling, the underlying mechanisms have not been explored. The data reported here are important for defining mechanistic details to explain signaling suppression by RNAs containing modified nucleotides. The results suggest that RNAs containing modified nucleotides interrupt signaling at early steps of the RIG-I-like innate immune activation pathway and also that nucleotide modifications with similar chemical structures can be organized into classes that suppress or evade innate immune signaling steps. These data contribute to defining the molecular basis for innate immune signaling suppression by RNAs containing modified nucleotides. The results have important implications for designing therapeutic RNAs that evade innate immune detection.
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65
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Liddicoat BJ, Hartner JC, Piskol R, Ramaswami G, Chalk AM, Kingsley PD, Sankaran VG, Wall M, Purton LE, Seeburg PH, Palis J, Orkin SH, Lu J, Li JB, Walkley CR. Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis. Exp Hematol 2016; 44:947-63. [PMID: 27373493 DOI: 10.1016/j.exphem.2016.06.250] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/17/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) convert adenosine residues to inosine in double-stranded RNA. In vivo, ADAR1 is essential for the maintenance of hematopoietic stem/progenitors. Whether other hematopoietic cell types also require ADAR1 has not been assessed. Using erythroid- and myeloid-restricted deletion of Adar1, we demonstrate that ADAR1 is dispensable for myelopoiesis but is essential for normal erythropoiesis. Adar1-deficient erythroid cells display a profound activation of innate immune signaling and high levels of cell death. No changes in microRNA levels were found in ADAR1-deficient erythroid cells. Using an editing-deficient allele, we demonstrate that RNA editing is the essential function of ADAR1 during erythropoiesis. Mapping of adenosine-to-inosine editing in purified erythroid cells identified clusters of hyperedited adenosines located in long 3'-untranslated regions of erythroid-specific transcripts and these are ADAR1-specific editing events. ADAR1-mediated RNA editing is essential for normal erythropoiesis.
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Affiliation(s)
- Brian J Liddicoat
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Jochen C Hartner
- Taconic Biosciences, Cologne, Germany; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Robert Piskol
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alistair M Chalk
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Paul D Kingsley
- Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Vijay G Sankaran
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, Fitzroy, Victoria, Australia
| | - Louise E Purton
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Peter H Seeburg
- Department of Molecular Neurobiology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James Palis
- Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology and Stem Cell Program, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA
| | - Jun Lu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia.
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66
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Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 482] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
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Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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67
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Buers I, Nitschke Y, Rutsch F. Novel interferonopathies associated with mutations in RIG-I like receptors. Cytokine Growth Factor Rev 2016; 29:101-7. [PMID: 26993858 DOI: 10.1016/j.cytogfr.2016.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Type I interferonopathies are a relatively new class of inherited autoimmune disorders associated with an inborn elevated interferon response. Activation of cytosolic receptors which recognize viral double stranded RNA including the RIG-I (retinoic acid-inducible gene I) like receptors RIG-I and MDA5 (melanoma differentiation-associated gene 5) has been shown to induce the transcription of type I interferon genes. Within recent years, with the help of next generation sequencing techniques in syndromic families, mutations in the genes encoding for RIG-I and MDA5 have been identified to cause rare diseases including Aicardi-Goutières syndrome, Systemic Lupus Erythematosus in certain individuals as well as classic and atypical Singleton-Merten syndrome. Patients carrying mono-allelic mutations in MDA5 and RIG-I show constitutive activation of the RIG-I receptors and downstream signalling associated with increased type I interferon production. Although differing in the degree of phenotypic expression and severity, the phenotype of these "novel" diseases shows a considerable overlap reflecting their common pathogenetic pathway.
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Affiliation(s)
- Insa Buers
- Department of General Pediatrics, Muenster University Children's Hospital, Albert-Schweitzer-Campus 1, Building A1, 48149 Muenster, Germany.
| | - Yvonne Nitschke
- Department of General Pediatrics, Muenster University Children's Hospital, Albert-Schweitzer-Campus 1, Building A1, 48149 Muenster, Germany.
| | - Frank Rutsch
- Department of General Pediatrics, Muenster University Children's Hospital, Albert-Schweitzer-Campus 1, Building A1, 48149 Muenster, Germany.
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68
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Xu C, Evensen Ø, Munang'andu H. De Novo Transcriptome Analysis Shows That SAV-3 Infection Upregulates Pattern Recognition Receptors of the Endosomal Toll-Like and RIG-I-Like Receptor Signaling Pathways in Macrophage/Dendritic Like TO-Cells. Viruses 2016; 8:114. [PMID: 27110808 PMCID: PMC4848607 DOI: 10.3390/v8040114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/05/2016] [Accepted: 04/14/2016] [Indexed: 12/28/2022] Open
Abstract
A fundamental step in cellular defense mechanisms is the recognition of “danger signals” made of conserved pathogen associated molecular patterns (PAMPs) expressed by invading pathogens, by host cell germ line coded pattern recognition receptors (PRRs). In this study, we used RNA-seq and the Kyoto encyclopedia of genes and genomes (KEGG) to identify PRRs together with the network pathway of differentially expressed genes (DEGs) that recognize salmonid alphavirus subtype 3 (SAV-3) infection in macrophage/dendritic like TO-cells derived from Atlantic salmon (Salmo salar L) headkidney leukocytes. Our findings show that recognition of SAV-3 in TO-cells was restricted to endosomal Toll-like receptors (TLRs) 3 and 8 together with RIG-I-like receptors (RLRs) and not the nucleotide-binding oligomerization domain-like receptors NOD-like receptor (NLRs) genes. Among the RLRs, upregulated genes included the retinoic acid inducible gene I (RIG-I), melanoma differentiation association 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2). The study points to possible involvement of the tripartite motif containing 25 (TRIM25) and mitochondrial antiviral signaling protein (MAVS) in modulating RIG-I signaling being the first report that links these genes to the RLR pathway in SAV-3 infection in TO-cells. Downstream signaling suggests that both the TLR and RLR pathways use interferon (IFN) regulatory factors (IRFs) 3 and 7 to produce IFN-a2. The validity of RNA-seq data generated in this study was confirmed by quantitative real time qRT-PCR showing that genes up- or downregulated by RNA-seq were also up- or downregulated by RT-PCR. Overall, this study shows that de novo transcriptome assembly identify key receptors of the TLR and RLR sensors engaged in host pathogen interaction at cellular level. We envisage that data presented here can open a road map for future intervention strategies in SAV infection of salmon.
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Affiliation(s)
- Cheng Xu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Ullevålsveien 72, P.O. Box 8146 Dep NO-0033 Oslo, Norway.
| | - Øystein Evensen
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Ullevålsveien 72, P.O. Box 8146 Dep NO-0033 Oslo, Norway.
| | - Hetron Munang'andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Ullevålsveien 72, P.O. Box 8146 Dep NO-0033 Oslo, Norway.
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69
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Ahmad S, Hur S. Helicases in Antiviral Immunity: Dual Properties as Sensors and Effectors. Trends Biochem Sci 2016; 40:576-585. [PMID: 26410598 DOI: 10.1016/j.tibs.2015.08.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/01/2023]
Abstract
Many helicases have a unique ability to couple cognate RNA binding to ATP hydrolysis, which can induce a large conformational change that affects its interaction with RNA, position along RNA, or oligomeric state. A growing number of these helicases contribute to the innate immune system, either as sensors that detect foreign nucleic acids and/or as effectors that directly participate in the clearance of such foreign species. In this review, we discuss a few examples, including retinoic acid-inducible gene-I (RIG-I), melanoma differentiation-associated gene 5 (MDA5), and Dicer, focusing on their dual functions as both sensors and effectors. We will also discuss the closely related, but less understood, helicases, laboratory of genetics and physiology 2 (LGP2) and Dicer-related helicase-1 and -3 (DRH-1 and -3).
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Affiliation(s)
- Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
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70
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The role of RNA editing by ADAR1 in prevention of innate immune sensing of self-RNA. J Mol Med (Berl) 2016; 94:1095-1102. [PMID: 27044320 DOI: 10.1007/s00109-016-1416-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/16/2016] [Accepted: 03/24/2016] [Indexed: 12/25/2022]
Abstract
The innate immune system is the first line of the cellular defence against invading pathogens. A critical component of this defence is the capacity to discriminate foreign RNA molecules, which are distinct from most cellular RNAs in structure and/or modifications. However, a series of rare autoimmune/autoinflammatory diseases in humans highlight the propensity for the innate immune sensing system to be activated by endogenous cellular double-stranded RNAs (dsRNAs), underscoring the fine line between distinguishing self from non-self. The RNA editing enzyme ADAR1 has recently emerged as a key regulator that prevents innate immune pathway activation, principally the cytosolic dsRNA sensor MDA5, from inducing interferon in response to double-stranded RNA structures within endogenous RNAs. Adenosine-to-Inosine RNA editing by ADAR1 is proposed to destabilise duplexes formed from inverted repetitive elements within RNAs, which appear to prevent MDA5 from sensing these RNA as virus-like in the cytoplasm. Aberrant activation of these pathways has catastrophic effects at both a cellular and organismal level, contributing to one of the causes of the conditions collectively known as the type I interferonopathies.
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71
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Yoneyama M, Jogi M, Onomoto K. Regulation of antiviral innate immune signaling by stress-induced RNA granules. J Biochem 2016; 159:279-86. [PMID: 26748340 PMCID: PMC4763080 DOI: 10.1093/jb/mvv122] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/24/2015] [Indexed: 12/17/2022] Open
Abstract
Activation of antiviral innate immunity is triggered by cellular pattern recognition receptors. Retinoic acid inducible gene-I (RIG-I)-like receptors (RLRs) detect viral non-self RNA in cytoplasm of virus-infected cells and play a critical role in the clearance of the invaded viruses through production of antiviral cytokines. Among the three known RLRs, RIG-I and melanoma differentiation-associated gene 5 recognize distinct non-self signatures of viral RNA and activate antiviral signaling. Recent reports have clearly described the molecular machinery underlying the activation of RLRs and interactions with the downstream adaptor, mitochondrial antiviral signaling protein (MAVS). RLRs and MAVS are thought to form large multimeric filaments around cytoplasmic organelles depending on the presence of Lys63-linked ubiquitin chains. Furthermore, RLRs have been shown to localize to stress-induced ribonucleoprotein aggregate known as stress granules and utilize them as a platform for recognition/activation of signaling. In this review, we will focus on the current understanding of RLR-mediated signal activation and the interactions with stress-induced RNA granules.
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Affiliation(s)
- Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Michihiko Jogi
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - Koji Onomoto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
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72
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Sohn J, Hur S. Filament assemblies in foreign nucleic acid sensors. Curr Opin Struct Biol 2016; 37:134-44. [PMID: 26859869 DOI: 10.1016/j.sbi.2016.01.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/24/2022]
Abstract
Helical filamentous assembly is ubiquitous in biology, but was only recently realized to be broadly employed in the innate immune system of vertebrates. Accumulating evidence suggests that the filamentous assemblies and helical oligomerization play important roles in detection of foreign nucleic acids and activation of the signaling pathways to produce antiviral and inflammatory mediators. In this review, we focus on the helical assemblies observed in the signaling pathways of RIG-I-like receptors (RLRs) and AIM2-like receptors (ALRs). We describe ligand-dependent oligomerization of receptor, receptor-dependent oligomerization of signaling adaptor molecules, and their functional implications and regulations.
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Affiliation(s)
- Jungsan Sohn
- Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Sun Hur
- Harvard Medical School, Boston, MA, USA.
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73
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Leung DW, Amarasinghe GK. When your cap matters: structural insights into self vs non-self recognition of 5' RNA by immunomodulatory host proteins. Curr Opin Struct Biol 2016; 36:133-41. [PMID: 26916433 PMCID: PMC5218996 DOI: 10.1016/j.sbi.2016.02.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 12/13/2022]
Abstract
Cytosolic recognition of viral RNA is important for host innate immune responses. Differential recognition of self vs non-self RNA is a considerable challenge as the inability to differentiate may trigger aberrant immune responses. Recent work identified the composition of the RNA 5', including the 5' cap and its methylation state, as an important determinant of recognition by the host. Recent studies have advanced our understanding of the modified 5' RNA recognition and viral antagonism of RNA receptors. Here, we will discuss RIG-I and IFIT proteins as examples of host proteins that detect dsRNA and ssRNA, respectively.
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Affiliation(s)
- Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, United States.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, United States.
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74
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Heaton SM, Borg NA, Dixit VM. Ubiquitin in the activation and attenuation of innate antiviral immunity. J Exp Med 2015; 213:1-13. [PMID: 26712804 PMCID: PMC4710203 DOI: 10.1084/jem.20151531] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/02/2015] [Indexed: 01/01/2023] Open
Abstract
Viral infection activates danger signals that are transmitted via the retinoic acid-inducible gene 1-like receptor (RLR), nucleotide-binding oligomerization domain-like receptor (NLR), and Toll-like receptor (TLR) protein signaling cascades. This places host cells in an antiviral posture by up-regulating antiviral cytokines including type-I interferon (IFN-I). Ubiquitin modifications and cross-talk between proteins within these signaling cascades potentiate IFN-I expression, and inversely, a growing number of viruses are found to weaponize the ubiquitin modification system to suppress IFN-I. Here we review how host- and virus-directed ubiquitin modification of proteins in the RLR, NLR, and TLR antiviral signaling cascades modulate IFN-I expression.
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Affiliation(s)
- Steven M Heaton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Natalie A Borg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, CA 94080
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75
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Liddicoat BJ, Chalk AM, Walkley CR. ADAR1, inosine and the immune sensing system: distinguishing self from non-self. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:157-72. [PMID: 26692549 DOI: 10.1002/wrna.1322] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 11/10/2022]
Abstract
The conversion of genomically encoded adenosine to inosine in dsRNA is termed as A-to-I RNA editing. This process is catalyzed by two of the three mammalian ADAR proteins (ADAR1 and ADAR2) both of which have essential functions for normal organismal homeostasis. The phenotype of ADAR2 deficiency can be primarily ascribed to a lack of site-selective editing of a single transcript in the brain. In contrast, the biology and substrates responsible for the Adar1(-/-) phenotype have remained more elusive. Several recent studies have identified that a feature of absence or reductions of ADAR1 activity, conserved across human and mouse models, is a profound activation of interferon-stimulated gene signatures and innate immune responses. Further analysis of this observation has lead to the conclusion that editing by ADAR1 is required to prevent activation of the cytosolic innate immune system, primarily focused on the dsRNA sensor MDA5 and leading to downstream signaling via MAVS. The delineation of this mechanism places ADAR1 at the interface between the cells ability to differentiate self- from non-self dsRNA. Based on MDA5 dsRNA recognition requisites, the mechanism indicates that the type of dsRNA must fulfil a particular structural characteristic, rather than a sequence-specific requirement. While additional studies are required to molecularly verify the genetic model, the observations to date collectively identify A-to-I editing by ADAR1 as a key modifier of the cellular response to endogenous dsRNA.
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Affiliation(s)
- Brian J Liddicoat
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Alistair M Chalk
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
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76
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Looney BM, Xia CQ, Concannon P, Ostrov DA, Clare-Salzler MJ. Effects of type 1 diabetes-associated IFIH1 polymorphisms on MDA5 function and expression. Curr Diab Rep 2015; 15:96. [PMID: 26385483 DOI: 10.1007/s11892-015-0656-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent evidence has highlighted the role of the innate immune system in type 1 diabetes (T1D) pathogenesis. Specifically, aberrant activation of the interferon response prior to seroconversion of T1D-associated autoantibodies supports a role for the interferon response as a precipitating event toward activation of autoimmunity. Melanoma differentiation-associated protein 5 (MDA5), encoded by IFIH1, mediates the innate immune system's interferon response to certain viral species that form double-stranded RNA (dsRNA), the MDA5 ligand, during their life cycle. Extensive research has associated single nucleotide polymorphisms (SNPs) within the coding region of IFIH1 with T1D. This review discusses the different risk and protective IFIH1 alleles in the context of recent structural and functional analysis that relate to MDA5 regulation of interferon responses. These studies have provided a functional hypothesis for IFIH1 T1D-associated SNPs' effects on MDA5-mediated interferon responses as well as supporting the genome-wide association (GWA) studies that first associated IFIH1 with T1D.
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Affiliation(s)
- Benjamin M Looney
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine Interdisciplinary Program in Biomedical Sciences, University of Florida, 1600 SW Archer Rd., Gainesville, FL, 32610, USA.
| | - Chang-Qing Xia
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, 1600 SW Archer Rd., Gainesville, FL, 32610, USA.
| | - Patrick Concannon
- University of Florida Genetics Institute, 2033 Mowry Rd., P.O. Box 103610, Gainesville, FL, 32611, USA.
| | - David A Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, 2033 Mowry Rd., P.O. Box 103633, Gainesville, FL, 32611, USA.
| | - Michael J Clare-Salzler
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, 2033 Mowry Rd., P.O. Box 103633, Gainesville, FL, 32611, USA.
- Center for Immunology and Transplantation, University of Florida, 1600 SW Archer Rd., P.O. Box 100275, Gainesville, FL, 32610, USA.
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77
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Bruns AM, Horvath CM. LGP2 synergy with MDA5 in RLR-mediated RNA recognition and antiviral signaling. Cytokine 2015; 74:198-206. [PMID: 25794939 PMCID: PMC4475439 DOI: 10.1016/j.cyto.2015.02.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 12/24/2022]
Abstract
Mammalian cells have the ability to recognize virus infection and mount a powerful antiviral response. Pattern recognition receptor proteins detect molecular signatures of virus infection and activate antiviral signaling. The RIG-I-like receptor (RLR) proteins are expressed in the cytoplasm of nearly all cells and specifically recognize virus-derived RNA species as a molecular feature discriminating the pathogen from the host. The RLR family is composed of three homologous proteins, RIG-I, MDA5, and LGP2. All RLRs have the ability to detect virus-derived dsRNA and hydrolyze ATP, but display individual differences in enzymatic activity, intrinsic ability to recognize RNA, and mechanisms of activation. Emerging evidence suggests that MDA5 and RIG-I utilize distinct mechanisms to form oligomeric complexes along dsRNA. Aligning of their signaling domains creates a platform capable of propagating and amplifying antiviral signaling responses. LGP2 with intact ATP hydrolysis is critical for the MDA5-mediated antiviral response, but LGP2 lacks the domains essential for activation of antiviral signaling, leaving the role of LGP2 in antiviral signaling unclear. Recent studies revealed a mechanistic basis of synergy between LGP2 and MDA5 leading to enhanced antiviral signaling. This review briefly summarizes the RLR system, and focuses on the relationship between LGP2 and MDA5, describing in detail how these two proteins work together to detect foreign RNA and generate a fully functional antiviral response.
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Affiliation(s)
- Annie M Bruns
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Curt M Horvath
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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Louber J, Brunel J, Uchikawa E, Cusack S, Gerlier D. Kinetic discrimination of self/non-self RNA by the ATPase activity of RIG-I and MDA5. BMC Biol 2015; 13:54. [PMID: 26215161 PMCID: PMC4517655 DOI: 10.1186/s12915-015-0166-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/11/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The cytoplasmic RIG-like receptors are responsible for the early detection of viruses and other intracellular microbes by activating the innate immune response mediated by type I interferons (IFNs). RIG-I and MDA5 detect virus-specific RNA motifs with short 5'-tri/diphosphorylated, blunt-end double-stranded RNA (dsRNA) and >0.5-2 kb long dsRNA as canonical agonists, respectively. However, in vitro, they can bind to many RNA species, while in cells there is an activation threshold. As SF2 helicase/ATPase family members, ATP hydrolysis is dependent on co-operative RNA and ATP binding. Whereas simultaneous ATP and cognate RNA binding is sufficient to activate RIG-I by releasing autoinhibition of the signaling domains, the physiological role of the ATPase activity of RIG-I and MDA5 remains controversial. RESULTS A cross-analysis of a rationally designed panel of RNA binding and ATPase mutants and truncated receptors, using type I IFN promoter activation as readout, allows us to refine our understanding of the structure-function relationships of RIG-I and MDA5. RNA activation of RIG-I depends on multiple critical RNA binding sites in its helicase domain as confirmed by functional evidence using novel mutations. We found that RIG-I or MDA5 mutants with low ATP hydrolysis activity exhibit constitutive activity but this was fully reverted when associated with mutations preventing RNA binding to the helicase domain. We propose that the turnover kinetics of the ATPase domain enables the discrimination of self/non-self RNA by both RIG-I and MDA5. Non-cognate, possibly self, RNA binding would lead to fast ATP turnover and RNA disassociation and thus insufficient time for the caspase activation and recruitment domains (CARDs) to promote downstream signaling, whereas tighter cognate RNA binding provides a longer time window for downstream events to be engaged. CONCLUSIONS The exquisite fine-tuning of RIG-I and MDA5 RNA-dependent ATPase activity coupled to CARD release allows a robust IFN response from a minor subset of non-self RNAs within a sea of cellular self RNAs. This avoids the eventuality of deleterious autoimmunity effects as have been recently described to arise from natural gain-of-function alleles of RIG-I and MDA5.
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Affiliation(s)
- Jade Louber
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France.
- INSERM, U1111, Lyon, France.
- Ecole Normale Supérieure de Lyon, Lyon, France.
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.
- CNRS, UMR5308, Lyon, France.
| | - Joanna Brunel
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France.
- INSERM, U1111, Lyon, France.
- Ecole Normale Supérieure de Lyon, Lyon, France.
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.
- CNRS, UMR5308, Lyon, France.
| | - Emiko Uchikawa
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, BP 181, 38042, Grenoble, Cedex 9, France.
- Unit of Virus Host Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, BP 181, 38042, Grenoble, Cedex 9, France.
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, BP 181, 38042, Grenoble, Cedex 9, France.
- Unit of Virus Host Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, BP 181, 38042, Grenoble, Cedex 9, France.
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France.
- INSERM, U1111, Lyon, France.
- Ecole Normale Supérieure de Lyon, Lyon, France.
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.
- CNRS, UMR5308, Lyon, France.
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79
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Morrone SR, Matyszewski M, Yu X, Delannoy M, Egelman EH, Sohn J. Assembly-driven activation of the AIM2 foreign-dsDNA sensor provides a polymerization template for downstream ASC. Nat Commun 2015. [PMID: 26197926 PMCID: PMC4525163 DOI: 10.1038/ncomms8827] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AIM2 recognizes foreign dsDNA and assembles into the inflammasome, a filamentous supramolecular signalling platform required to launch innate immune responses. We show here that the pyrin domain of AIM2 (AIM2PYD) drives both filament formation and dsDNA binding. In addition, the dsDNA-binding domain of AIM2 also oligomerizes and assists in filament formation. The ability to oligomerize is critical for binding dsDNA, and in turn permits the size of dsDNA to regulate the assembly of the AIM2 polymers. The AIM2PYD oligomers define the filamentous structure, and the helical symmetry of the AIM2PYD filament is consistent with the filament assembled by the PYD of the downstream adaptor ASC. Our results suggest that the role of AIM2PYD is not autoinhibitory, but generating a structural template by coupling ligand binding and oligomerization is a key signal transduction mechanism in the AIM2 inflammasome. The AIM2 inflammasome complex is essential for defence against a number of human pathogens but how it assembles upon recognition of foreign DNA remains incompletely understood. Here Morrone et al. suggest the AIM2 pyrin domain acts in both DNA binding and filament assembly to generate a structural template for complex assembly.
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Affiliation(s)
- Seamus R Morrone
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA
| | - Mariusz Matyszewski
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA
| | - Xiong Yu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine Charlottesville, Virginia 22908, USA
| | - Michael Delannoy
- Microscope Core Facilities, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine Charlottesville, Virginia 22908, USA
| | - Jungsan Sohn
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA
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80
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Yao H, Dittmann M, Peisley A, Hoffmann HH, Gilmore RH, Schmidt T, Schmidt-Burgk J, Hornung V, Rice CM, Hur S. ATP-dependent effector-like functions of RIG-I-like receptors. Mol Cell 2015; 58:541-548. [PMID: 25891073 PMCID: PMC4427555 DOI: 10.1016/j.molcel.2015.03.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/05/2015] [Accepted: 03/11/2015] [Indexed: 01/24/2023]
Abstract
The vertebrate antiviral innate immune system is often considered to consist of two distinct groups of proteins: pattern recognition receptors (PRRs) that detect viral infection and induce the interferon (IFN) signaling, and effectors that directly act against viral replication. Accordingly, previous studies on PRRs, such as RIG-I and MDA5, have primarily focused on their functions in viral double-stranded RNA (dsRNA) detection and consequent antiviral signaling. We report here that both RIG-I and MDA5 efficiently displace viral proteins pre-bound to dsRNA in a manner dependent on their ATP hydrolysis, and that this activity assists a dsRNA-dependent antiviral effector protein, PKR, and allows RIG-I to promote MDA5 signaling. Furthermore, truncated RIG-I/MDA5 lacking the signaling domain, and hence the IFN stimulatory activity, displaces viral proteins and suppresses replication of certain viruses in an ATP-dependent manner. Thus, this study reveals novel "effector-like" functions of RIG-I and MDA5 that challenge the conventional view of PRRs.
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MESH Headings
- Adenosine Triphosphate/metabolism
- Antiviral Agents/metabolism
- Base Sequence
- Blotting, Western
- Cell Line, Tumor
- DEAD Box Protein 58
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- HEK293 Cells
- Humans
- Interferon-Induced Helicase, IFIH1
- Interferon-beta/genetics
- Interferon-beta/metabolism
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- Phosphorylation
- RNA Interference
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Immunologic
- Receptors, Pattern Recognition/genetics
- Receptors, Pattern Recognition/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Diseases/genetics
- Virus Diseases/metabolism
- eIF-2 Kinase/genetics
- eIF-2 Kinase/metabolism
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Affiliation(s)
- Hui Yao
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, MA 02115, USA
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences Nankai University, Tianjin 300071, China
| | - Meike Dittmann
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C The Rockefeller University, New York, New York 10065, USA
| | - Alys Peisley
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School, Boston, MA 02115, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C The Rockefeller University, New York, New York 10065, USA
| | - Rachel H. Gilmore
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C The Rockefeller University, New York, New York 10065, USA
| | - Tobias Schmidt
- Institut für Molekulare Medizin, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | | | - Veit Hornung
- Institut für Molekulare Medizin, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C The Rockefeller University, New York, New York 10065, USA
| | - Sun Hur
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School, Boston, MA 02115, USA
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81
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Bosch PJ, Corrêa IR, Sonntag MH, Ibach J, Brunsveld L, Kanger JS, Subramaniam V. Evaluation of fluorophores to label SNAP-tag fused proteins for multicolor single-molecule tracking microscopy in live cells. Biophys J 2015; 107:803-14. [PMID: 25140415 DOI: 10.1016/j.bpj.2014.06.040] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/22/2014] [Accepted: 06/10/2014] [Indexed: 11/19/2022] Open
Abstract
Single-molecule tracking has become a widely used technique for studying protein dynamics and their organization in the complex environment of the cell. In particular, the spatiotemporal distribution of membrane receptors is an active field of study due to its putative role in the regulation of signal transduction. The SNAP-tag is an intrinsically monovalent and highly specific genetic tag for attaching a fluorescent label to a protein of interest. Little information is currently available on the choice of optimal fluorescent dyes for single-molecule microscopy utilizing the SNAP-tag labeling system. We surveyed 6 green and 16 red excitable dyes for their suitability in single-molecule microscopy of SNAP-tag fusion proteins in live cells. We determined the nonspecific binding levels and photostability of these dye conjugates when bound to a SNAP-tag fused membrane protein in live cells. We found that only a limited subset of the dyes tested is suitable for single-molecule tracking microscopy. The results show that a careful choice of the dye to conjugate to the SNAP-substrate to label SNAP-tag fusion proteins is very important, as many dyes suffer from either rapid photobleaching or high nonspecific staining. These characteristics appear to be unpredictable, which motivated the need to perform the systematic survey presented here. We have developed a protocol for evaluating the best dyes, and for the conditions that we evaluated, we find that Dy 549 and CF 640 are the best choices tested for single-molecule tracking. Using an optimal dye pair, we also demonstrate the possibility of dual-color single-molecule imaging of SNAP-tag fusion proteins. This survey provides an overview of the photophysical and imaging properties of a range of SNAP-tag fluorescent substrates, enabling the selection of optimal dyes and conditions for single-molecule imaging of SNAP-tagged fusion proteins in eukaryotic cell lines.
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Affiliation(s)
- Peter J Bosch
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | | | - Michael H Sonntag
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jenny Ibach
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Johannes S Kanger
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands.
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82
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Nellimarla S, Mossman KL. Extracellular dsRNA: its function and mechanism of cellular uptake. J Interferon Cytokine Res 2015; 34:419-26. [PMID: 24905198 DOI: 10.1089/jir.2014.0002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Double-stranded RNA (dsRNA) is arguably the most potent viral trigger of innate immune signaling. Its activity has been recognized for over 5 decades, first as a toxin, then as a central component of the interferon system, as an efficient activator of antiviral responses and an immunomodulator for therapeutic applications. Nucleic acid sensing is the main basis for antiviral defense systems throughout the diverse forms of life from bacteria to plants and animals. Pattern recognition receptors of the host defense system not only sense viral dsRNA as a pathogen-associated molecular pattern in infected cells, but also recognize circulating endogenous dsRNA, a nonmicrobial signal, as a danger-associated molecular pattern, often leading to autoimmunity. Despite the effects of extracellular viral and host dsRNA associated with infection and autoimmunity, respectively, the understanding of cellular mechanisms for its recognition and uptake has only been appreciated in recent years. This review presents an overview of this unique form of nucleic acid, addressing its roles in infection, autoimmunity, and host sensing mechanisms. The goal of this review is to highlight the novel findings with a focus on extracellular recognition and uptake by the cell.
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Affiliation(s)
- Srinivas Nellimarla
- 1 Department of Pathology and Molecular Medicine, McMaster Immunology Research Center, Michael DeGroote Institute for Infectious Disease Research, McMaster University , Hamilton, Ontario, Canada
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83
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del Toro Duany Y, Wu B, Hur S. MDA5-filament, dynamics and disease. Curr Opin Virol 2015; 12:20-5. [PMID: 25676875 DOI: 10.1016/j.coviro.2015.01.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 01/22/2015] [Indexed: 12/22/2022]
Abstract
Melanoma Differentiation-Associated gene 5 (MDA5), encoded by the gene IFIH1, is a cytoplasmic sensor for viral double-stranded RNAs (dsRNAs). MDA5 activates the type I interferon signaling pathway upon detection of long viral dsRNA generated during replication of picornaviruses. Studies have shown that MDA5 forms a filament along the length of dsRNA and utilizes ATP-dependent filament dynamics to discriminate between self versus non-self on the basis of dsRNA length. This review summarizes our current understanding of how the MDA5 filament assembles and disassembles, how this filament dynamics are utilized in dsRNA length-dependent signaling, and how dysregulated filament dynamics lead to pathogenesis of immune disorders.
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Affiliation(s)
- Yoandris del Toro Duany
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, United States; Program in Cellular and Molecular Medicine, Boston Children's Hospital, United States
| | - Bin Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, United States; Program in Cellular and Molecular Medicine, Boston Children's Hospital, United States
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, United States; Program in Cellular and Molecular Medicine, Boston Children's Hospital, United States.
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84
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Viral RNA detection by RIG-I-like receptors. Curr Opin Immunol 2015; 32:48-53. [PMID: 25594890 DOI: 10.1016/j.coi.2014.12.012] [Citation(s) in RCA: 324] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 12/17/2014] [Accepted: 12/30/2014] [Indexed: 12/12/2022]
Abstract
In higher vertebrates, recognition of the non-self signature of invading viruses by genome-encoded pattern recognition receptors initiates antiviral innate immunity. Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) detect viral RNA as a non-self pattern in the cytoplasm and activate downstream signaling. Detection of viral RNA also activates stress responses resulting in stress granule-like aggregates, which facilitate RLR-mediated antiviral immunity. Among the three RLR family members RIG-I and melanoma differentiation-associated gene 5 (MDA5) recognize distinct viral RNA species with differential molecular machinery and activate signaling through mitochondrial antiviral signaling (MAVS, also known as IPS-1/VISA/Cardif), which leads to the expression of cytokines including type I and III interferons (IFNs) to restrict viral propagation. In this review, we summarize recent knowledge regarding RNA recognition and signal transduction by RLRs and MAVS/IPS-1.
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85
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Zheng J, Yong HY, Panutdaporn N, Liu C, Tang K, Luo D. High-resolution HDX-MS reveals distinct mechanisms of RNA recognition and activation by RIG-I and MDA5. Nucleic Acids Res 2015; 43:1216-30. [PMID: 25539915 PMCID: PMC4333383 DOI: 10.1093/nar/gku1329] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 12/07/2014] [Accepted: 12/09/2014] [Indexed: 12/25/2022] Open
Abstract
RIG-I and MDA5 are the major intracellular immune receptors that recognize viral RNA species and undergo a series of conformational transitions leading to the activation of the interferon-mediated antiviral response. However, to date, full-length RLRs have resisted crystallographic efforts and a molecular description of their activation pathways remains hypothetical. Here we employ hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) to probe the apo states of RIG-I and MDA5 and to dissect the molecular details with respect to distinct RNA species recognition, ATP binding and hydrolysis and CARDs activation. We show that human RIG-I maintains an auto-inhibited resting state owing to the intra-molecular HEL2i-CARD2 interactions while apo MDA5 lacks the analogous intra-molecular interactions and therefore adopts an extended conformation. Our work demonstrates that RIG-I binds and responds differently to short triphosphorylated RNA and long duplex RNA and that sequential addition of RNA and ATP triggers specific allosteric effects leading to RIG-I CARDs activation. We also present a high-resolution protein surface mapping technique that refines the cooperative oligomerization model of neighboring MDA5 molecules on long duplex RNA. Taken together, our data provide a high-resolution view of RLR activation in solution and offer new evidence for the molecular mechanism of RLR activation.
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Affiliation(s)
- Jie Zheng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Hui Yee Yong
- Lee Kong Chian School of Medicine, Nanyang Technological University, 61 Biopolis Drive, Proteos Building, #07-03, 138673, Singapore
| | - Nantika Panutdaporn
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Chuanfa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Kai Tang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 61 Biopolis Drive, Proteos Building, #07-03, 138673, Singapore
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86
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Chiang JJ, Davis ME, Gack MU. Regulation of RIG-I-like receptor signaling by host and viral proteins. Cytokine Growth Factor Rev 2014; 25:491-505. [PMID: 25023063 PMCID: PMC7108356 DOI: 10.1016/j.cytogfr.2014.06.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/16/2014] [Indexed: 12/17/2022]
Abstract
Vertebrate innate immunity is characterized by an effective immune surveillance apparatus, evolved to sense foreign structures, such as proteins or nucleic acids of invading microbes. RIG-I-like receptors (RLRs) are key sensors of viral RNA species in the host cell cytoplasm. Activation of RLRs in response to viral RNA triggers an antiviral defense program through the production of hundreds of antiviral effector proteins including cytokines, chemokines, and host restriction factors that directly interfere with distinct steps in the virus life cycle. To avoid premature or abnormal antiviral and proinflammatory responses, which could have harmful consequences for the host, the signaling activities of RLRs and their common adaptor molecule, MAVS, are delicately controlled by cell-intrinsic regulatory mechanisms. Furthermore, viruses have evolved multiple strategies to modulate RLR-MAVS signal transduction to escape from immune surveillance. Here, we summarize recent progress in our understanding of the regulation of RLR signaling through host factors and viral antagonistic proteins.
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Affiliation(s)
- Jessica J Chiang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, United States
| | - Meredith E Davis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, United States
| | - Michaela U Gack
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, United States.
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87
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Schmitz ML, Kracht M, Saul VV. The intricate interplay between RNA viruses and NF-κB. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2754-2764. [PMID: 25116307 PMCID: PMC7114235 DOI: 10.1016/j.bbamcr.2014.08.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 12/19/2022]
Abstract
RNA viruses have rapidly evolving genomes which often allow cross-species transmission and frequently generate new virus variants with altered pathogenic properties. Therefore infections by RNA viruses are a major threat to human health. The infected host cell detects trace amounts of viral RNA and the last years have revealed common principles in the biochemical mechanisms leading to signal amplification that is required for mounting of a powerful antiviral response. Components of the RNA sensing and signaling machinery such as RIG-I-like proteins, MAVS and the inflammasome inducibly form large oligomers or even fibers that exhibit hallmarks of prions. Following a nucleation event triggered by detection of viral RNA, these energetically favorable and irreversible polymerization events trigger signaling cascades leading to the induction of antiviral and inflammatory responses, mediated by interferon and NF-κB pathways. Viruses have evolved sophisticated strategies to manipulate these host cell signaling pathways in order to ensure their replication. We will discuss at the examples of influenza and HTLV-1 viruses how a fascinating diversity of biochemical mechanisms is employed by viral proteins to control the NF-κB pathway at all levels.
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Affiliation(s)
- M Lienhard Schmitz
- Institute of Biochemistry, Medical Faculty, Friedrichstrasse 24, Justus-Liebig-University, 35392 Giessen, Germany.
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, D-35392 Giessen, Germany
| | - Vera V Saul
- Institute of Biochemistry, Medical Faculty, Friedrichstrasse 24, Justus-Liebig-University, 35392 Giessen, Germany
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88
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The innate immune sensor LGP2 activates antiviral signaling by regulating MDA5-RNA interaction and filament assembly. Mol Cell 2014; 55:771-81. [PMID: 25127512 DOI: 10.1016/j.molcel.2014.07.003] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/11/2014] [Accepted: 07/03/2014] [Indexed: 12/24/2022]
Abstract
Cytoplasmic pattern recognition receptors detect non-self RNAs during virus infections and initiate antiviral signaling. One receptor, MDA5, possesses essential signaling domains, but weak RNA binding. A second receptor, LGP2, rapidly detects diverse dsRNA species, but lacks signaling domains. Accumulating evidence suggests LGP2 and MDA5 work together to detect viral RNA and generate a complete antiviral response, but the basis for their cooperation has been elusive. Experiments presented here address this gap in antiviral signaling, revealing that LGP2 assists MDA5-RNA interactions leading to enhanced MDA5-mediated antiviral signaling. LGP2 increases the initial rate of MDA5-RNA interaction and regulates MDA5 filament assembly, resulting in the formation of more numerous, shorter MDA5 filaments that are shown to generate equivalent or greater signaling activity in vivo than the longer filaments containing only MDA5. These findings provide a mechanism for LGP2 coactivation of MDA5 and a biological context for MDA5-RNA filaments in antiviral responses.
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89
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Reikine S, Nguyen JB, Modis Y. Pattern Recognition and Signaling Mechanisms of RIG-I and MDA5. Front Immunol 2014; 5:342. [PMID: 25101084 PMCID: PMC4107945 DOI: 10.3389/fimmu.2014.00342] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/05/2014] [Indexed: 12/25/2022] Open
Abstract
Most organisms rely on innate immune receptors to recognize conserved molecular structures from invading microbes. Two essential innate immune receptors, RIG-I and MDA5, detect viral double-stranded RNA in the cytoplasm. The inflammatory response triggered by these RIG-I-like receptors (RLRs) is one of the first and most important lines of defense against infection. RIG-I recognizes short RNA ligands with 5′-triphosphate caps. MDA5 recognizes long kilobase-scale genomic RNA and replication intermediates. Ligand binding induces conformational changes and oligomerization of RLRs that activate the signaling partner MAVS on the mitochondrial and peroxisomal membranes. This signaling process is under tight regulation, dependent on post-translational modifications of RIG-I and MDA5, and on regulatory proteins including unanchored ubiquitin chains and a third RLR, LGP2. Here, we review recent advances that have shifted the paradigm of RLR signaling away from the conventional linear signaling cascade. In the emerging RLR signaling model, large multimeric signaling platforms generate a highly cooperative, self-propagating, and context-dependent signal, which varies with the subcellular localization of the signaling platform.
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Affiliation(s)
- Stephanie Reikine
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT , USA
| | - Jennifer B Nguyen
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT , USA
| | - Yorgo Modis
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT , USA
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90
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Bruns AM, Horvath CM. Antiviral RNA recognition and assembly by RLR family innate immune sensors. Cytokine Growth Factor Rev 2014; 25:507-12. [PMID: 25081315 DOI: 10.1016/j.cytogfr.2014.07.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 12/24/2022]
Abstract
Virus-encoded molecular signatures, such as cytosolic double-stranded or otherwise biochemically distinct RNA species, trigger cellular antiviral signaling. Cytoplasmic proteins recognize these non-self RNAs and activate signal transduction pathways that drive the expression of virus-induced genes, including the primary antiviral cytokine, IFNβ, and diverse direct and indirect antiviral effectors. One important group of cytosolic RNA sensors known as the RIG-I-like receptors (RLRs) is comprised of three proteins that are similar in structure and function. The RLR proteins, RIG-I, MDA5, and LGP2, share the ability to recognize nucleic acid signatures produced by virus infections and activate antiviral signaling. Emerging evidence indicates that RNA detection by RLRs culminates in the assembly of dynamic multimeric ribonucleoprotein (RNP) complexes. These RNPs can act as signaling platforms that are capable of propagating and amplifying antiviral signaling responses. Despite their common domain structures and similar abilities to induce antiviral responses, the RLRs differ in their enzymatic properties, their intrinsic abilities to recognize RNA, and their ability to assemble into filamentous complexes. This molecular specialization has enabled the RLRs to recognize and respond to diverse virus infections, and to mediate both unique and overlapping functions in immune regulation.
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Affiliation(s)
- Annie M Bruns
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Curt M Horvath
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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91
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Wu B, Peisley A, Tetrault D, Li Z, Egelman EH, Magor KE, Walz T, Penczek PA, Hur S. Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I. Mol Cell 2014; 55:511-23. [PMID: 25018021 DOI: 10.1016/j.molcel.2014.06.010] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/12/2014] [Accepted: 06/02/2014] [Indexed: 12/24/2022]
Abstract
RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires its interaction with the tandem CARDs of RIG-I (2CARD(RIG-I)). However, the precise nature of the interaction between 2CARD(RIG-I) and CARD(MAVS), and how this interaction leads to CARD(MAVS) filament assembly, has been unclear. Here we report a 3.6 Å electron microscopy structure of the CARD(MAVS) filament and a 3.4 Å crystal structure of the 2CARD(RIG-I):CARD(MAVS) complex, representing 2CARD(RIG-I) "caught in the act" of nucleating the CARD(MAVS) filament. These structures, together with functional analyses, show that 2CARD(RIG-I) acts as a template for the CARD(MAVS) filament assembly, by forming a helical tetrameric structure and recruiting CARD(MAVS) along its helical trajectory. Our work thus reveals that signal activation by RIG-I occurs by imprinting its helical assembly architecture on MAVS, a previously uncharacterized mechanism of signal transmission.
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Affiliation(s)
- Bin Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115, USA
| | - Alys Peisley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115, USA
| | - David Tetrault
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Zongli Li
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Katharine E Magor
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas-Houston Medical School, Houston, TX 77030, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115, USA.
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92
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MDA5 and LGP2: accomplices and antagonists of antiviral signal transduction. J Virol 2014; 88:8194-200. [PMID: 24850739 DOI: 10.1128/jvi.00640-14] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mammalian cells have the ability to recognize virus infection and mount a powerful antiviral transcriptional response that provides an initial barrier to replication and impacts both innate and adaptive immune responses. Retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) proteins mediate intracellular virus recognition and are activated by viral RNA ligands to induce antiviral signal transduction. While the mechanisms of RIG-I regulation are already well understood, less is known about the more enigmatic melanoma differentiation-associated 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2). Emerging evidence suggests that these two RLRs are intimately associated as both accomplices and antagonists of antiviral signal transduction.
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93
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Cui J, Song Y, Li Y, Zhu Q, Tan P, Qin Y, Wang HY, Wang RF. USP3 inhibits type I interferon signaling by deubiquitinating RIG-I-like receptors. Cell Res 2014; 24:400-16. [PMID: 24366338 PMCID: PMC3975496 DOI: 10.1038/cr.2013.170] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/15/2013] [Accepted: 11/11/2013] [Indexed: 02/04/2023] Open
Abstract
Lysine 63 (K63)-linked ubiquitination of RIG-I plays a critical role in the activation of type I interferon pathway, yet the molecular mechanism responsible for its deubiquitination is still poorly understood. Here we report that the deubiquitination enzyme ubiquitin-specific protease 3 (USP3) negatively regulates the activation of type I interferon signaling by targeting RIG-I. Knockdown of USP3 specifically enhanced K63-linked ubiquitination of RIG-I, upregulated the phosphorylation of IRF3 and augmented the production of type I interferon cytokines and antiviral immunity. We further show that there is no interaction between USP3 and RIG-I-like receptors (RLRs) in unstimulated or uninfected cells, but upon viral infection or ligand stimulation, USP3 binds to the caspase activation recruitment domain of RLRs and then cleaves polyubiquitin chains through cooperation of its zinc-finger Ub-binding domain and USP catalytic domains. Mutation analysis reveals that binding of USP3 to polyubiquitin chains on RIG-I is a prerequisite step for its cleavage of polyubiquitin chains. Our findings identify a previously unrecognized role of USP3 in RIG-I activation and provide insights into the mechanisms by which USP3 inhibits RIG-I signaling and antiviral immunity.
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Affiliation(s)
- Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Yanxia Song
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, TX 77030, USA
- Central Laboratory, The First Affiliated Hospital, Jilin University, Changchun 130012, China
| | - Yinyin Li
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, TX 77030, USA
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Qingyuan Zhu
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Peng Tan
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, TX 77030, USA
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Yunfei Qin
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Helen Y Wang
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Rong-Fu Wang
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, TX 77030, USA
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94
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Rice GI, Del Toro Duany Y, Jenkinson EM, Forte GM, Anderson BH, Ariaudo G, Bader-Meunier B, Baildam EM, Battini R, Beresford MW, Casarano M, Chouchane M, Cimaz R, Collins AE, Cordeiro NJ, Dale RC, Davidson JE, De Waele L, Desguerre I, Faivre L, Fazzi E, Isidor B, Lagae L, Latchman AR, Lebon P, Li C, Livingston JH, Lourenço CM, Mancardi MM, Masurel-Paulet A, McInnes IB, Menezes MP, Mignot C, O'Sullivan J, Orcesi S, Picco PP, Riva E, Robinson RA, Rodriguez D, Salvatici E, Scott C, Szybowska M, Tolmie JL, Vanderver A, Vanhulle C, Vieira JP, Webb K, Whitney RN, Williams SG, Wolfe LA, Zuberi SM, Hur S, Crow YJ. Gain-of-function mutations in IFIH1 cause a spectrum of human disease phenotypes associated with upregulated type I interferon signaling. Nat Genet 2014; 46:503-509. [PMID: 24686847 PMCID: PMC4004585 DOI: 10.1038/ng.2933] [Citation(s) in RCA: 439] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 03/05/2014] [Indexed: 12/23/2022]
Abstract
The type I interferon system is integral to human antiviral immunity. However, inappropriate stimulation or defective negative regulation of this system can lead to inflammatory disease. We sought to determine the molecular basis of genetically uncharacterized cases of the type I interferonopathy Aicardi-Goutières syndrome, and of other patients with undefined neurological and immunological phenotypes also demonstrating an upregulated type I interferon response. We found that heterozygous mutations in the cytosolic double-stranded RNA receptor gene IFIH1 (MDA5) cause a spectrum of neuro-immunological features consistently associated with an enhanced interferon state. Cellular and biochemical assays indicate that these mutations confer a gain-of-function - so that mutant IFIH1 binds RNA more avidly, leading to increased baseline and ligand-induced interferon signaling. Our results demonstrate that aberrant sensing of nucleic acids can cause immune upregulation.
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Affiliation(s)
- Gillian I Rice
- Manchester Academic Health Science Centre, University of Manchester, Genetic Medicine, Manchester, UK
| | - Yoandris Del Toro Duany
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Boston Children's Hospital, Boston, MA 02115, USA
| | - Emma M Jenkinson
- Manchester Academic Health Science Centre, University of Manchester, Genetic Medicine, Manchester, UK
| | - Gabriella Ma Forte
- Manchester Academic Health Science Centre, University of Manchester, Genetic Medicine, Manchester, UK
| | - Beverley H Anderson
- Manchester Academic Health Science Centre, University of Manchester, Genetic Medicine, Manchester, UK
| | - Giada Ariaudo
- Child Neurology and Psychiatry Unit, C. Mondino National Neurological Institute, Pavia, Italy.,Department of Brain and Behavioral Sciences, Unit of Child Neurology and Psychiatry, University of Pavia, Pavia, Italy
| | - Brigitte Bader-Meunier
- Department of pediatric Immunology and Rheumatology, INSERM U 768, Imagine Foundation, APHP, Hôpital Necker, Paris, France
| | - Eileen M Baildam
- Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris, Pisa, Italy
| | - Michael W Beresford
- Institute of Translational Medicine, University of Liverpool; Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Manuela Casarano
- Department of Developmental Neuroscience, IRCCS Stella Maris, Pisa, Italy
| | | | | | - Abigail E Collins
- Department of Pediatrics, Division of Pediatric Neurology, University of Colorado, Denver, School of Medicine, USA
| | - Nuno Jv Cordeiro
- Department of Paediatrics, Rainbow House NHS Ayrshire & Arran, Scotland, UK
| | - Russell C Dale
- Neuroimmunology group, the Children's Hospital at Westmead, University of Sydney, Australia
| | - Joyce E Davidson
- Department of Paediatric Rheumatology, Royal Hospital for Sick Children, Glasgow, UK
| | - Liesbeth De Waele
- Department of Development and Regeneration, KU Leuven, Paediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Isabelle Desguerre
- Department of pediatric Immunology and Rheumatology, INSERM U 768, Imagine Foundation, APHP, Hôpital Necker, Paris, France
| | - Laurence Faivre
- Centre de Génétique, Hôpital d'Enfants, CHU de Dijon et Université de Bourgogne, Dijon, France
| | - Elisa Fazzi
- Child Neurology and Psychiatry Unit. Civil Hospital. Department of Clinical and Experimental Sciences, University of Brescia, Italy
| | - Bertrand Isidor
- Service de Génétique Médicale, Inserm, CHU Nantes, UMR-S 957, Nantes, France
| | - Lieven Lagae
- Department of Development and Regeneration, KU Leuven, Paediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Andrew R Latchman
- Division of General Pediatrics, Department of Pediatrics, McMaster Children's Hospital, McMaster University, Hamilton, Canada
| | - Pierre Lebon
- Université et Faculté de Medecine Paris Descartes, Paris, France
| | - Chumei Li
- Department of Pediatrics, Clinical Genetics Program, McMaster Children's Hospital, McMaster University, Hamilton, Canada
| | - John H Livingston
- Department of Paediatric Neurology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | | | - Alice Masurel-Paulet
- Centre de Génétique, Hôpital d'Enfants, CHU de Dijon et Université de Bourgogne, Dijon, France
| | - Iain B McInnes
- Institute of Infection Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Manoj P Menezes
- Institute for Neuroscience and Muscle Research, the Children's Hospital at Westmead, University of Sydney, Australia
| | - Cyril Mignot
- AP-HP, Department of Genetics, Groupe Hospitalier Pitié Salpêtrière, F-75013, Paris, France
| | - James O'Sullivan
- Manchester Academic Health Science Centre, University of Manchester, Genetic Medicine, Manchester, UK
| | - Simona Orcesi
- Child Neurology and Psychiatry Unit, C. Mondino National Neurological Institute, Pavia, Italy
| | - Paolo P Picco
- Paediatric Rheumatology, Giannina Gaslini Institute, Genoa, Italy
| | - Enrica Riva
- Clinical Department of Pediatrics, San Paolo Hospital, University of Milan, Italy
| | - Robert A Robinson
- Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Diana Rodriguez
- AP-HP, Service de Neuropédiatrie & Centre de Référence de Neurogénétique, Hôpital A. Trousseau, HUEP, F-75012 Paris, France.,UPMC Univ Paris 06, F-75012 Paris; Inserm U676, F-75019 Paris, France
| | - Elisabetta Salvatici
- Clinical Department of Pediatrics, San Paolo Hospital, University of Milan, Italy
| | - Christiaan Scott
- University of Cape Town, Red Cross War Memorial Children's Hospital, Republic of South Africa
| | - Marta Szybowska
- Department of Pediatrics, Clinical Genetics Program, McMaster Children's Hospital, McMaster University, Hamilton, Canada
| | - John L Tolmie
- Department of Clinical Genetics, Southern General Hospital, Glasgow, Scotland, UK
| | - Adeline Vanderver
- Department of Paediatric Neurology, Children's National Medical Center, Washington DC, USA
| | - Catherine Vanhulle
- Service de Néonatalogie et Réanimation, Hôpital Charles Nicolle, CHU Rouen, F-76031 Rouen, France
| | - Jose Pedro Vieira
- Neurology Department. Hospital Dona Estefânia, Centro Hospitalar de Lisboa Central, Portugal
| | - Kate Webb
- University of Cape Town, Red Cross War Memorial Children's Hospital, Republic of South Africa
| | - Robyn N Whitney
- Division of Pediatric Neurology, Department of Pediatrics, McMaster Children's Hospital, McMaster University, Hamilton, Canada
| | - Simon G Williams
- Manchester Academic Health Science Centre, University of Manchester, Genetic Medicine, Manchester, UK
| | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, Fraser of Allander Neurosciences Unit, Royal Hospital for Sick Children, Glasgow, UK.,School of Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, UK
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Boston Children's Hospital, Boston, MA 02115, USA
| | - Yanick J Crow
- Manchester Academic Health Science Centre, University of Manchester, Genetic Medicine, Manchester, UK
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95
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Deddouche S, Goubau D, Rehwinkel J, Chakravarty P, Begum S, Maillard PV, Borg A, Matthews N, Feng Q, van Kuppeveld FJM, Reis e Sousa C. Identification of an LGP2-associated MDA5 agonist in picornavirus-infected cells. eLife 2014; 3:e01535. [PMID: 24550253 PMCID: PMC3967861 DOI: 10.7554/elife.01535] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/07/2014] [Indexed: 12/24/2022] Open
Abstract
The RIG-I-like receptors RIG-I, LGP2, and MDA5 initiate an antiviral response that includes production of type I interferons (IFNs). The nature of the RNAs that trigger MDA5 activation in infected cells remains unclear. Here, we purify and characterise LGP2/RNA complexes from cells infected with encephalomyocarditis virus (EMCV), a picornavirus detected by MDA5 and LGP2 but not RIG-I. We show that those complexes contain RNA that is highly enriched for MDA5-stimulatory activity and for a specific sequence corresponding to the L region of the EMCV antisense RNA. Synthesis of this sequence by in vitro transcription is sufficient to generate an MDA5 stimulatory RNA. Conversely, genomic deletion of the L region in EMCV generates viruses that are less potent at stimulating MDA5-dependent IFN production. Thus, the L region antisense RNA of EMCV is a key determinant of innate immunity to the virus and represents an RNA that activates MDA5 in virally-infected cells. DOI: http://dx.doi.org/10.7554/eLife.01535.001.
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MESH Headings
- Animals
- Antiviral Agents/pharmacology
- Chlorocebus aethiops
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Encephalomyocarditis virus/drug effects
- Encephalomyocarditis virus/genetics
- Encephalomyocarditis virus/immunology
- Encephalomyocarditis virus/metabolism
- Gene Expression Regulation, Viral
- HEK293 Cells
- HeLa Cells
- Host-Pathogen Interactions
- Humans
- Immunity, Innate
- Influenza A virus/genetics
- Influenza A virus/metabolism
- Interferon-Induced Helicase, IFIH1
- Interferons/genetics
- Interferons/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mutation
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptor, Interferon alpha-beta/deficiency
- Receptor, Interferon alpha-beta/genetics
- Signal Transduction
- Transfection
- Vero Cells
- Virus Replication
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Affiliation(s)
- Safia Deddouche
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Delphine Goubau
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Jan Rehwinkel
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Probir Chakravarty
- Bioinformatics Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Sharmin Begum
- Clonal Sequencing Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Pierre V Maillard
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Annabel Borg
- Protein Purification Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Nik Matthews
- Clonal Sequencing Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
| | - Qian Feng
- Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
| | - Caetano Reis e Sousa
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom
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96
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Luo D. Toward a crystal-clear view of the viral RNA sensing and response by RIG-I-like receptors. RNA Biol 2014; 11:25-32. [PMID: 24457940 DOI: 10.4161/rna.27717] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The RIG-I-like receptors (RLRs)--RIG-I, MDA5, and LGP2--detect intracellular pathogenic RNA and elicit an antiviral immune response during viral infection. The protein architecture of the RLR family consists of multiple functional domains, including N-terminal Caspase Activation and Recruitment Domains (CARDs) for signaling initiation, a central RNA helicase core, and a C-terminal domain for RNA sensing. With these specialized sensing-and-responding modules, RLRs are able to selectively bind non-self RNA species and trigger downstream signaling events leading to interferon production. This article summarizes the recent progress toward defining the precise mechanisms of RNA recognition and subsequent signal induction by RLRs.
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Affiliation(s)
- Dahai Luo
- Lee Kong Chian School of Medicine; Nanyang Technological University; Singapore
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97
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Fitzgerald ME, Vela A, Pyle AM. Dicer-related helicase 3 forms an obligate dimer for recognizing 22G-RNA. Nucleic Acids Res 2014; 42:3919-30. [PMID: 24435798 PMCID: PMC3973318 DOI: 10.1093/nar/gkt1383] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dicer is a specialized nuclease that produces RNA molecules of specific lengths for use in gene silencing pathways. Dicer relies on the correct measurement of RNA target duplexes to generate products of specific lengths. It is thought that Dicer uses its multidomain architecture to calibrate RNA product length. However, this measurement model is derived from structural information from a protozoan Dicer, and does not account for the helicase domain present in higher organisms. The Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) is an ortholog of the Dicer and RIG-I family of double-strand RNA activated ATPases essential for secondary siRNA production. We find that DRH-3 specifies 22 bp RNAs by dimerization of the helicase domain, a process mediated by ATPase activity and the N-terminal domain. This mechanism for RNA length discrimination by a Dicer family protein suggests an alternative model for RNA length measurement by Dicer, with implications for recognition of siRNA and miRNA targets.
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Affiliation(s)
- Megan E Fitzgerald
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA, Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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98
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Cooperative assembly of IFI16 filaments on dsDNA provides insights into host defense strategy. Proc Natl Acad Sci U S A 2013; 111:E62-71. [PMID: 24367117 DOI: 10.1073/pnas.1313577111] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whether host DNA receptors have any capacity to distinguish self from nonself at the molecular level is an outstanding question in the innate immunity of mammals. Here, by using quantitative assays and electron microscopy, we show that cooperatively assembling into filaments on dsDNA may serve as an integral mechanism by which human IFN-inducible protein-16 (IFI16) engages foreign DNA. IFI16 is essential for defense against a number of different pathogens, and its aberrant activity is also implicated in several autoimmune disorders, such as Sjögren syndrome. IFI16 cooperatively binds dsDNA in a length-dependent manner and clusters into distinct protein filaments even in the presence of excess dsDNA. Consequently, the assembled IFI16⋅dsDNA oligomers are clearly different from the conventional noninteracting entities resembling beads on a string. The isolated DNA-binding domains of IFI16 engage dsDNA without forming filaments and with weak affinity, and it is the non-DNA-binding pyrin domain of IFI16 that drives the cooperative filament assembly. The surface residues on the pyrin domain that mediate the cooperative DNA binding are conserved, suggesting that related receptors use a common mechanism. These results suggest that IFI16 clusters into signaling foci in a switch-like manner and that it is capable of using the size of naked dsDNA as a molecular ruler to distinguish self from nonself.
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99
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Rustagi A, Gale M. Innate antiviral immune signaling, viral evasion and modulation by HIV-1. J Mol Biol 2013; 426:1161-77. [PMID: 24326250 DOI: 10.1016/j.jmb.2013.12.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 02/08/2023]
Abstract
The intracellular innate antiviral response in human cells is an essential component of immunity against virus infection. As obligate intracellular parasites, all viruses must evade the actions of the host cell's innate immune response in order to replicate and persist. Innate immunity is induced when pathogen recognition receptors of the host cell sense viral products including nucleic acid as "non-self". This process induces downstream signaling through adaptor proteins to activate latent transcription factors that drive the expression of genes encoding antiviral and immune modulatory effector proteins that restrict virus replication and regulate adaptive immunity. The interferon regulatory factors (IRFs) are transcription factors that play major roles in innate immunity. In particular, IRF3 is activated in response to infection by a range of viruses including RNA viruses, DNA viruses and retroviruses. Among these viruses, human immunodeficiency virus type 1 (HIV-1) remains a major global health problem mediating chronic infection in millions of people wherein recent studies show that viral persistence is linked with the ability of the virus to dysregulate and evade the innate immune response. In this review, we discuss viral pathogen sensing, innate immune signaling pathways and effectors that respond to viral infection, the role of IRF3 in these processes and how it is regulated by pathogenic viruses. We present a contemporary overview of the interplay between HIV-1 and innate immunity, with a focus on understanding how innate immune control impacts infection outcome and disease.
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Affiliation(s)
- Arjun Rustagi
- Departments of Immunology and Global Health, University of Washington, Seattle, WA 98195-8059, USA
| | - Michael Gale
- Departments of Immunology and Global Health, University of Washington, Seattle, WA 98195-8059, USA.
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100
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Peisley A, Wu B, Yao H, Walz T, Hur S. RIG-I forms signaling-competent filaments in an ATP-dependent, ubiquitin-independent manner. Mol Cell 2013; 51:573-83. [PMID: 23993742 DOI: 10.1016/j.molcel.2013.07.024] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/27/2013] [Accepted: 07/25/2013] [Indexed: 12/24/2022]
Abstract
Retinoic acid-inducible gene 1 (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) are paralogous receptors for viral double-stranded RNA (dsRNA) with divergent specificity. We have previously shown that MDA5 forms filaments upon viral dsRNA recognition and that this filament formation is essential for interferon signal activation. Here, we show that while RIG-I binds to a dsRNA end as a monomer in the absence of ATP, it assembles in the presence of ATP into a filament that propagates from the dsRNA end to the interior. Furthermore, RIG-I filaments directly stimulate mitochondrial antiviral signaling (MAVS) filament formation without any cofactor, such as polyubiquitin chains, and forced juxtaposition of the isolated signaling domain of RIG-I, as it would be in the filament, is sufficient to activate interferon signaling. Our findings thus define filamentous architecture as a common yet versatile molecular platform for divergent viral RNA detection and proximity-induced signal activation by RIG-I and MDA5.
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Affiliation(s)
- Alys Peisley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115, USA
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