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Yu JH, Moon EY, Kim J, Koo JH. Identification of Small GTPases That Phosphorylate IRF3 through TBK1 Activation Using an Active Mutant Library Screen. Biomol Ther (Seoul) 2023; 31:48-58. [PMID: 36579460 PMCID: PMC9810446 DOI: 10.4062/biomolther.2022.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022] Open
Abstract
Interferon regulatory factor 3 (IRF3) integrates both immunological and non-immunological inputs to control cell survival and death. Small GTPases are versatile functional switches that lie on the very upstream in signal transduction pathways, of which duration of activation is very transient. The large number of homologous proteins and the requirement for site-directed mutagenesis have hindered attempts to investigate the link between small GTPases and IRF3. Here, we constructed a constitutively active mutant expression library for small GTPase expression using Gibson assembly cloning. Small-scale screening identified multiple GTPases capable of promoting IRF3 phosphorylation. Intriguingly, 27 of 152 GTPases, including ARF1, RHEB, RHEBL1, and RAN, were found to increase IRF3 phosphorylation. Unbiased screening enabled us to investigate the sequence-activity relationship between the GTPases and IRF3. We found that the regulation of IRF3 by small GTPases was dependent on TBK1. Our work reveals the significant contribution of GTPases in IRF3 signaling and the potential role of IRF3 in GTPase function, providing a novel therapeutic approach against diseases with GTPase overexpression or active mutations, such as cancer.
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Affiliation(s)
- Jae-Hyun Yu
- Department of Pharmacology and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea,College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Yi Moon
- Department of Bioscience and Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Jiyoon Kim
- Department of Pharmacology and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea,Corresponding Authors E-mail: (Kim J), (Koo JH), Tel: +82-2-3147-8358 (Kim J), +82-2-880-7839 (Koo JH), Fax: +82-2-536-2485 (Kim J), +82-2-888-9122 (Koo JH)
| | - Ja Hyun Koo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea,Corresponding Authors E-mail: (Kim J), (Koo JH), Tel: +82-2-3147-8358 (Kim J), +82-2-880-7839 (Koo JH), Fax: +82-2-536-2485 (Kim J), +82-2-888-9122 (Koo JH)
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2
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Baesjou JP, Wellenreuther M. Genomic Signatures of Domestication Selection in the Australasian Snapper ( Chrysophrys auratus). Genes (Basel) 2021; 12:1737. [PMID: 34828341 PMCID: PMC8623400 DOI: 10.3390/genes12111737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 10/26/2021] [Indexed: 01/10/2023] Open
Abstract
Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of FST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations FST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.
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Affiliation(s)
- Jean-Paul Baesjou
- The New Zealand Institute for Plant and Food Research Ltd., 1025 Auckland, New Zealand;
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd., 7010 Nelson, New Zealand
- School of Biological Sciences, University of Auckland, 1010 Auckland, New Zealand
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3
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Vargová R, Wideman JG, Derelle R, Klimeš V, Kahn RA, Dacks JB, Eliáš M. A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family. Genome Biol Evol 2021; 13:6319025. [PMID: 34247240 PMCID: PMC8358228 DOI: 10.1093/gbe/evab157] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.
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Affiliation(s)
- Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Romain Derelle
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, United Kingdom
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
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4
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Chan TW, Fu T, Bahn JH, Jun HI, Lee JH, Quinones-Valdez G, Cheng C, Xiao X. RNA editing in cancer impacts mRNA abundance in immune response pathways. Genome Biol 2020; 21:268. [PMID: 33106178 PMCID: PMC7586670 DOI: 10.1186/s13059-020-02171-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND RNA editing generates modifications to the RNA sequences, thereby increasing protein diversity and shaping various layers of gene regulation. Recent studies have revealed global shifts in editing levels across many cancer types, as well as a few specific mechanisms implicating individual sites in tumorigenesis or metastasis. However, most tumor-associated sites, predominantly in noncoding regions, have unknown functional relevance. RESULTS Here, we carry out integrative analysis of RNA editing profiles between epithelial and mesenchymal tumors, since epithelial-mesenchymal transition is a key paradigm for metastasis. We identify distinct editing patterns between epithelial and mesenchymal tumors in seven cancer types using TCGA data, an observation further supported by single-cell RNA sequencing data and ADAR perturbation experiments in cell culture. Through computational analyses and experimental validations, we show that differential editing sites between epithelial and mesenchymal phenotypes function by regulating mRNA abundance of their respective genes. Our analysis of RNA-binding proteins reveals ILF3 as a potential regulator of this process, supported by experimental validations. Consistent with the known roles of ILF3 in immune response, epithelial-mesenchymal differential editing sites are enriched in genes involved in immune and viral processes. The strongest target of editing-dependent ILF3 regulation is the transcript encoding PKR, a crucial player in immune and viral response. CONCLUSIONS Our study reports widespread differences in RNA editing between epithelial and mesenchymal tumors and a novel mechanism of editing-dependent regulation of mRNA abundance. It reveals the broad impact of RNA editing in cancer and its relevance to cancer-related immune pathways.
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Affiliation(s)
- Tracey W Chan
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Ting Fu
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, USA
| | - Hyun-Ik Jun
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, USA
| | - Jae-Hyung Lee
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, USA
- Department of Life and Nanopharmaceutical Sciences & Oral Microbiology, School of Dentistry, Kyung Hee University, Seoul, South Korea
| | | | - Chonghui Cheng
- Lester & Sue Smith Breast Center & Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA.
- Molecular, Cellular and Integrative Physiology Interdepartmental Program, UCLA, Los Angeles, CA, USA.
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
- Institute for Quantitative and Computational Sciences, UCLA, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
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5
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Yang Q, Bai SY, Li LF, Li S, Zhang Y, Munir M, Qiu HJ. Human Hemoglobin Subunit Beta Functions as a Pleiotropic Regulator of RIG-I/MDA5-Mediated Antiviral Innate Immune Responses. J Virol 2019; 93:e00718-19. [PMID: 31167908 PMCID: PMC6675906 DOI: 10.1128/jvi.00718-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 05/20/2019] [Indexed: 12/28/2022] Open
Abstract
Hemoglobin is an important oxygen-carrying protein and plays crucial roles in establishing host resistance against pathogens and in regulating innate immune responses. The hemoglobin subunit beta (HB) is an essential component of hemoglobin, and we have previously demonstrated that the antiviral role of the porcine HB (pHB) is mediated by promoting type I interferon pathways. Thus, considering the high homology between human HB (hHB) and pHB, we hypothesized that hHB also plays an important role in the antiviral innate immunity. In this study, we characterized hHB as a regulatory factor for the replication of RNA viruses by differentially regulating the RIG-I- and MDA5-mediated antiviral signaling pathways. Furthermore, we showed that hHB directly inhibited MDA5-mediated signaling by reducing the MDA5-double-stranded RNA (dsRNA) interaction. Additionally, hHB required hHB-induced reactive oxygen species (ROS) to promote RIG-I-mediated signaling through enhancement of K63-linked RIG-I ubiquitination. Taken together, our findings suggest that hHB is a pleiotropic regulator of RIG-I/MDA5-mediated antiviral responses and further highlight the importance of the intercellular microenvironment, including the redox state, in regulating antiviral innate immune responses.IMPORTANCE Hemoglobin, the most important oxygen-carrying protein, is involved in the regulation of innate immune responses. We have previously reported that the porcine hemoglobin subunit beta (HB) exerts antiviral activity through regulation of type I interferon production. However, the antiviral activities and the underlying mechanisms of HBs originating from other animals have been poorly understood. Here, we identified human HB (hHB) as a pleiotropic regulator of the replication of RNA viruses through regulation of RIG-I/MDA5-mediated signaling pathways. hHB enhances RIG-I-mediated antiviral responses by promoting RIG-I ubiquitination depending on the hHB-induced reactive oxygen species (ROS), while it blocks MDA5-mediated antiviral signaling by suppressing the MDA5-dsRNA interaction. Our results contribute to an understanding of the crucial roles of hHB in the regulation of the RIG-I/MDA5-mediated signaling pathways. We also provide novel insight into the correlation of the intercellular redox state with the regulation of antiviral innate immunity.
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Affiliation(s)
- Qian Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Si-Yu Bai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lian-Feng Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Su Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuexiu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, United Kingdom
| | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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6
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Brisse M, Ly H. Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5. Front Immunol 2019; 10:1586. [PMID: 31379819 PMCID: PMC6652118 DOI: 10.3389/fimmu.2019.01586] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. While RIG-I and MDA5 share many genetic, structural and functional similarities, there is increasing evidence that they can have significantly different strategies to recognize different pathogens, PAMPs, and in different host species. This review article discusses the similarities and differences between RIG-I and MDA5 from multiple perspectives, including their structures, evolution and functional relationships with other cellular proteins, their differential mechanisms of distinguishing between host and viral dsRNAs and interactions with host and viral protein factors, and their immunogenic signaling. A comprehensive comparative analysis can help inform future studies of RIG-I and MDA5 in order to fully understand their functions in order to optimize potential therapeutic approaches targeting them.
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Affiliation(s)
- Morgan Brisse
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Twin Cities, St. Paul, MN, United States
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
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7
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Browne JA, Leir SH, Eggener SE, Harris A. Region-specific innate antiviral responses of the human epididymis. Mol Cell Endocrinol 2018; 473:72-78. [PMID: 29339104 PMCID: PMC6045438 DOI: 10.1016/j.mce.2018.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 01/08/2018] [Accepted: 01/08/2018] [Indexed: 12/27/2022]
Abstract
Viral infections of the epididymis are associated with epididymitis, which damages the epithelium and impairs fertility. We showed previously that innate immune response genes were differentially expressed in the corpus and cauda region of the human epididymis in comparison to the caput. Here we investigate the antiviral defense response mechanisms of human epididymis epithelial (HEE) cells. Toll-like receptor (TLR) 3 and retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are enriched in HEE cells from the corpus and cauda region. These HEE cells show an enhanced response to antiviral ligands (poly(I:C) and HSV-60), as shown by increased IFN-β mRNA expression and IFN-β secretion. Nuclear translocation of phosphorylated p65 occurs after poly(I:C) exposure. In addition, paired box 2 (PAX2), which was implicated in regulating antiviral response pathways, is required for basal expression of the DNA sensor, Z-DNA binding protein (ZBP1) and type I interferon, in caput but not in cauda cells.
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Affiliation(s)
- James A Browne
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Scott E Eggener
- Section of Urology, University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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8
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Quicke KM, Diamond MS, Suthar MS. Negative regulators of the RIG-I-like receptor signaling pathway. Eur J Immunol 2017; 47:615-628. [PMID: 28295214 DOI: 10.1002/eji.201646484] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/18/2017] [Accepted: 03/01/2017] [Indexed: 12/13/2022]
Abstract
Upon recognition of specific molecular patterns on microbes, host cells trigger an innate immune response, which culminates in the production of type I interferons, proinflammatory cytokines and chemokines, and restricts pathogen replication and spread within the host. At each stage of this response, there are stimulatory and inhibitory signals that regulate the magnitude, quality, and character of the response. Positive regulation promotes an antiviral state to control and eventually clear infection, whereas negative regulation dampens inflammation and prevents immune-mediated tissue damage. An overexuberant innate response can lead to cell and tissue destruction, and the development of spontaneous autoimmunity. The retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), RIG-I and melanoma differentiation-associated gene 5 (MDA5), belong to a family of cytosolic host RNA helicases that recognize distinct nonself RNA signatures and trigger innate immune responses against several RNA viruses by signaling through the essential adaptor protein mitochondrial antiviral signaling (MAVS). The RLR signaling pathway is tightly regulated to maximize antiviral immunity and minimize immune-mediated pathology. This review highlights contemporary findings on negative regulators of the RLR signaling pathway, with specific focus on the proteins and biological processes that directly regulate RIG-I, MDA5 and MAVS signaling function.
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Affiliation(s)
- Kendra M Quicke
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.,Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Mehul S Suthar
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.,Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
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9
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Kim N, Now H, Nguyen NTH, Yoo JY. Multilayered regulations of RIG-I in the anti-viral signaling pathway. J Microbiol 2016; 54:583-587. [PMID: 27572506 DOI: 10.1007/s12275-016-6322-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 10/21/2022]
Abstract
RIG-I is a cytosolic receptor recognizing virus-specific RNA structures and initiates an antiviral signaling that induces the production of interferons and proinflammatory cytokines. Because inappropriate RIG-I signaling affects either viral clearance or immune toxicity, multiple regulations of RIG-I have been investigated since its discovery as the viral RNA detector. In this review, we describe the recent progress in research on the regulation of RIG-I activity or abundance. Specifically, we focus on the mechanism that modulates RIG-I-dependent antiviral response through post-translational modifications of or protein-protein interactions with RIG-I.
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Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.
| | - Hesung Now
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Nhung T H Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.
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10
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Wang S, Yang YK, Chen T, Zhang H, Yang WW, Song SS, Zhai ZH, Chen DY. RNF123 has an E3 ligase-independent function in RIG-I-like receptor-mediated antiviral signaling. EMBO Rep 2016; 17:1155-68. [PMID: 27312109 PMCID: PMC4967948 DOI: 10.15252/embr.201541703] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 05/09/2016] [Accepted: 05/19/2016] [Indexed: 12/21/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are cytoplasmic sensors crucial for recognizing different species of viral RNAs, which triggers the production of type I interferons (IFNs) and inflammatory cytokines. Here, we identify RING finger protein 123 (RNF123) as a negative regulator of RIG-I and MDA5. Overexpression of RNF123 inhibits IFN-β production triggered by Sendai virus (SeV) and encephalomyocarditis picornavirus (EMCV). Knockdown or knockout of endogenous RNF123 potentiates IFN-β production triggered by SeV and EMCV, but not by the sensor of DNA viruses cGAS RNF123 associates with RIG-I and MDA5 in both endogenous and exogenous cases in a viral infection-inducible manner. The SPRY and coiled-coil, but not the RING, domains of RNF123 are required for the inhibitory function. RNF123 interacts with the N-terminal CARD domains of RIG-I/MDA5 and competes with the downstream adaptor VISA/MAVS/IPS-1/Cardif for RIG-I/MDA5 CARD binding. These findings suggest that RNF123 functions as a novel inhibitor of innate antiviral signaling mediated by RIG-I and MDA5, a function that does not depend on its E3 ligase activity.
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Affiliation(s)
- Shuai Wang
- Key Laboratory of Cell Proliferation and Differentiation of The Ministry of Education, School of Life Sciences, Peking University, Beijing, China
| | - Yong-Kang Yang
- Key Laboratory of Cell Proliferation and Differentiation of The Ministry of Education, School of Life Sciences, Peking University, Beijing, China
| | - Tao Chen
- Key Laboratory of Cell Proliferation and Differentiation of The Ministry of Education, School of Life Sciences, Peking University, Beijing, China
| | - Heng Zhang
- Key Laboratory of Cell Proliferation and Differentiation of The Ministry of Education, School of Life Sciences, Peking University, Beijing, China
| | - Wei-Wei Yang
- Key Laboratory of Cell Proliferation and Differentiation of The Ministry of Education, School of Life Sciences, Peking University, Beijing, China
| | - Sheng-Sheng Song
- Key Laboratory of Cell Proliferation and Differentiation of The Ministry of Education, School of Life Sciences, Peking University, Beijing, China
| | - Zhong-He Zhai
- Key Laboratory of Cell Proliferation and Differentiation of The Ministry of Education, School of Life Sciences, Peking University, Beijing, China
| | - Dan-Ying Chen
- Key Laboratory of Cell Proliferation and Differentiation of The Ministry of Education, School of Life Sciences, Peking University, Beijing, China
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11
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Kitai Y, Takeuchi O, Kawasaki T, Ori D, Sueyoshi T, Murase M, Akira S, Kawai T. Negative regulation of melanoma differentiation-associated gene 5 (MDA5)-dependent antiviral innate immune responses by Arf-like protein 5B. J Biol Chem 2015; 290:1269-80. [PMID: 25451939 PMCID: PMC4294491 DOI: 10.1074/jbc.m114.611053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 11/14/2014] [Indexed: 11/06/2022] Open
Abstract
RIG-I-like receptors (RLRs), including retinoic acid-inducible gene-I (RIG-I) and MDA5, constitute a family of cytoplasmic RNA helicases that senses viral RNA and mounts antiviral innate immunity by producing type I interferons and inflammatory cytokines. Despite their essential roles in antiviral host defense, RLR signaling is negatively regulated to protect the host from excessive inflammation and autoimmunity. Here, we identified ADP-ribosylation factor-like protein 5B (Arl5B), an Arl family small GTPase, as a regulator of RLR signaling through MDA5 but not RIG-I. Overexpression of Arl5B repressed interferon β promoter activation by MDA5 but not RIG-I, and its knockdown enhanced MDA5-mediated responses. Furthermore, Arl5B-deficient mouse embryonic fibroblast cells exhibited increased type I interferon expression in response to MDA5 agonists such as poly(I:C) and encephalomyocarditis virus. Arl5B-mediated negative regulation of MDA5 signaling does not require its GTP binding ability but requires Arl5B binding to the C-terminal domain of MDA5, which prevents interaction between MDA5 and poly(I:C). Our results, therefore, suggest that Arl5B is a negative regulator for MDA5.
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Affiliation(s)
- Yuichi Kitai
- From the Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan, the Laboratory of Host Defense, Immunology Frontier Research Center (IFReC) and Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan, and
| | - Osamu Takeuchi
- the Laboratory of Infection and Prevention, Institute for Virus Research, Kyoto University, 53 Shogoin Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takumi Kawasaki
- From the Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Daisuke Ori
- the Laboratory of Infection and Prevention, Institute for Virus Research, Kyoto University, 53 Shogoin Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takuya Sueyoshi
- From the Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Motoya Murase
- From the Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Shizuo Akira
- the Laboratory of Host Defense, Immunology Frontier Research Center (IFReC) and Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan, and
| | - Taro Kawai
- From the Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan,
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12
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Abstract
The ARF-like (ARL) proteins, within the ARF family, are a collection of functionally diverse GTPases that share extensive (>40 %) identity with the ARFs and each other and are assumed to share basic mechanisms of regulation and a very incompletely documented degree of overlapping regulators. At least four ARLs were already present in the last eukaryotic common ancestor, along with one ARF, and these have been expanded to >20 members in mammals. We know little about the majority of these proteins so our review will focus on those about which the most is known, including ARL1, ARL2, ARL3, ARL4s, ARL6, ARL13s, and ARFRP1. From this fragmentary information we extract some generalizations and conclusions regarding the sources and extent of specificity and functions of the ARLs.
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Affiliation(s)
- Alfred Wittinghofer
- Max-Planck-Institute of Molecular Physiology, Dortmund, Nordrhein-Westfalen Germany
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13
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Li MT, Di W, Xu H, Yang YK, Chen HW, Zhang FX, Zhai ZH, Chen DY. Negative regulation of RIG-I-mediated innate antiviral signaling by SEC14L1. J Virol 2013; 87:10037-46. [PMID: 23843640 PMCID: PMC3754010 DOI: 10.1128/jvi.01073-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/26/2013] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) is a key sensor for recognizing nucleic acids derived from RNA viruses and triggers beta interferon (IFN-β) production. Because of its important role in antiviral innate immunity, the activity of RIG-I must be tightly controlled. Here, we used yeast two-hybrid screening to identify a SEC14 family member, SEC14L1, as a RIG-I-associated negative regulator. Transfected SEC14L1 interacted with RIG-I, and endogenous SEC14L1 associated with RIG-I in a viral infection-inducible manner. Overexpression of SEC14L1 inhibited transcriptional activity of the IFN-β promoter induced by RIG-I but not TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3). Knockdown of endogenous SEC14L1 in both HEK293T cells and HT1080 cells potentiated RIG-I and Sendai virus-triggered IFN-β production as well as attenuated the replication of Newcastle disease virus. SEC14L1 interacted with the N-terminal domain of RIG-I (RIG-I caspase activation and recruitment domain [RIG-I-CARD]) and competed with VISA/MAVS/IPS-1/Cardif for RIG-I-CARD binding. Domain mapping further indicated that the PRELI-MSF1 and CRAL-TRIO domains but not the GOLD domain of SEC14L1 are required for interaction and inhibitory function. These findings suggest that SEC14L1 functions as a novel negative regulator of RIG-I-mediated antiviral signaling by preventing RIG-I interaction with the downstream effector.
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Affiliation(s)
- Meng-Tong Li
- The Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Wei Di
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Hao Xu
- The Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Yong-Kang Yang
- The Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Hai-Wei Chen
- The Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Fei-Xiong Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhong-He Zhai
- The Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Dan-Ying Chen
- The Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
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14
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Wang J, Yang B, Hu Y, Zheng Y, Zhou H, Wang Y, Ma Y, Mao K, Yang L, Lin G, Ji Y, Wu X, Sun B. Negative regulation of Nmi on virus-triggered type I IFN production by targeting IRF7. THE JOURNAL OF IMMUNOLOGY 2013; 191:3393-9. [PMID: 23956435 DOI: 10.4049/jimmunol.1300740] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Viral infection causes host cells to produce type I IFNs, which play a critical role in viral clearance. IFN regulatory factor (IRF) 7 is the master regulator of type I IFN-dependent immune responses. In this article, we report that N-Myc and STATs interactor (Nmi), a Sendai virus-inducible protein, interacted with IRF7 and inhibited virus-triggered type I IFN production. The overexpression of Nmi inhibited the Sendai virus-triggered induction of type I IFNs, whereas the knockdown of Nmi promoted IFN production. Furthermore, the enhanced production of IFNs resulting from Nmi knockdown was sufficient to protect cells from infection by vesicular stomatitis virus. In addition, Nmi was found to promote the K48-linked ubiquitination of IRF7 and the proteasome-dependent degradation of this protein. Finally, an impairment of antiviral responses is also detectable in Nmi-transgenic mice. These findings suggest that Nmi is a negative regulator of the virus-triggered induction of type I IFNs that targets IRF7.
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Affiliation(s)
- Jie Wang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
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15
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Wang L, Zhao W, Zhang M, Wang P, Zhao K, Zhao X, Yang S, Gao C. USP4 positively regulates RIG-I-mediated antiviral response through deubiquitination and stabilization of RIG-I. J Virol 2013; 87:4507-15. [PMID: 23388719 PMCID: PMC3624380 DOI: 10.1128/jvi.00031-13] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 01/30/2013] [Indexed: 12/22/2022] Open
Abstract
Protein ubiquitination plays an essential role in the regulation of retinoic acid-inducible gene I (RIG-I) activation and the antiviral immune response. However, the function of the opposite process of deubiquitination in RIG-I activation remains elusive. In this study, we have identified the deubiquitinating enzyme ubiquitin-specific protease 4 (USP4) as a new regulator for RIG-I activation through deubiquitination and stabilization of RIG-I. USP4 expression was attenuated after virus-induced RIG-I activation. Overexpression of USP4 significantly enhanced RIG-I protein expression and RIG-I-triggered beta interferon (IFN-β) signaling and, at the same time, inhibited vesicular stomatitis virus (VSV) replication. Small interfering RNA (siRNA) knockdown of USP4 expression had an opposite effect. Furthermore, USP4 was found to interact with RIG-I and remove K48-linked polyubiquitination chains from RIG-I. Therefore, we identified USP4 as a new positive regulator for RIG-I that acts through deubiquitinating K48-linked ubiquitin chains and stabilizing RIG-I.
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Affiliation(s)
- Lijuan Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education & Department of Immunology, Shandong University School of Medicine, Jinan, Shandong, China
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16
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Chen H, Li Y, Zhang J, Ran Y, Wei J, Yang Y, Shu HB. RAVER1 is a coactivator of MDA5-mediated cellular antiviral response. J Mol Cell Biol 2013; 5:111-9. [PMID: 23390309 DOI: 10.1093/jmcb/mjt006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Detection of viral nucleic acids by pattern recognition receptors initiates type I interferon (IFN) induction and innate antiviral response. The RIG-I-like receptors (RLRs), including RIG-I and MDA5, recognize cytoplasmic viral RNA in most cell types and are critically involved in innate antiviral response. RIG-I and MDA5 are structurally related and mediate similar signaling pathways. While the regulation of RIG-I activity has been extensively investigated, little is known about the regulatory mechanisms of MDA5 activity. Here we identified ribonucleoprotein PTB-binding 1 (RAVER1) as a specific MDA5-interacting protein. RAVER1 was associated with MDA5 upon viral infection. Overexpression of RAVER1 at low dosages enhanced MDA5- but not RIG-I-mediated activation of the IFN-β promoter, whereas knockdown of RAVER1 inhibited MDA5- but not RIG-I-mediated induction of downstream antiviral genes. Mechanistically, overexpression of RAVER1 enhanced the binding of MDA5 to its ligand poly(I:C), whereas knockdown of RAVER1 had opposite effect. Our findings suggest that RAVER1 specifically regulates MDA5 activity, revealing a mechanism of differential regulation of MDA5- and RIG-I-mediated innate antiviral response.
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Affiliation(s)
- He Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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17
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Sin WX, Li P, Yeong JPS, Chin KC. Activation and regulation of interferon-β in immune responses. Immunol Res 2012; 53:25-40. [PMID: 22411096 DOI: 10.1007/s12026-012-8293-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Interferons (IFNs) were discovered more than half a century ago, and extensive research has since identified multifarious roles for type I IFN in human immune responses. Here, we review the functions of IFN-β in innate and adaptive immunity. We also discuss the activation and influence of IFN-β on myeloid cell types, including monocytes and dendritic cells, as well as address the effects of IFN-β on T cells and B cells. Findings from our own laboratory, which explores the molecular mechanisms of IFN-β activation by LPS and viruses, as well as from other groups investigating the regulation of IFN-β by viral proteins and endogenous factors are described. The effects of post-translational modifications of the interferon regulatory factor (IRF)-3 on IFN-β induction are also highlighted. Many unanswered questions remain concerning the regulation of the type I IFN response in inflammation, especially the role of transcription factors in the modulation of inflammatory gene expression, and these questions will form the basis for exciting avenues of future research.
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Affiliation(s)
- Wei-Xiang Sin
- Laboratory of Gene Regulation and Inflammation, Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #04 Immunos, Biopolis, Singapore
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18
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Gerlier D, Lyles DS. Interplay between innate immunity and negative-strand RNA viruses: towards a rational model. Microbiol Mol Biol Rev 2011; 75:468-90, second page of table of contents. [PMID: 21885681 PMCID: PMC3165544 DOI: 10.1128/mmbr.00007-11] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The discovery of a new class of cytosolic receptors recognizing viral RNA, called the RIG-like receptors (RLRs), has revolutionized our understanding of the interplay between viruses and host cells. A tremendous amount of work has been accumulating to decipher the RNA moieties required for an RLR agonist, the signal transduction pathway leading to activation of the innate immunity orchestrated by type I interferon (IFN), the cellular and viral regulators of this pathway, and the viral inhibitors of the innate immune response. Previous reviews have focused on the RLR signaling pathway and on the negative regulation of the interferon response by viral proteins. The focus of this review is to put this knowledge in the context of the virus replication cycle within a cell. Likewise, there has been an expansion of knowledge about the role of innate immunity in the pathophysiology of viral infection. As a consequence, some discrepancies have arisen between the current models of cell-intrinsic innate immunity and current knowledge of virus biology. This holds particularly true for the nonsegmented negative-strand viruses (Mononegavirales), which paradoxically have been largely used to build presently available models. The aim of this review is to bridge the gap between the virology and innate immunity to favor the rational building of a relevant model(s) describing the interplay between Mononegavirales and the innate immune system.
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Affiliation(s)
- Denis Gerlier
- INSERM U758, CERVI, 21 avenue Tony Garnier, 69007 Lyon, France.
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