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Jin K, Dai Y, Ouyang K, Huang H, Jiang Z, Yang Z, Zhou T, Lin H, Wang C, Wang C, Sun X, Lu D, Liu X, Hu N, Zhu C, Zhu J, Li J. TRIM3 attenuates cytokine storm caused by Dabie bandavirus via promoting Toll-like receptor 3 degradation. Front Microbiol 2023; 14:1209870. [PMID: 37520369 PMCID: PMC10375709 DOI: 10.3389/fmicb.2023.1209870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease that was caused by the Dabie bandavirus (DBV), and it has become a global public health threat. Cytokine storm is considered to be an important pathogenesis of critical SFTS. Tripartite motif-containing 3 (TRIM3), as a member of the TRIM protein family, may contribute to the regulation of the immune and inflammatory responses after viral infection. However, whether TRIM3 plays a major role in the pathogenesis of SFTS has not yet been investigated. Methods TRIM3 mRNA levels were detected in PBMCs between 29 SFTS patients and 29 healthy controls by qRT-PCR. We established the pathogenic IFNAR-/- SFTS mouse model successfully by inoculating subcutaneously with DBV and testing the expression levels of TRIM3 mRNA and protein by qRT-PCR and immunofluorescence in the livers, spleens, lungs, and kidneys. TRIM3OE THP-1 cells and peritoneal macrophages extracted from TRIM3-/- mice were infected with DBV. The effect of TRIM3 on cytokines was detected by qRT-PCR and ELISA. Then we examined Toll-like receptor 3 (TLR3) and protein phosphorylation in the MAPK pathway after DBV infection using Western blot. Flow cytometry was used to verify TLR3 expression on peripheral blood monocytes in SFTS patients. We further explored the interaction between TRIM3 and TLR3 using CO-IP and Western blot. Results Compared to healthy controls, TRIM3 mRNA expression in PBMCs is decreased in SFTS patients, especially in severe cases. TRIM3 mRNA and protein were synchronously reduced in the livers, spleens, lungs, and kidney tissues of the IFNAR-/- SFTS mice model. In the DBV-infected cell model, TRIM3 overexpression can inhibit the DBV-induced release of IL-1β, IL-6, and TNF-α, the expression of TLR3, and protein phosphorylation in the MAPK pathway, which plays an anti-inflammatory role, while TRIM3 deficiency exacerbates the pro-inflammatory effects. We further found that TRIM3 can promote TLR3 degradation through K48-linked ubiquitination. Conclusion TRIM3 can inhibit the production of cytokines by regulating the degradation of TLR3 through K48-linked ubiquitination, which can be a therapeutic target for improving the prognosis of SFTS.
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Affiliation(s)
- Ke Jin
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Dai
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ke Ouyang
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huaying Huang
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhengyi Jiang
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhan Yang
- Epidemiological Department, Huadong Medical Institute of Biotechniques, Nanjing, China
| | - Tingting Zhou
- Epidemiological Department, Huadong Medical Institute of Biotechniques, Nanjing, China
| | - Hong Lin
- Department of Transfusion Research, Jiangsu Province Blood Center, Nanjing, China
| | - Chunhui Wang
- Epidemiological Department, Huadong Medical Institute of Biotechniques, Nanjing, China
| | - Chunyan Wang
- Epidemiological Department, Huadong Medical Institute of Biotechniques, Nanjing, China
| | - Xuewei Sun
- School of Basic Medicine, Binzhou Medical University, Yantai, China
| | - Dafeng Lu
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaoguang Liu
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Nannan Hu
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chuanlong Zhu
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jin Zhu
- Epidemiological Department, Huadong Medical Institute of Biotechniques, Nanjing, China
| | - Jun Li
- Department of Infectious Disease, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Li Z, Zheng M, He Z, Qin Y, Chen M. Morphogenesis and functional organization of viral inclusion bodies. CELL INSIGHT 2023; 2:100103. [PMID: 37193093 PMCID: PMC10164783 DOI: 10.1016/j.cellin.2023.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/18/2023]
Abstract
Eukaryotic viruses are obligate intracellular parasites that rely on the host cell machinery to carry out their replication cycle. This complex process involves a series of steps, starting with virus entry, followed by genome replication, and ending with virion assembly and release. Negative strand RNA and some DNA viruses have evolved to alter the organization of the host cell interior to create a specialized environment for genome replication, known as IBs, which are precisely orchestrated to ensure efficient viral replication. The biogenesis of IBs requires the cooperation of both viral and host factors. These structures serve multiple functions during infection, including sequestering viral nucleic acids and proteins from innate immune responses, increasing the local concentration of viral and host factors, and spatially coordinating consecutive replication cycle steps. While ultrastructural and functional studies have improved our understanding of IBs, much remains to be learned about the precise mechanisms of IB formation and function. This review aims to summarize the current understanding of how IBs are formed, describe the morphology of these structures, and highlight the mechanism of their functions. Given that the formation of IBs involves complex interactions between the virus and the host cell, the role of both viral and cellular organelles in this process is also discussed.
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Affiliation(s)
- Zhifei Li
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
| | - Miaomiao Zheng
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
| | - Zhicheng He
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, 430200, China
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Forsberg KJ. Anti-CRISPR Discovery: Using Magnets to Find Needles in Haystacks. J Mol Biol 2023; 435:167952. [PMID: 36638909 PMCID: PMC10073268 DOI: 10.1016/j.jmb.2023.167952] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
CRISPR-Cas immune systems in bacteria and archaea protect against viral infection, which has spurred viruses to develop dedicated inhibitors of these systems called anti-CRISPRs (Acrs). Like most host-virus arms races, many diverse examples of these immune and counter-immune proteins are encoded by the genomes of bacteria, archaea, and their viruses. For the case of Acrs, it is almost certain that just a small minority of nature's true diversity has been described. In this review, I discuss the various approaches used to identify these Acrs and speculate on the future for Acr discovery. Because Acrs can determine infection outcomes in nature and regulate CRISPR-Cas activities in applied settings, they have a dual importance to both host-virus conflicts and emerging biotechnologies. Thus, revealing the largely hidden world of Acrs should provide important lessons in microbiology that have the potential to ripple far beyond the field.
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Affiliation(s)
- Kevin J Forsberg
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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4
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Potential health risks of mRNA-based vaccine therapy: A hypothesis. Med Hypotheses 2023; 171:111015. [PMID: 36718314 PMCID: PMC9876036 DOI: 10.1016/j.mehy.2023.111015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/08/2022] [Accepted: 01/24/2023] [Indexed: 01/26/2023]
Abstract
Therapeutic applications of synthetic mRNA were proposed more than 30 years ago, and are currently the basis of one of the vaccine platforms used at a massive scale as part of the public health strategy to get COVID-19 under control. To date, there are no published studies on the biodistribution, cellular uptake, endosomal escape, translation rates, functional half-life and inactivation kinetics of synthetic mRNA, rates and duration of vaccine-induced antigen expression in different cell types. Furthermore, despite the assumption that there is no possibility of genomic integration of therapeutic synthetic mRNA, only one recent study has examined interactions between vaccine mRNA and the genome of transfected cells, and reported that an endogenous retrotransposon, LINE-1 is unsilenced following mRNA entry to the cell, leading to reverse transcription of full length vaccine mRNA sequences, and nuclear entry. This finding should be a major safety concern, given the possibility of synthetic mRNA-driven epigenetic and genomic modifications arising. We propose that in susceptible individuals, cytosolic clearance of nucleotide modified synthetic (nms-mRNAs) is impeded. Sustained presence of nms-mRNA in the cytoplasm deregulates and activates endogenous transposable elements (TEs), causing some of the mRNA copies to be reverse transcribed. The cytosolic accumulation of the nms-mRNA and the reverse transcribed cDNA molecules activates RNA and DNA sensory pathways. Their concurrent activation initiates a synchronized innate response against non-self nucleic acids, prompting type-I interferon and pro-inflammatory cytokine production which, if unregulated, leads to autoinflammatory and autoimmune conditions, while activated TEs increase the risk of insertional mutagenesis of the reverse transcribed molecules, which can disrupt coding regions, enhance the risk of mutations in tumour suppressor genes, and lead to sustained DNA damage. Susceptible individuals would then expectedly have an increased risk of DNA damage, chronic autoinflammation, autoimmunity and cancer. In light of the current mass administration of nms-mRNA vaccines, it is essential and urgent to fully understand the intracellular cascades initiated by cellular uptake of synthetic mRNA and the consequences of these molecular events.
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Wen Y, Ma J. Phase separation drives the formation of biomolecular condensates in the immune system. Front Immunol 2022; 13:986589. [PMID: 36439121 PMCID: PMC9685520 DOI: 10.3389/fimmu.2022.986589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/19/2022] [Indexed: 08/12/2023] Open
Abstract
When the external conditions change, such as the temperature or the pressure, the multi-component system sometimes separates into several phases with different components and structures, which is called phase separation. Increasing studies have shown that cells condense related biomolecules into independent compartments in order to carry out orderly and efficient biological reactions with the help of phase separation. Biomolecular condensates formed by phase separation play a significant role in a variety of cellular processes, including the control of signal transduction, the regulation of gene expression, and the stress response. In recent years, many phase separation events have been discovered in the immune response process. In this review, we provided a comprehensive and detailed overview of the role and mechanism of phase separation in the innate and adaptive immune responses, which will help the readers to appreciate the advance and importance of this field.
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Affiliation(s)
- Yuqing Wen
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
| | - Jian Ma
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, China
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Wu C, Holehouse AS, Leung DW, Amarasinghe GK, Dutch RE. Liquid Phase Partitioning in Virus Replication: Observations and Opportunities. Annu Rev Virol 2022; 9:285-306. [PMID: 35709511 DOI: 10.1146/annurev-virology-093020-013659] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses frequently carry out replication in specialized compartments within cells. The effect of these structures on virus replication is poorly understood. Recent research supports phase separation as a foundational principle for organization of cellular components with the potential to influence viral replication. In this review, phase separation is described in the context of formation of viral replication centers, with an emphasis on the nonsegmented negative-strand RNA viruses. Consideration is given to the interplay between phase separation and the critical processes of viral transcription and genome replication, and the role of these regions in pathogen-host interactions is discussed. Finally, critical questions that must be addressed to fully understand how phase separation influences viral replication and the viral life cycle are presented, along with information about new approaches that could be used to make important breakthroughs in this emerging field.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Science and Engineering Living Systems, Washington University, St. Louis, Missouri, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA;
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Chan CP, Jin DY. Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations. RNA (NEW YORK, N.Y.) 2022; 28:449-477. [PMID: 35031583 PMCID: PMC8925969 DOI: 10.1261/rna.079016.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sensing of pathogen-associated molecular patterns including viral RNA by innate immunity represents the first line of defense against viral infection. In addition to RIG-I-like receptors and NOD-like receptors, several other RNA sensors are known to mediate innate antiviral response in the cytoplasm. Double-stranded RNA-binding protein PACT interacts with prototypic RNA sensor RIG-I to facilitate its recognition of viral RNA and induction of host interferon response, but variations of this theme are seen when the functions of RNA sensors are modulated by other RNA-binding proteins to impinge on antiviral defense, proinflammatory cytokine production and cell death programs. Their discrete and coordinated actions are crucial to protect the host from infection. In this review, we will focus on cytoplasmic RNA sensors with an emphasis on their interplay with RNA-binding partners. Classical sensors such as RIG-I will be briefly reviewed. More attention will be brought to new insights on how RNA-binding partners of RNA sensors modulate innate RNA sensing and how viruses perturb the functions of RNA-binding partners.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
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8
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Brice AM, Watts E, Hirst B, Jans DA, Ito N, Moseley GW. Implication of the nuclear trafficking of rabies virus P3 protein in viral pathogenicity. Traffic 2021; 22:482-489. [PMID: 34622522 DOI: 10.1111/tra.12821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/27/2021] [Accepted: 10/04/2021] [Indexed: 11/27/2022]
Abstract
Although the majority of viruses of the family Mononegvirales replicate exclusively in the host cell cytoplasm, many of these viruses encode proteins that traffic between the nucleus and cytoplasm, which is believed to enable accessory functions in modulating the biology of the infected host cell. Among these, the P3 protein of rabies virus localizes to the nucleus through the activity of several specific nuclear localization and nuclear export signals. The major defined functions of P3 are in evasion of interferon (IFN)-mediated antiviral responses, including through inhibition of DNA-binding by IFN-activated STAT1. P3 also localizes to nucleoli and promyelocytic leukemia (PML) nuclear bodies, and interacts with nucleolin and PML protein, indicative of several intranuclear roles. The relationship of P3 nuclear localization with pathogenicity, however, is unresolved. We report that nucleocytoplasmic localization of P3 proteins from a pathogenic RABV strain, Nishigahara (Ni) and a non-pathogenic Ni-derived strain, Ni-CE, differs significantly, with nuclear accumulation defective for Ni-CE-P3. Molecular mapping indicates that altered localization derives from a coordinated effect, including two residue substitutions that independently disable nuclear localization and augment nuclear export signals, collectively promoting nuclear exclusion. Intriguingly, this appears to relate to effects on protein conformation or regulatory mechanisms, rather than direct modification of defined trafficking signal sequences. These data provide new insights into the role of regulated nuclear trafficking of a viral protein in the pathogenicity of a virus that replicates in the cytoplasm.
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Affiliation(s)
- Aaron M Brice
- Viral Pathogenesis Laboratory, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Ericka Watts
- Viral Pathogenesis Laboratory, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Bevan Hirst
- Viral Pathogenesis Laboratory, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - David A Jans
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Naoto Ito
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, and United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Gregory W Moseley
- Viral Pathogenesis Laboratory, Department of Microbiology, Monash University, Clayton, Victoria, Australia
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Abstract
The necessity of viruses to modulate the innate immune response often dictates the outcome of viral infection. As such, viruses encode many factors that undermine these potent antiviral responses. A recent study by Bouvet et al. (M. Bouvet, S. Voigt, T. Tagawa, M. Albanese, et al., mBio 12:e03440-20, 2021, https://doi.org/10.1128/mBio.03440-20) revisits the impact of virus-encoded noncoding RNAs on key components of the interferon pathway and sheds light on how the extensive biological functions of Epstein-Barr virus (EBV) microRNAs (miRNAs) are on targeting both the induction and signaling cascades of interferon.
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10
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Dolnik O, Gerresheim GK, Biedenkopf N. New Perspectives on the Biogenesis of Viral Inclusion Bodies in Negative-Sense RNA Virus Infections. Cells 2021; 10:cells10061460. [PMID: 34200781 PMCID: PMC8230417 DOI: 10.3390/cells10061460] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Infections by negative strand RNA viruses (NSVs) induce the formation of viral inclusion bodies (IBs) in the host cell that segregate viral as well as cellular proteins to enable efficient viral replication. The induction of those membrane-less viral compartments leads inevitably to structural remodeling of the cellular architecture. Recent studies suggested that viral IBs have properties of biomolecular condensates (or liquid organelles), as have previously been shown for other membrane-less cellular compartments like stress granules or P-bodies. Biomolecular condensates are highly dynamic structures formed by liquid-liquid phase separation (LLPS). Key drivers for LLPS in cells are multivalent protein:protein and protein:RNA interactions leading to specialized areas in the cell that recruit molecules with similar properties, while other non-similar molecules are excluded. These typical features of cellular biomolecular condensates are also a common characteristic in the biogenesis of viral inclusion bodies. Viral IBs are predominantly induced by the expression of the viral nucleoprotein (N, NP) and phosphoprotein (P); both are characterized by a special protein architecture containing multiple disordered regions and RNA-binding domains that contribute to different protein functions. P keeps N soluble after expression to allow a concerted binding of N to the viral RNA. This results in the encapsidation of the viral genome by N, while P acts additionally as a cofactor for the viral polymerase, enabling viral transcription and replication. Here, we will review the formation and function of those viral inclusion bodies upon infection with NSVs with respect to their nature as biomolecular condensates.
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Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. Biomolecules 2021; 11:biom11050622. [PMID: 33922087 PMCID: PMC8143464 DOI: 10.3390/biom11050622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.
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Nonsegmented Negative-Sense RNA Viruses Utilize N 6-Methyladenosine (m 6A) as a Common Strategy To Evade Host Innate Immunity. J Virol 2021; 95:JVI.01939-20. [PMID: 33536170 DOI: 10.1128/jvi.01939-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/22/2021] [Indexed: 12/22/2022] Open
Abstract
N 6-Methyladenosine (m6A) is the most abundant internal RNA modification catalyzed by host RNA methyltransferases. As obligate intracellular parasites, many viruses acquire m6A methylation in their RNAs. However, the biological functions of viral m6A methylation are poorly understood. Here, we found that viral m6A methylation serves as a molecular marker for host innate immunity to discriminate self from nonself RNA and that this novel biological function of viral m6A methylation is universally conserved in several families in nonsegmented negative-sense (NNS) RNA viruses. Using m6A methyltransferase (METTL3) knockout cells, we produced m6A-deficient virion RNAs from the representative members of the families Pneumoviridae, Paramyxoviridae, and Rhabdoviridae and found that these m6A-deficient viral RNAs triggered significantly higher levels of type I interferon compared to the m6A-sufficient viral RNAs, in a RIG-I-dependent manner. Reconstitution of the RIG-I pathway revealed that m6A-deficient virion RNA induced higher expression of RIG-I, bound to RIG-I more efficiently, enhanced RIG-I ubiquitination, and facilitated RIG-I conformational rearrangement and oligomerization. Furthermore, the m6A binding protein YTHDF2 is essential for suppression of the type I interferon signaling pathway, including by virion RNA. Collectively, our results suggest that several families in NNS RNA viruses acquire m6A in viral RNA as a common strategy to evade host innate immunity.IMPORTANCE The nonsegmented negative-sense (NNS) RNA viruses share many common replication and gene expression strategies. There are no vaccines or antiviral drugs for many of these viruses. We found that representative members of the families Pneumoviridae, Paramyxoviridae, and Rhabdoviridae among the NNS RNA viruses acquire m6A methylation in their genome and antigenome as a means to escape recognition by host innate immunity via a RIG-I-dependent signaling pathway. Viral RNA lacking m6A methylation induces a significantly higher type I interferon response than m6A-sufficient viral RNA. In addition to uncovering m6A methylation as a common mechanism for many NNS RNA viruses to evade host innate immunity, this study discovered a novel strategy to enhance type I interferon responses, which may have important applications in vaccine development, as robust innate immunity will likely promote the subsequent adaptive immunity.
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Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages. J Virol 2020; 94:JVI.00178-20. [PMID: 32188729 PMCID: PMC7269425 DOI: 10.1128/jvi.00178-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022] Open
Abstract
Macrophages are an important cell type during coronavirus infections because they “notice” the infection and respond by inducing type I interferons, which limits virus replication. In turn, coronaviruses encode proteins that mitigate the cell’s ability to signal an interferon response. Here, we evaluated the host macrophage response to two independent mutant coronaviruses, one with reduced deubiquitinating activity (DUBmut) and the other containing an inactivated endoribonuclease (EndoUmut). We observed a rapid, robust, and focused response to the EndoUmut virus, which was characterized by enhanced expression of interferon and interferon-related genes. In contrast, wild-type virus and the DUBmut virus elicited a more limited interferon response and ultimately activated over 2,800 genes, including players in the unfolded protein response and proinflammatory pathways associated with progression of significant disease. This study reveals that EndoU activity substantially contributes to the ability of coronaviruses to evade the host innate response and to replicate in macrophages. Coronaviruses (CoVs) encode multiple interferon (IFN) antagonists that modulate the host response to virus replication. Here, we evaluated the host transcriptional response to infection with murine coronaviruses encoding independent mutations in one of two different viral antagonists, the deubiquitinase (DUB) within nonstructural protein 3 or the endoribonuclease (EndoU) within nonstructural protein 15. We used transcriptomics approaches to compare the scope and kinetics of the host response to the wild-type (WT), DUBmut, and EndoUmut viruses in infected macrophages. We found that the EndoUmut virus activates a focused response that predominantly involves type I interferons and interferon-related genes, whereas the WT and DUBmut viruses more broadly stimulate upregulation of over 2,800 genes, including networks associated with activating the unfolded protein response (UPR) and the proinflammatory response associated with viral pathogenesis. This study highlights the role of viral interferon antagonists in shaping the kinetics and magnitude of the host response during virus infection and demonstrates that inactivating a dominant viral antagonist, the coronavirus endoribonuclease, dramatically alters the host response in macrophages. IMPORTANCE Macrophages are an important cell type during coronavirus infections because they “notice” the infection and respond by inducing type I interferons, which limits virus replication. In turn, coronaviruses encode proteins that mitigate the cell’s ability to signal an interferon response. Here, we evaluated the host macrophage response to two independent mutant coronaviruses, one with reduced deubiquitinating activity (DUBmut) and the other containing an inactivated endoribonuclease (EndoUmut). We observed a rapid, robust, and focused response to the EndoUmut virus, which was characterized by enhanced expression of interferon and interferon-related genes. In contrast, wild-type virus and the DUBmut virus elicited a more limited interferon response and ultimately activated over 2,800 genes, including players in the unfolded protein response and proinflammatory pathways associated with progression of significant disease. This study reveals that EndoU activity substantially contributes to the ability of coronaviruses to evade the host innate response and to replicate in macrophages.
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Ezzikouri S, Hoque Kayesh ME, Benjelloun S, Kohara M, Tsukiyama-Kohara K. Targeting Host Innate and Adaptive Immunity to Achieve the Functional Cure of Chronic Hepatitis B. Vaccines (Basel) 2020; 8:vaccines8020216. [PMID: 32403281 PMCID: PMC7349973 DOI: 10.3390/vaccines8020216] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
Despite the availability of an effective preventive vaccine for hepatitis B virus (HBV) for over 38 years, chronic HBV (CHB) infection remains a global health burden with around 257 million patients. The ideal treatment goal for CHB infection would be to achieve complete cure; however, current therapies such as peg-interferon and nucleos(t)ide analogs are unable to achieve the functional cure, the newly set target for HBV chronic infection. Considering the fact functional cure has been accepted as an endpoint in the treatment of chronic hepatitis B by scientific committee, the development of alternative therapeutic strategies is urgently needed to functionally cure CHB infection. A promising target for future therapeutic strategies is immune modulation to restore dysfunctional HBV-specific immunity. In this review, we provide an overview of the progress in alternative therapeutic strategies, including immune-based therapeutic approaches that enhance host innate and adaptive immunity to achieve and increase the functional cure from CHB infection.
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Affiliation(s)
- Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca 20250, Morocco;
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan;
- Correspondence: (S.E.); (K.T.-K.); Tel.: +212-5-2243-4470 (S.E.); Tel./Fax: +81-99-285-3589 (K.T.-K.)
| | - Mohammad Enamul Hoque Kayesh
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan;
- Department of Microbiology and Public Health, Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal 8210, Bangladesh
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca 20250, Morocco;
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, The Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan;
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan;
- Correspondence: (S.E.); (K.T.-K.); Tel.: +212-5-2243-4470 (S.E.); Tel./Fax: +81-99-285-3589 (K.T.-K.)
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15
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Vesicular Stomatitis Virus Phosphoprotein Dimerization Domain Is Dispensable for Virus Growth. J Virol 2020; 94:JVI.01789-19. [PMID: 31852780 DOI: 10.1128/jvi.01789-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/06/2019] [Indexed: 02/08/2023] Open
Abstract
The phosphoprotein (P) of the nonsegmented negative-sense RNA viruses is a multimeric modular protein that is essential for RNA transcription and replication. Despite great variability in length and sequence, the architecture of this protein is conserved among the different viral families, with a long N-terminal intrinsically disordered region comprising a nucleoprotein chaperone module, a central multimerization domain (PMD), connected by a disordered linker to a C-terminal nucleocapsid-binding domain. The P protein of vesicular stomatitis virus (VSV) forms dimers, and here we investigate the importance of its dimerization domain, PMD, for viral gene expression and virus growth. A truncated P protein lacking the central dimerization domain (PΔMD) loses its ability to form dimers both in vitro and in a yeast two-hybrid system but conserves its ability to bind N. In a minireplicon system, the truncated monomeric protein performs almost as well as the full-length dimeric protein, while a recombinant virus harboring the same truncation in the P protein has been rescued and follows replication kinetics similar to those seen with the wild-type virus, showing that the dimerization domain of P is dispensable for viral gene expression and virus replication in cell culture. Because RNA viruses have high mutation rates, it is unlikely that a structured domain such as a VSV dimerization domain would persist in the absence of a function(s), but our work indicates that it is not required for the functioning of the RNA polymerase machinery or for the assembly of new viruses.IMPORTANCE The phosphoprotein (P) is an essential and conserved component of all nonsegmented negative-sense RNA viruses, including some major human pathogens (e.g., rabies virus, measles virus, respiratory syncytial virus [RSV], Ebola virus, and Nipah virus). P is a modular protein with intrinsically disordered regions and folded domains that plays specific and similar roles in the replication of the different viruses and, in some cases, hijacks cell components to the advantage of the virus and is involved in immune evasion. All P proteins are multimeric, but the role of this multimerization is still unclear. Here, we demonstrate that the dimerization domain of VSV P is dispensable for the expression of virally encoded proteins and for virus growth in cell culture. This provides new insights into and raises questions about the functioning of the RNA-synthesizing machinery of the nonsegmented negative-sense RNA viruses.
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Kikkert M. Innate Immune Evasion by Human Respiratory RNA Viruses. J Innate Immun 2019; 12:4-20. [PMID: 31610541 PMCID: PMC6959104 DOI: 10.1159/000503030] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
The impact of respiratory virus infections on the health of children and adults can be very significant. Yet, in contrast to most other childhood infections as well as other viral and bacterial diseases, prophylactic vaccines or effective antiviral treatments against viral respiratory infections are either still not available, or provide only limited protection. Given the widespread prevalence, a general lack of natural sterilizing immunity, and/or high morbidity and lethality rates of diseases caused by influenza, respiratory syncytial virus, coronaviruses, and rhinoviruses, this difficult situation is a genuine societal challenge. A thorough understanding of the virus-host interactions during these respiratory infections will most probably be pivotal to ultimately meet these challenges. This review attempts to provide a comparative overview of the knowledge about an important part of the interaction between respiratory viruses and their host: the arms race between host innate immunity and viral innate immune evasion. Many, if not all, viruses, including the respiratory viruses listed above, suppress innate immune responses to gain a window of opportunity for efficient virus replication and setting-up of the infection. The consequences for the host's immune response are that it is often incomplete, delayed or diminished, or displays overly strong induction (after the delay) that may cause tissue damage. The affected innate immune response also impacts subsequent adaptive responses, and therefore viral innate immune evasion often undermines fully protective immunity. In this review, innate immune responses relevant for respiratory viruses with an RNA genome will briefly be summarized, and viral innate immune evasion based on shielding viral RNA species away from cellular innate immune sensors will be discussed from different angles. Subsequently, viral enzymatic activities that suppress innate immune responses will be discussed, including activities causing host shut-off and manipulation of stress granule formation. Furthermore, viral protease-mediated immune evasion and viral manipulation of the ubiquitin system will be addressed. Finally, perspectives for use of the reviewed knowledge for the development of novel antiviral strategies will be sketched.
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Affiliation(s)
- Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, Molecular Virology Laboratory, Leiden, The Netherlands,
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Chanthamontri CK, Jordan DS, Wang W, Wu C, Lin Y, Brett TJ, Gross ML, Leung DW. The Ebola Viral Protein 35 N-Terminus Is a Parallel Tetramer. Biochemistry 2019; 58:657-664. [PMID: 30592210 DOI: 10.1021/acs.biochem.8b01154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Members of Mononegavirales, the order that includes nonsegmented negative sense RNA viruses (NNSVs), encode a small number of multifunctional proteins. In members of the Filoviridae family, virus protein 35 (VP35) facilitates immune evasion and functions as an obligatory cofactor for viral RNA synthesis. VP35 functions in a manner orthologous to that of phosphoproteins from other NNSVs. Although the critical roles of Ebola viral VP35 (eVP35) in immune evasion and RNA synthesis are well-appreciated, a complete understanding of its organization and its role in carrying out its many functions has yet to be fully realized. In particular, we currently lack information about the role of the oligomerization domain within eVP35. To address this limitation, we report here an investigation of the oligomer structure of eVP35 using hybrid methods that include multiangle light scattering, small-angle X-ray scattering, and cross-linking coupled with mass spectrometry to determine the shape and orientation of the eVP35 oligomer. Our integrative results are consistent with a parallel tetramer in which the N-terminal regions that are required for RNA synthesis are all oriented in the same direction. Furthermore, these results define a framework for targeting the symmetric tetramer for structure-based antiviral discovery.
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Affiliation(s)
- Chamnongsak Ken Chanthamontri
- Department of Chemistry , Washington University in St. Louis , Box 1134, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - David S Jordan
- Department of Pathology and Immunology , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| | - Wenjie Wang
- Department of Pathology and Immunology , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| | - Chao Wu
- Department of Pathology and Immunology , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| | - Yanchun Lin
- Department of Chemistry , Washington University in St. Louis , Box 1134, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Tom J Brett
- Department of Medicine , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
| | - Michael L Gross
- Department of Chemistry , Washington University in St. Louis , Box 1134, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Daisy W Leung
- Department of Pathology and Immunology , Washington University School of Medicine in St. Louis , St. Louis , Missouri 63110 , United States
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Hong Y, Bai M, Qi X, Li C, Liang M, Li D, Cardona CJ, Xing Z. Suppression of the IFN-α and -β Induction through Sequestering IRF7 into Viral Inclusion Bodies by Nonstructural Protein NSs in Severe Fever with Thrombocytopenia Syndrome Bunyavirus Infection. THE JOURNAL OF IMMUNOLOGY 2018; 202:841-856. [DOI: 10.4049/jimmunol.1800576] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022]
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Banerjee A, Pal A, Pal D, Mitra P. Ebolavirus interferon antagonists—protein interaction perspectives to combat pathogenesis. Brief Funct Genomics 2017; 17:392-401. [DOI: 10.1093/bfgp/elx034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Ribaudo M, Barik S. The nonstructural proteins of Pneumoviruses are remarkably distinct in substrate diversity and specificity. Virol J 2017; 14:215. [PMID: 29110727 PMCID: PMC5674761 DOI: 10.1186/s12985-017-0881-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/27/2017] [Indexed: 11/23/2022] Open
Abstract
Background Interferon (IFN) inhibits viruses by inducing several hundred cellular genes, aptly named ‘interferon (IFN)-stimulated genes’ (ISGs). The only two RNA viruses of the Pneumovirus genus of the Paramyxoviridae family, namely Respiratory Syncytial Virus (RSV) and Pneumonia Virus of Mice (PVM), each encode two nonstructural (NS) proteins that share no sequence similarity but yet suppress IFN. Since suppression of IFN underlies the ability of these viruses to replicate in the host cells, the mechanism of such suppression has become an important area of research. This Short Report is an important extension of our previous efforts in defining this mechanism. Results We show that, like their PVM counterparts, the RSV NS proteins also target multiple members of the ISG family. While significantly extending the substrate repertoire of the RSV NS proteins, these results, unexpectedly, also reveal that the target preferences of the NS proteins of the two viruses are entirely different. This is surprising since the two Pneumoviruses are phylogenetically close with similar genome organization and gene function, and the NS proteins of both also serve as suppressors of host IFN response. Conclusion The finding that the NS proteins of the two highly similar viruses suppress entirely different members of the ISG family raises intriguing questions of pneumoviral NS evolution and mechanism of action.
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Affiliation(s)
- Michael Ribaudo
- Department of Biological, Geological and Environmental Sciences, and Center for Gene Regulation in Health and Disease, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA
| | - Sailen Barik
- Department of Biological, Geological and Environmental Sciences, and Center for Gene Regulation in Health and Disease, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH, 44115, USA. .,3780 Pelham Drive, Mobile, AL, 36619, USA.
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The Many Faces of the Flavivirus NS5 Protein in Antagonism of Type I Interferon Signaling. J Virol 2017; 91:JVI.01970-16. [PMID: 27881649 DOI: 10.1128/jvi.01970-16] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The vector-borne flaviviruses cause severe disease in humans on every inhabited continent on earth. Their transmission by arthropods, particularly mosquitoes, facilitates large emergence events such as witnessed with Zika virus (ZIKV) or West Nile virus in the Americas. Every vector-borne flavivirus examined thus far that causes disease in humans, from dengue virus to ZIKV, antagonizes the host type I interferon (IFN-I) response by preventing JAK-STAT signaling, suggesting that suppression of this pathway is an important determinant of infection. The most direct and potent viral inhibitor of this pathway is the nonstructural protein NS5. However, the mechanisms utilized by NS5 from different flaviviruses are often quite different, sometimes despite close evolutionary relationships between viruses. The varied mechanisms of NS5 as an IFN-I antagonist are also surprising given that the evolution of NS5 is restrained by the requirement to maintain function of two enzymatic activities critical for virus replication, the methyltransferase and RNA-dependent RNA polymerase. This review discusses the different strategies used by flavivirus NS5 to evade the antiviral effects of IFN-I and how this information can be used to better model disease and develop antiviral countermeasures.
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Schulz KS, Mossman KL. Viral Evasion Strategies in Type I IFN Signaling - A Summary of Recent Developments. Front Immunol 2016; 7:498. [PMID: 27891131 PMCID: PMC5104748 DOI: 10.3389/fimmu.2016.00498] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/26/2016] [Indexed: 12/13/2022] Open
Abstract
The immune system protects the organism against infections and the damage associated with them. The first line of defense against pathogens is the innate immune response. In the case of a viral infection, it induces the interferon (IFN) signaling cascade and eventually the expression of type I IFN, which then causes an antiviral state in the cells. However, many viruses have developed strategies to counteract this mechanism and prevent the production of IFN. In order to modulate or inhibit the IFN signaling cascade in their favor, viruses have found ways to interfere at every single step of the cascade, for example, by inducing protein degradation or cleavage, or by mediate protein polyubiquitination. In this article, we will review examples of viruses that modulate the IFN response and describe the mechanisms they use.
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Affiliation(s)
- Katharina S Schulz
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre, Institute for Infectious Disease Research, McMaster University , Hamilton, ON , Canada
| | - Karen L Mossman
- Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre, Institute for Infectious Disease Research, McMaster University , Hamilton, ON , Canada
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Hodak H. Down to the Molecular Mechanisms of Host–Pathogen Interactions. J Mol Biol 2016; 428:3353-4. [DOI: 10.1016/j.jmb.2016.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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