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Cai ZY, Wu P, Liang H, Xie YZ, Zhang BX, He CL, Yang CR, Li H, Mo W, Yang ZH. A ZBP1 isoform blocks ZBP1-mediated cell death. Cell Rep 2024; 43:114221. [PMID: 38748877 DOI: 10.1016/j.celrep.2024.114221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/10/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
ZBP1 is an interferon (IFN)-induced nucleic acid (NA) sensor that senses unusual Z-form NA (Z-NA) to promote cell death and inflammation. However, the mechanisms that dampen ZBP1 activation to fine-tune inflammatory responses are unclear. Here, we characterize a short isoform of ZBP1 (referred to as ZBP1-S) as an intrinsic suppressor of the inflammatory signaling mediated by full-length ZBP1. Mechanistically, ZBP1-S depresses ZBP1-mediated cell death by competitive binding with Z-NA for Zα domains of ZBP1. Cells from mice (Ripk1D325A/D325A) with cleavage-resistant RIPK1-induced autoinflammatory (CRIA) syndrome are alive but sensitive to IFN-induced and ZBP1-dependent cell death. Intriguingly, Ripk1D325A/D325A cells die spontaneously when ZBP1-S is deleted, indicating that cell death driven by ZBP1 is under the control of ZBP1-S. Thus, our findings reveal that alternative splicing of Zbp1 represents autogenic inhibition for regulating ZBP1 signaling and indicate that uncoupling of Z-NA with ZBP1 could be an effective strategy against autoinflammations.
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Affiliation(s)
- Zhi-Yu Cai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 310012, China
| | - Puqi Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hao Liang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yu-Ze Xie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Bo-Xin Zhang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 310012, China
| | - Cai-Ling He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Cong-Rong Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hongda Li
- Institute for Brain Science and Disease, Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Wei Mo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 310012, China; Department of Immunology, School of Basic Medical Science, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310012, China; Institute for Brain Science and Disease, Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing Medical University, Chongqing 400016, China.
| | - Zhang-Hua Yang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 310012, China.
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Zhang M, Zeng Y, Wang F, Feng H, Liu Q, Li F, Zhao S, Zhao J, Liu Z, Zheng F, Liu H. Effects of the Nonstructural Protein-Nucleolar and Coiled-Body Phosphoprotein 1 Protein Interaction on rRNA Synthesis Through Telomeric Repeat-Binding Factor 2 Regulation Under Nucleolar Stress. AIDS Res Hum Retroviruses 2024. [PMID: 38062753 DOI: 10.1089/aid.2023.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024] Open
Abstract
To investigate the effects and underlying molecular mechanisms of the interaction between the non-structural protein 1 (NS1) and nucleolar and coiled-body phosphoprotein 1 (NOLC1) on rRNA synthesis through nucleolar telomeric repeat-binding factor 2 (TRF2) under nucleolar stress in avian influenza A virus infection. The analysis of TRF2 ties into the exploration of ribosomal protein L11 (RPL11) and mouse double minute 2 (MDM2) because TRF2 has been found to interact with NOLC1, and the RPL11-MDM2 pathway plays an important role in nucleolar regulation and cellular processes. Both human embryonic kidney 293T cells and human lung adenocarcinoma A549 cells were transfected with the plasmids pCAGGS-HA and pCAGGS-HA-NS1, respectively. In addition, A549 cells were transfected with the plasmids pEGFP-N1, pEGFP-N1-NS1, and pDsRed2-N1-TRF2. The cell cycle was detected by flow cytometry, and coimmunoprecipitation was applied to examine the interactions between different proteins. The effect of NS1 on TRF2 was detected by immunoprecipitation, and the colocalization of NOLC1 and TRF2 or NS1 and TRF2 was visualized by immunofluorescence. Quantitative real-time PCR was conducted to detect the expression of the TRF2 and p21. There is a strong interaction between NOLC1 and TRF2, and the colocalization of NOLC1 and TRF2 in the nucleus. The protein expression of NOLC1 in A549-HA-NS1 cells was lower than that in A549-HA cells, which was accompanied by the upregulated protein expression of p53 in A549-HA-NS1 cells (all p < .05). TRF2 was scattered throughout the nucleus without clear nucleolar aggregation. RPL11 specifically interacted with MDM2 in the NS1 group, and expression of the p21 gene was significantly increased in the HA-NS1 group compared with the HA group (p < .01). NS1 protein can lead to the reduced aggregation of TRF2 in the nucleolus, inhibition of rRNA expression, and cell cycle blockade by interfering with the NOLC1 protein and generating nucleolar stress.
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Affiliation(s)
- Man Zhang
- School of Life Science, Liaoning University, Shenyang, China
| | - Yingyue Zeng
- School of Life Science, Liaoning University, Shenyang, China
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
| | - Fengchao Wang
- School of Life Science, Liaoning University, Shenyang, China
| | - Huawei Feng
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
| | - Qingqing Liu
- School of Life Science, Liaoning University, Shenyang, China
| | - Feng Li
- School of Life Science, Liaoning University, Shenyang, China
| | - Shan Zhao
- School of Life Science, Liaoning University, Shenyang, China
| | - Jian Zhao
- School of Life Science, Liaoning University, Shenyang, China
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
| | - Zhikui Liu
- Liaoning Huikang Testing and Evaluation Technology Co., Shenyang, China
| | - Fangliang Zheng
- School of Life Science, Liaoning University, Shenyang, China
| | - Hongsheng Liu
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
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3
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Mann JT, Riley BA, Baker SF. All differential on the splicing front: Host alternative splicing alters the landscape of virus-host conflict. Semin Cell Dev Biol 2023; 146:40-56. [PMID: 36737258 DOI: 10.1016/j.semcdb.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Alternative RNA splicing is a co-transcriptional process that richly increases proteome diversity, and is dynamically regulated based on cell species, lineage, and activation state. Virus infection in vertebrate hosts results in rapid host transcriptome-wide changes, and regulation of alternative splicing can direct a combinatorial effect on the host transcriptome. There has been a recent increase in genome-wide studies evaluating host alternative splicing during viral infection, which integrates well with prior knowledge on viral interactions with host splicing proteins. A critical challenge remains in linking how these individual events direct global changes, and whether alternative splicing is an overall favorable pathway for fending off or supporting viral infection. Here, we introduce the process of alternative splicing, discuss how to analyze splice regulation, and detail studies on genome-wide and splice factor changes during viral infection. We seek to highlight where the field can focus on moving forward, and how incorporation of a virus-host co-evolutionary perspective can benefit this burgeoning subject.
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Affiliation(s)
- Joshua T Mann
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Brent A Riley
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Steven F Baker
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA.
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Lee MC, Yu CP, Chen XH, Liu MT, Yang JR, Chen AY, Huang CH. Influenza A virus NS1 protein represses antiviral immune response by hijacking NF-κB to mediate transcription of type III IFN. Front Cell Infect Microbiol 2022; 12:998584. [PMID: 36189352 PMCID: PMC9519859 DOI: 10.3389/fcimb.2022.998584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Background Non-structural protein 1 (NS1), one of the viral proteins of influenza A viruses (IAVs), plays a crucial role in evading host antiviral immune response. It is known that the IAV NS1 protein regulates the antiviral genes response mainly through several different molecular mechanisms in cytoplasm. Current evidence suggests that NS1 represses the transcription of IFNB1 gene by inhibiting the recruitment of Pol II to its exons and promoters in infected cells. However, IAV NS1 whether can utilize a common mechanism to antagonize antiviral response by interacting with cellular DNA and immune-related transcription factors in the nucleus, is not yet clear. Methods Chromatin immunoprecipitation and sequencing (ChIP-seq) was used to determine genome-wide transcriptional DNA-binding sites for NS1 and NF-κB in viral infection. Next, we used ChIP-reChIP, luciferase reporter assay and secreted embryonic alkaline phosphatase (SEAP) assay to provide information on the dynamic binding of NS1 and NF-κB to chromatin. RNA sequencing (RNA-seq) transcriptomic analyses were used to explore the critical role of NS1 and NF-κB in IAV infection as well as the detailed processes governing host antiviral response. Results Herein, NS1 was found to co-localize with NF-κB using ChIP-seq. ChIP-reChIP and luciferase reporter assay confirmed the co-localization of NS1 and NF-κB at type III IFN genes, such as IFNL1, IFNL2, and IFNL3. We discovered that NS1 disturbed binding manners of NF-κB to inhibit IFNL1 expression. NS1 hijacked NF-κB from a typical IFNL1 promoter to the exon-intron region of IFNL1 and decreased the enrichment of RNA polymerase II and H3K27ac, a chromatin accessibility marker, in the promoter region of IFNL1 during IAV infection, consequently reducing IFNL1 gene expression. NS1 deletion enhanced the enrichment of RNA polymerase II at the IFNL1 promoter and promoted its expression. Conclusion Overall, NS1 hijacked NF-κB to prevent its interaction with the IFNL1 promoter and restricted the open chromatin architecture of the promoter, thereby abating antiviral gene expression.
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Affiliation(s)
- Meng-Chang Lee
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Ping Yu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Xing-Hong Chen
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Ming-Tsan Liu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Ji-Rong Yang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - An-Yu Chen
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Heng Huang
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
- *Correspondence: Chih-Heng Huang,
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5
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Angiotensin-Converting Enzyme 2 SNPs as Common Genetic Loci and Optimal Early Identification Genetic Markers for COVID-19. Pathogens 2022; 11:pathogens11080947. [PMID: 36015068 PMCID: PMC9415427 DOI: 10.3390/pathogens11080947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/08/2022] [Accepted: 08/16/2022] [Indexed: 12/15/2022] Open
Abstract
Background: Angiotensin-converting enzyme 2 (ACE2) is implicated as a host cell receptor that causes infection in the pathogenesis of coronavirus disease 2019 (COVID-19), and its genetic polymorphisms in the ACE2 gene may promote cardiovascular disease and systemic inflammatory injury in COVID-19 patients. Hence, the genetic background may potentially explain the broad interindividual variation in disease susceptibility and/or severity. Methods: Genetic susceptibility to COVID-19 was analyzed by examining single-nucleotide polymorphisms (SNPs) of ACE2 in 246 patients with COVID-19 and 210 normal controls using the TaqMan genotyping assay. Results: We demonstrated that the ACE2 SNPs rs4646142, rs6632677, and rs2074192 were associated with COVID-19 (for all, p < 0.05), and the differences in the ACE2 SNPs rs4646142 and rs6632677 were correlated with COVID-19-related systemic inflammatory injury and cardiovascular risk. Specifically, rs4646142 was associated with high-sensitivity C-reactive protein (hs-CRP), prealbumin (PAB), apolipoprotein A (APOA), high-density lipoprotein (HDL), and acid glycoprotein (AGP) levels. Rs6632677 was also associated with elevated CRP, acid glycoprotein (AGP), and haptoglobin (HPT). Conclusions: Our results suggest that the ACE2 SNPs rs4646142 and rs6632677 may be common genetic loci and optimal early identification genetic markers for COVID-19 with cardiovascular risk.
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Karlebach G, Aronow B, Baylin SB, Butler D, Foox J, Levy S, Meydan C, Mozsary C, Saravia-Butler AM, Taylor DM, Wurtele E, Mason CE, Beheshti A, Robinson PN. Betacoronavirus-specific alternate splicing. Genomics 2022; 114:110270. [PMID: 35074468 PMCID: PMC8782732 DOI: 10.1016/j.ygeno.2022.110270] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/15/2021] [Accepted: 01/16/2022] [Indexed: 11/04/2022]
Abstract
Viruses can subvert a number of cellular processes including splicing in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection, datasets from the betacoronaviruses SARS-CoV and MERS, as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification, and have a smaller number of exons as compared with differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by differential alternative splicing and gene expression in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS. The alternative splicing changes observed in betacoronaviruses infection potentially modify a broad range of cellular functions, via changes in the functions of the products of a diverse set of genes involved in different biological processes.
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7
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Hale BG. Antiviral immunity triggered by infection-induced host transposable elements. Curr Opin Virol 2021; 52:211-216. [PMID: 34959082 DOI: 10.1016/j.coviro.2021.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
Abstract
Host silencing of transposable elements (TEs) is critical to prevent genome damage and inappropriate inflammation. However, new evidence suggests that a virus-infected host may re-activate TEs and co-opt them for antiviral defense. RNA-Seq and specialized bioinformatics have revealed the diversity of virus infections that induce TEs. Furthermore, studies with influenza virus have uncovered how infection-triggered changes to the SUMOylation of TRIM28, an epigenetic co-repressor, lead to TE de-repression. Importantly, there is a growing appreciation of how de-repressed TEs stimulate antiviral gene expression, either via cis-acting enhancer functions or via their recognition as viral mimetics by innate immune nucleic acid sensors (e.g. RIG-I, mda-5 and cGAS). Understanding how viruses trigger, and counteract, TE-based antiviral immunity should provide insights into pathogenic mechanisms.
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Affiliation(s)
- Benjamin G Hale
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.
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8
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Xiao Y, Lidsky PV, Shirogane Y, Aviner R, Wu CT, Li W, Zheng W, Talbot D, Catching A, Doitsh G, Su W, Gekko CE, Nayak A, Ernst JD, Brodsky L, Brodsky E, Rousseau E, Capponi S, Bianco S, Nakamura R, Jackson PK, Frydman J, Andino R. A defective viral genome strategy elicits broad protective immunity against respiratory viruses. Cell 2021; 184:6037-6051.e14. [PMID: 34852237 PMCID: PMC8598942 DOI: 10.1016/j.cell.2021.11.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022]
Abstract
RNA viruses generate defective viral genomes (DVGs) that can interfere with replication of the parental wild-type virus. To examine their therapeutic potential, we created a DVG by deleting the capsid-coding region of poliovirus. Strikingly, intraperitoneal or intranasal administration of this genome, which we termed eTIP1, elicits an antiviral response, inhibits replication, and protects mice from several RNA viruses, including enteroviruses, influenza, and SARS-CoV-2. While eTIP1 replication following intranasal administration is limited to the nasal cavity, its antiviral action extends non-cell-autonomously to the lungs. eTIP1 broad-spectrum antiviral effects are mediated by both local and distal type I interferon responses. Importantly, while a single eTIP1 dose protects animals from SARS-CoV-2 infection, it also stimulates production of SARS-CoV-2 neutralizing antibodies that afford long-lasting protection from SARS-CoV-2 reinfection. Thus, eTIP1 is a safe and effective broad-spectrum antiviral generating short- and long-term protection against SARS-CoV-2 and other respiratory infections in animal models.
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Affiliation(s)
- Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuta Shirogane
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Ranen Aviner
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Chien-Ting Wu
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Weiyi Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Weihao Zheng
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Dale Talbot
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Aleph Therapeutics, Inc., Stanford, CA 94305, USA
| | - Adam Catching
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gilad Doitsh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Weiheng Su
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; School of Life Sciences, Jilin University, Changchun, China
| | - Colby E Gekko
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arabinda Nayak
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center and Department of Evolutionary & Environmental Biology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | | | - Elsa Rousseau
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Sara Capponi
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Simone Bianco
- Functional Genomics and Cellular Engineering, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA 95120, USA
| | | | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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9
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Liu W, Sun Y, Qiu X, Meng C, Song C, Tan L, Liao Y, Liu X, Ding C. Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken. Viruses 2021; 13:v13122409. [PMID: 34960678 PMCID: PMC8703359 DOI: 10.3390/v13122409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host-virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.
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Affiliation(s)
- Weiwei Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Yingjie Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Xusheng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Chunchun Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Cuiping Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Lei Tan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
| | - Xiufan Liu
- School of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (W.L.); (Y.S.); (X.Q.); (C.M.); (C.S.); (L.T.); (Y.L.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-21-3429-3441
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10
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Karlebach G, Aronow B, Baylin SB, Butler D, Foox J, Levy S, Meydan C, Mozsary C, Saravia-Butler AM, Taylor DM, Wurtele E, Mason CE, Beheshti A, Robinson PN. Betacoronavirus-specific alternate splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34230929 PMCID: PMC8259905 DOI: 10.1101/2021.07.02.450920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection as well as datasets from the betacoronaviruses SARS-CoV and MERS as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification and a smaller number of exons than differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by DAS and DGE in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS, potentially modifying a broad range of cellular functions and affecting a diverse set of genes and biological functions.
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11
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Ashraf U, Benoit-Pilven C, Navratil V, Ligneau C, Fournier G, Munier S, Sismeiro O, Coppée JY, Lacroix V, Naffakh N. Influenza virus infection induces widespread alterations of host cell splicing. NAR Genom Bioinform 2020; 2:lqaa095. [PMID: 33575639 PMCID: PMC7680258 DOI: 10.1093/nargab/lqaa095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/24/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022] Open
Abstract
Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here, we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3' end termination site, suggesting that IAVs can specifically manipulate cellular splicing. Among a randomly selected subset of 21 IAV-sensitive alternative splicing events, most are specific to IAV infection as they are not observed upon infection with VSV, induction of interferon expression or induction of an osmotic stress. Finally, the analysis of splicing changes in RED-depleted cells reveals a limited but significant overlap with the splicing changes in IAV-infected cells. This observation suggests that hijacking of RED by IAVs to promote splicing of the abundant viral NS1 mRNAs could partially divert RED from its target mRNAs. All our RNA-seq datasets and analyses are made accessible for browsing through a user-friendly Shiny interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing or https://github.com/cbenoitp/flu-splicing).
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Affiliation(s)
- Usama Ashraf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 75013 Paris, France
| | - Clara Benoit-Pilven
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR5292, 69675 Bron, France
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, 69622 Villeurbanne, France
- EPI ERABLE, INRIA Grenoble Rhône-Alpes, 38330 Montbonnot-Saint-Martin France
| | - Vincent Navratil
- PRABI, Rhône-Alpes Bioinformatics Center, Université Lyon 1, 69622 Villeurbanne, France
- European Virus Bioinformatics Center, 07743 Jena, Germany
- Institut Français de Bioinformatique, IFB-core, UMS 3601, 91057 Évry, France
| | - Cécile Ligneau
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Guillaume Fournier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Sandie Munier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Pôle BIOMICS, Plateforme Transcriptome et Epigenome, 75015 Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Pôle BIOMICS, Plateforme Transcriptome et Epigenome, 75015 Paris, France
| | - Vincent Lacroix
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, 69622 Villeurbanne, France
- EPI ERABLE, INRIA Grenoble Rhône-Alpes, 38330 Montbonnot-Saint-Martin France
| | - Nadia Naffakh
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
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12
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Schaack GA, Mehle A. Experimental Approaches to Identify Host Factors Important for Influenza Virus. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a038521. [PMID: 31871241 DOI: 10.1101/cshperspect.a038521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An ever-expanding toolkit of experimental methods provides the means to discover and characterize host factors important for influenza virus. Here, we describe common methods for investigating genetic relationships and physical interactions between virus and host. A comprehensive knowledge of host:virus interactions is key to understanding how influenza virus exploits the host cell and to potentially identify vulnerabilities that may be manipulated to prevent or treat disease.
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Affiliation(s)
- Grace A Schaack
- Department of Medical Microbiology and Immunology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
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13
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Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway. Cell Mol Life Sci 2020; 78:1423-1444. [PMID: 33084946 PMCID: PMC7576986 DOI: 10.1007/s00018-020-03671-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/14/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
Antiviral responses of interferons (IFNs) are crucial in the host immune response, playing a relevant role in controlling viralw infections. Three types of IFNs, type I (IFN-α, IFN-β), II (IFN-γ) and III (IFN-λ), are classified according to their receptor usage, mode of induction, biological activity and amino acid sequence. Here, we provide a comprehensive review of type I IFN responses and different mechanisms that viruses employ to circumvent this response. In the first part, we will give an overview of the different induction and signaling cascades induced in the cell by IFN-I after virus encounter. Next, highlights of some of the mechanisms used by viruses to counteract the IFN induction will be described. And finally, we will address different mechanism used by viruses to interference with the IFN signaling cascade and the blockade of IFN induced antiviral activities.
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14
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Banerjee AK, Blanco MR, Bruce EA, Honson DD, Chen LM, Chow A, Bhat P, Ollikainen N, Quinodoz SA, Loney C, Thai J, Miller ZD, Lin AE, Schmidt MM, Stewart DG, Goldfarb D, De Lorenzo G, Rihn SJ, Voorhees RM, Botten JW, Majumdar D, Guttman M. SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. Cell 2020; 183:1325-1339.e21. [PMID: 33080218 PMCID: PMC7543886 DOI: 10.1016/j.cell.2020.10.004] [Citation(s) in RCA: 358] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/26/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently identified coronavirus that causes the respiratory disease known as coronavirus disease 2019 (COVID-19). Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis. Here, we comprehensively define the interactions between SARS-CoV-2 proteins and human RNAs. NSP16 binds to the mRNA recognition domains of the U1 and U2 splicing RNAs and acts to suppress global mRNA splicing upon SARS-CoV-2 infection. NSP1 binds to 18S ribosomal RNA in the mRNA entry channel of the ribosome and leads to global inhibition of mRNA translation upon infection. Finally, NSP8 and NSP9 bind to the 7SL RNA in the signal recognition particle and interfere with protein trafficking to the cell membrane upon infection. Disruption of each of these essential cellular functions acts to suppress the interferon response to viral infection. Our results uncover a multipronged strategy utilized by SARS-CoV-2 to antagonize essential cellular processes to suppress host defenses. NSP16 binds mRNA recognition domains of U1/U2 snRNAs and disrupts mRNA splicing NSP1 binds in the mRNA entry channel of the ribosome to disrupt protein translation NSP8 and NSP9 bind the signal recognition particle and disrupt protein trafficking These disruptions of protein production suppress the interferon response to infection
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Affiliation(s)
- Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Emily A Bruce
- Departments of Medicine, Division of Immunobiology and Microbiology, and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Drew D Honson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Linlin M Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Jasmine Thai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zachary D Miller
- Department of Surgery and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Aaron E Lin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Madaline M Schmidt
- Departments of Medicine, Division of Immunobiology and Microbiology, and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Douglas G Stewart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Daniel Goldfarb
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Suzannah J Rihn
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jason W Botten
- Departments of Medicine, Division of Immunobiology and Microbiology, and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Devdoot Majumdar
- Department of Surgery and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA.
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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15
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Wacquiez A, Coste F, Kut E, Gaudon V, Trapp S, Castaing B, Marc D. Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1. Viruses 2020; 12:E947. [PMID: 32867106 PMCID: PMC7552008 DOI: 10.3390/v12090947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 11/16/2022] Open
Abstract
The non-structural protein NS1 of influenza A viruses is an RNA-binding protein of which its activities in the infected cell contribute to the success of the viral cycle, notably through interferon antagonism. We have previously shown that NS1 strongly binds RNA aptamers harbouring virus-specific sequence motifs (Marc et al., Nucleic Acids Res. 41, 434-449). Here, we started out investigating the putative role of one particular virus-specific motif through the phenotypic characterization of mutant viruses that were genetically engineered from the parental strain WSN. Unexpectedly, our data did not evidence biological importance of the putative binding of NS1 to this specific motif (UGAUUGAAG) in the 3'-untranslated region of its own mRNA. Next, we sought to identify specificity determinants in the NS1-RNA interaction through interaction assays in vitro with several RNA ligands and through solving by X-ray diffraction the 3D structure of several complexes associating NS1's RBD with RNAs of various affinities. Our data show that the RBD binds the GUAAC motif within double-stranded RNA helices with an apparent specificity that may rely on the sequence-encoded ability of the RNA to bend its axis. On the other hand, we showed that the RBD binds to the virus-specific AGCAAAAG motif when it is exposed in the apical loop of a high-affinity RNA aptamer, probably through a distinct mode of interaction that still requires structural characterization. Our data are consistent with more than one mode of interaction of NS1's RBD with RNAs, recognizing both structure and sequence determinants.
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MESH Headings
- 3' Untranslated Regions
- Animals
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Cell Line
- Humans
- Influenza A Virus, H1N1 Subtype/chemistry
- Influenza A Virus, H7N1 Subtype/chemistry
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Domains
- RNA/chemistry
- RNA/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- SELEX Aptamer Technique
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Alan Wacquiez
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Franck Coste
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Emmanuel Kut
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Sascha Trapp
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 02, 45071 Orléans, France; (F.C.); (V.G.)
| | - Daniel Marc
- Equipe 3IMo, UMR1282 Infectiologie et Santé Publique, INRAE, F-37380 Nouzilly, France; (A.W.); (E.K.); (S.T.)
- UMR1282 Infectiologie et Santé Publique, Université de Tours, F-37000 Tours, France
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16
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He Y, Fu W, Cao K, He Q, Ding X, Chen J, Zhu L, Chen T, Ding L, Yang Y, Zhu C, Yuan S, Li Z, Zhao C, Zhang X, Xu J. IFN-κ suppresses the replication of influenza A viruses through the IFNAR-MAPK-Fos-CHD6 axis. Sci Signal 2020; 13:13/626/eaaz3381. [PMID: 32265337 DOI: 10.1126/scisignal.aaz3381] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Type I interferons (IFNs) are the first line of defense against viral infection. Using a mouse model of influenza A virus infection, we found that IFN-κ was one of the earliest responding type I IFNs after infection with H9N2, a low-pathogenic avian influenza A virus, whereas this early induction did not occur upon infection with the epidemic-causing H7N9 virus. IFN-κ efficiently suppressed the replication of various influenza viruses in cultured human lung cells, and chromodomain helicase DNA binding protein 6 (CHD6) was the major effector for the antiviral activity of IFN-κ, but not for that of IFN-α or IFN-β. The induction of CHD6 required both of the type I IFN receptor subunits IFNAR1 and IFNAR2, the mitogen-activated protein kinase (MAPK) p38, and the transcription factor c-Fos but was independent of signal transducer and activator of transcription 1 (STAT1) activity. In addition, we showed that pretreatment with IFN-κ protected mice from lethal influenza viral challenge. Together, our findings identify an IFN-κ-specific pathway that constrains influenza A virus and provide evidence that IFN-κ may have potential as a preventative and therapeutic agent against influenza A virus.
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Affiliation(s)
- Yongquan He
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Weihui Fu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Kangli Cao
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Qian He
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Xiangqing Ding
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Jian Chen
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Lingyan Zhu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Tianyue Chen
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Longfei Ding
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Yu Yang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Cuisong Zhu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Songhua Yuan
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China
| | - Zejun Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, P. R. China
| | - Chen Zhao
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China.
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China. .,State Key Laboratory for Infectious Disease Prevention and Control, China Centers for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, P. R. China. .,State Key Laboratory for Infectious Disease Prevention and Control, China Centers for Disease Control and Prevention, Beijing 102206, P. R. China
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17
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Kumari R, Guo Z, Kumar A, Wiens M, Gangappa S, Katz JM, Cox NJ, Lal RB, Sarkar D, Fisher PB, García-Sastre A, Fujita T, Kumar V, Sambhara S, Ranjan P, Lal SK. Influenza virus NS1- C/EBPβ gene regulatory complex inhibits RIG-I transcription. Antiviral Res 2020; 176:104747. [PMID: 32092305 PMCID: PMC10773002 DOI: 10.1016/j.antiviral.2020.104747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 01/23/2020] [Accepted: 02/14/2020] [Indexed: 12/25/2022]
Abstract
Influenza virus non-structural protein 1 (NS1) counteracts host antiviral innate immune responses by inhibiting Retinoic acid inducible gene-I (RIG-I) activation. However, whether NS1 also specifically regulates RIG-I transcription is unknown. Here, we identify a CCAAT/Enhancer Binding Protein beta (C/EBPβ) binding site in the RIG-I promoter as a repressor element, and show that NS1 promotes C/EBPβ phosphorylation and its recruitment to the RIG-I promoter as a C/EBPβ/NS1 complex. C/EBPβ overexpression and siRNA knockdown in human lung epithelial cells resulted in suppression and activation of RIG-I expression respectively, implying a negative regulatory role of C/EBPβ. Further, C/EBPβ phosphorylation, its interaction with NS1 and occupancy at the RIG-I promoter was associated with RIG-I transcriptional inhibition. These findings provide an important insight into the molecular mechanism by which influenza NS1 commandeers RIG-I transcriptional regulation and suppresses host antiviral responses.
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Affiliation(s)
- Rashmi Kumari
- Virology Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, 110067, India
| | - Zhu Guo
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Amrita Kumar
- Virology Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, 110067, India
| | - Mayim Wiens
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shivaprakash Gangappa
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jacqueline M Katz
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nancy J Cox
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Renu B Lal
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine and VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine and VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, 23298, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Department of Medicine Division of Infectious Diseases and Global Health, Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Vijay Kumar
- Virology Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, 110067, India; Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences (ILBS), New Delhi, 110070, India
| | - Suryaprakash Sambhara
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Priya Ranjan
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Sunil K Lal
- Virology Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, 110067, India; School of Science, Tropical Medicine and Biology Multidisciplinary Plateform, Monash University Malaysia, 47500, Bandar Sunway, Selangor DE, Malaysia.
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18
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Esparza M, Mor A, Niederstrasser H, White K, White A, Zhang K, Gao S, Wang J, Liang J, Sho S, Sakthivel R, Sathe AA, Xing C, Muñoz-Moreno R, Shay JW, García-Sastre A, Ready J, Posner B, Fontoura BMA. Chemical intervention of influenza virus mRNA nuclear export. PLoS Pathog 2020; 16:e1008407. [PMID: 32240278 PMCID: PMC7117665 DOI: 10.1371/journal.ppat.1008407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/17/2020] [Indexed: 02/05/2023] Open
Abstract
Influenza A viruses are human pathogens with limited therapeutic options. Therefore, it is crucial to devise strategies for the identification of new classes of antiviral medications. The influenza A virus genome is constituted of 8 RNA segments. Two of these viral RNAs are transcribed into mRNAs that are alternatively spliced. The M1 mRNA encodes the M1 protein but is also alternatively spliced to yield the M2 mRNA during infection. M1 to M2 mRNA splicing occurs at nuclear speckles, and M1 and M2 mRNAs are exported to the cytoplasm for translation. M1 and M2 proteins are critical for viral trafficking, assembly, and budding. Here we show that gene knockout of the cellular protein NS1-BP, a constituent of the M mRNA speckle-export pathway and a binding partner of the virulence factor NS1 protein, inhibits M mRNA nuclear export without altering bulk cellular mRNA export, providing an avenue to preferentially target influenza virus. We performed a high-content, image-based chemical screen using single-molecule RNA-FISH to label viral M mRNAs followed by multistep quantitative approaches to assess cellular mRNA and cell toxicity. We identified inhibitors of viral mRNA biogenesis and nuclear export that exhibited no significant activity towards bulk cellular mRNA at non-cytotoxic concentrations. Among the hits is a small molecule that preferentially inhibits nuclear export of a subset of viral and cellular mRNAs without altering bulk cellular mRNA export. These findings underscore specific nuclear export requirements for viral mRNAs and phenocopy down-regulation of the mRNA export factor UAP56. This RNA export inhibitor impaired replication of diverse influenza A virus strains at non-toxic concentrations. Thus, this screening strategy yielded compounds that alone or in combination may serve as leads to new ways of treating influenza virus infection and are novel tools for studying viral RNA trafficking in the nucleus.
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Affiliation(s)
- Matthew Esparza
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Amir Mor
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Hanspeter Niederstrasser
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Alexander White
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Juan Wang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jue Liang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Sei Sho
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ramanavelan Sakthivel
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Adwait A. Sathe
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Raquel Muñoz-Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jerry W. Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Joseph Ready
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Bruce Posner
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Beatriz M. A. Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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19
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Chen G, Ma LC, Wang S, Woltz RL, Grasso EM, Montelione GT, Krug RM. A double-stranded RNA platform is required for the interaction between a host restriction factor and the NS1 protein of influenza A virus. Nucleic Acids Res 2020; 48:304-315. [PMID: 31754723 PMCID: PMC6943125 DOI: 10.1093/nar/gkz1094] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/18/2019] [Accepted: 11/05/2019] [Indexed: 01/02/2023] Open
Abstract
Influenza A viruses cause widespread human respiratory disease. The viral multifunctional NS1 protein inhibits host antiviral responses. This inhibition results from the binding of specific cellular antiviral proteins at various positions on the NS1 protein. Remarkably, binding of several proteins also requires the two amino-acid residues in the NS1 N-terminal RNA-binding domain (RBD) that are required for binding double-stranded RNA (dsRNA). Here we focus on the host restriction factor DHX30 helicase that is countered by the NS1 protein, and establish why the dsRNA-binding activity of NS1 is required for its binding to DHX30. We show that the N-terminal 152 amino-acid residue segment of DHX30, denoted DHX30N, possesses all the antiviral activity of DHX30 and contains a dsRNA-binding domain, and that the NS1-DHX30 interaction in vivo requires the dsRNA-binding activity of both DHX30N and the NS1 RBD. We demonstrate why this is the case using bacteria-expressed proteins: the DHX30N-NS1 RBD interaction in vitro requires the presence of a dsRNA platform that binds both NS1 RBD and DHX30N. We propose that a similar dsRNA platform functions in interactions of the NS1 protein with other proteins that requires these same two amino-acid residues required for NS1 RBD dsRNA-binding activity.
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Affiliation(s)
- Guifang Chen
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Li-Chung Ma
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Shanshan Wang
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ryan L Woltz
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Emily M Grasso
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.,Center for Biotechnology and Interdisciplinary Studies, and Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert M Krug
- Department of Molecular Biosciences, John Ring LaMontagne Center for Infectious Disease, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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20
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PA-X antagonises MAVS-dependent accumulation of early type I interferon messenger RNAs during influenza A virus infection. Sci Rep 2019; 9:7216. [PMID: 31076606 PMCID: PMC6510759 DOI: 10.1038/s41598-019-43632-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
The sensing of viral nucleic acids by the innate immune system activates a potent antiviral response in the infected cell, a key component of which is the expression of genes encoding type I interferons (IFNs). Many viruses counteract this response by blocking the activation of host nucleic acid sensors. The evolutionarily conserved influenza A virus (IAV) protein PA-X has been implicated in suppressing the host response to infection, including the expression of type I IFNs. Here, we characterise this further using a PA-X-deficient virus of the mouse-adapted PR8 strain to study activation of the innate immune response in a mouse model of the early response to viral infection. We show that levels of Ifna4 and Ifnb1 mRNAs in the lungs of infected mice were elevated in the absence of PA-X and that this was completely dependent on MAVS. This therefore suggests a role for PA-X in preventing the accumulation of early type I IFN mRNAs in the lung during IAV infection.
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21
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Thompson MG, Lynch KW. Functional and Mechanistic Interplay of Host and Viral Alternative Splicing Regulation during Influenza Infection. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019; 84:123-131. [PMID: 32703803 DOI: 10.1101/sqb.2019.84.039040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Alternative splicing is a pervasive gene regulatory mechanism utilized by both mammalian cells and viruses to expand their genomic coding capacity. The process of splicing and the RNA sequences that guide this process are the same in mammalian and viral transcripts; however, viruses lack the splicing machinery and therefore must usurp both the host spliceosome and many of the associated regulatory proteins in order to correctly process their genes. Here, we use the example of the influenza A virus to both describe how viruses utilize host splicing factors to regulate their own splicing and provide examples of how viral infection can, in turn, alter host splicing. Importantly, we show that at least some of the viral-induced changes in host splicing occur in genes that alter the efficiency of influenza replication. We emphasize the importance of increased understanding of the mechanistic interplay between host and viral splicing, and its functional consequences, in uncovering potential antiviral vulnerabilities.
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Affiliation(s)
- Matthew G Thompson
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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22
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Ashraf U, Benoit-Pilven C, Lacroix V, Navratil V, Naffakh N. Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing. Trends Microbiol 2018; 27:268-281. [PMID: 30577974 DOI: 10.1016/j.tim.2018.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/19/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022]
Abstract
Alteration of host cell splicing is a common feature of many viral infections which is underappreciated because of the complexity and technical difficulty of studying alternative splicing (AS) regulation. Recent advances in RNA sequencing technologies revealed that up to several hundreds of host genes can show altered mRNA splicing upon viral infection. The observed changes in AS events can be either a direct consequence of viral manipulation of the host splicing machinery or result indirectly from the virus-induced innate immune response or cellular damage. Analysis at a higher resolution with single-cell RNAseq, and at a higher scale with the integration of multiple omics data sets in a systems biology perspective, will be needed to further comprehend this complex facet of virus-host interactions.
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Affiliation(s)
- Usama Ashraf
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, F-75015 Paris, France; CNRS UMR3569, F-75015 Paris, France; Université Paris Diderot, Sorbonne Paris Cité EA302, F-75015 Paris, France
| | - Clara Benoit-Pilven
- INSERM U1028; CNRS UMR5292, Lyon Neuroscience Research Center, Genetic of Neuro-development Anomalies Team, F-69000 Lyon, France; Université Claude Bernard Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; EPI ERABLE, INRIA Grenoble Rhône-Alpes, F-38330 Montbonnot Saint-Martin, France
| | - Vincent Lacroix
- Université Claude Bernard Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; EPI ERABLE, INRIA Grenoble Rhône-Alpes, F-38330 Montbonnot Saint-Martin, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France; European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Nadia Naffakh
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, F-75015 Paris, France; CNRS UMR3569, F-75015 Paris, France; Université Paris Diderot, Sorbonne Paris Cité EA302, F-75015 Paris, France.
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