1
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Ortega-Prieto AM, Jimenez-Guardeño JM. Interferon-stimulated genes and their antiviral activity against SARS-CoV-2. mBio 2024; 15:e0210024. [PMID: 39171921 PMCID: PMC11389394 DOI: 10.1128/mbio.02100-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic remains an international health problem caused by the recent emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of May 2024, SARS-CoV-2 has caused more than 775 million cases and over 7 million deaths globally. Despite current vaccination programs, infections are still rapidly increasing, mainly due to the appearance and spread of new variants, variations in immunization rates, and limitations of current vaccines in preventing transmission. This underscores the need for pan-variant antivirals and treatments. The interferon (IFN) system is a critical element of the innate immune response and serves as a frontline defense against viruses. It induces a generalized antiviral state by transiently upregulating hundreds of IFN-stimulated genes (ISGs). To gain a deeper comprehension of the innate immune response to SARS-CoV-2, its connection to COVID-19 pathogenesis, and the potential therapeutic implications, this review provides a detailed overview of fundamental aspects of the diverse ISGs identified for their antiviral properties against SARS-CoV-2. It emphasizes the importance of these proteins in controlling viral replication and spread. Furthermore, we explore methodological approaches for the identification of ISGs and conduct a comparative analysis with other viruses. Deciphering the roles of ISGs and their interactions with viral pathogens can help identify novel targets for antiviral therapies and enhance our preparedness to confront current and future viral threats.
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Affiliation(s)
- Ana Maria Ortega-Prieto
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
| | - Jose M Jimenez-Guardeño
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, Málaga, Spain
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2
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Shao R, Visser I, Fros JJ, Yin X. Versatility of the Zinc-Finger Antiviral Protein (ZAP) As a Modulator of Viral Infections. Int J Biol Sci 2024; 20:4585-4600. [PMID: 39309436 PMCID: PMC11414379 DOI: 10.7150/ijbs.98029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 08/15/2024] [Indexed: 09/25/2024] Open
Abstract
The zinc-finger antiviral protein (ZAP) is a restriction factor that proficiently impedes the replication of a variety of RNA and DNA viruses. In recent years, the affinity of ZAP's zinc-fingers for single-stranded RNA (ssRNA) rich in CpG dinucleotides was uncovered. High frequencies of CpGs in RNA may suggest a non-self origin, which underscores the importance of ZAP as a potential cellular sensor of (viral) RNA. Upon binding viral RNA, ZAP recruits cellular cofactors to orchestrate a finely tuned antiviral response that limits virus replication via distinct mechanisms. These include promoting degradation of viral RNA, inhibiting RNA translation, and synergizing with other immune pathways. Depending on the viral species and experimental set-up, different isoforms and cellular cofactors have been reported to be dominant in shaping the ZAP-mediated antiviral response. Here we review how ZAP differentially affects viral replication depending on distinct interactions with RNA, cellular cofactors, and viral proteins to discuss how these interactions shape the antiviral mechanisms that have thus far been reported for ZAP. Importantly, we zoom in on the unknown aspects of ZAP's antiviral system and its therapeutic potential to be employed in vaccine design.
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Affiliation(s)
- Ran Shao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Imke Visser
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jelke J Fros
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Xin Yin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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3
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Huang S, Girdner J, Nguyen LP, Sandoval C, Fregoso OI, Enard D, Li MMH. Positive selection analyses identify a single WWE domain residue that shapes ZAP into a more potent restriction factor against alphaviruses. PLoS Pathog 2024; 20:e1011836. [PMID: 39207950 PMCID: PMC11361444 DOI: 10.1371/journal.ppat.1011836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
The host interferon pathway upregulates intrinsic restriction factors in response to viral infection. Many of them block a diverse range of viruses, suggesting that their antiviral functions might have been shaped by multiple viral families during evolution. Host-virus conflicts have led to the rapid adaptation of host and viral proteins at their interaction hotspots. Hence, we can use evolutionary genetic analyses to elucidate antiviral mechanisms and domain functions of restriction factors. Zinc finger antiviral protein (ZAP) is a restriction factor against RNA viruses such as alphaviruses, in addition to other RNA, retro-, and DNA viruses, yet its precise antiviral mechanism is not fully characterized. Previously, an analysis of 13 primate ZAP orthologs identified three positively selected residues in the poly(ADP-ribose) polymerase-like domain. However, selective pressure from ancient alphaviruses and others likely drove ZAP adaptation in a wider representation of mammals. We performed positive selection analyses in 261 mammalian ZAP using more robust methods with complementary strengths and identified seven positively selected sites in all domains of the protein. We generated ZAP inducible cell lines in which the positively selected residues of ZAP are mutated and tested their effects on alphavirus replication and known ZAP activities. Interestingly, the mutant in the second WWE domain of ZAP (N658A) is dramatically better than wild-type ZAP at blocking replication of Sindbis virus and other ZAP-sensitive alphaviruses due to enhanced viral translation inhibition. The N658A mutant is adjacent to the previously reported poly(ADP-ribose) (PAR) binding pocket, but surprisingly has reduced binding to PAR. In summary, the second WWE domain is critical for engineering a more potent ZAP and fluctuations in PAR binding modulate ZAP antiviral activity. Our study has the potential to unravel the role of ADP-ribosylation in the host innate immune defense and viral evolutionary strategies that antagonize this post-translational modification.
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Affiliation(s)
- Serina Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Juliana Girdner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - LeAnn P. Nguyen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Carina Sandoval
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Oliver I. Fregoso
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Melody M. H. Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
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4
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Smart A, Gilmer O, Caliskan N. Translation Inhibition Mediated by Interferon-Stimulated Genes during Viral Infections. Viruses 2024; 16:1097. [PMID: 39066259 PMCID: PMC11281336 DOI: 10.3390/v16071097] [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: 04/29/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Viruses often pose a significant threat to the host through the exploitation of cellular machineries for their own benefit. In the context of immune responses, myriad host factors are deployed to target viral RNAs and inhibit viral protein translation, ultimately hampering viral replication. Understanding how "non-self" RNAs interact with the host translation machinery and trigger immune responses would help in the development of treatment strategies for viral infections. In this review, we explore how interferon-stimulated gene products interact with viral RNA and the translation machinery in order to induce either global or targeted translation inhibition.
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Affiliation(s)
- Alexandria Smart
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Orian Gilmer
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Neva Caliskan
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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5
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Busa VF, Ando Y, Aigner S, Yee BA, Yeo GW, Leung AK. Transcriptome regulation by PARP13 in basal and antiviral states in human cells. iScience 2024; 27:109251. [PMID: 38495826 PMCID: PMC10943485 DOI: 10.1016/j.isci.2024.109251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
The RNA-binding protein PARP13 is a primary factor in the innate antiviral response, which suppresses translation and drives decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to activate antiviral pathways including co-translational addition of ISG15, or ISGylation. We performed enhanced crosslinking immunoprecipitation (eCLIP) and RNA-seq in human cells to investigate PARP13's role in transcriptome regulation for both basal and antiviral states. We find that the antiviral response shifts PARP13 target localization, but not its binding preferences, and that PARP13 supports the expression of ISGylation-related genes, including PARP13's cofactor, TRIM25. PARP13 associates with TRIM25 via RNA-protein interactions, and we elucidate a transcriptome-wide periodicity of PARP13 binding around TRIM25. Taken together, our study implicates PARP13 in creating and maintaining a cellular environment poised for an antiviral response through limiting PARP13 translation, regulating access to distinct mRNA pools, and elevating ISGylation machinery expression.
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Affiliation(s)
- Veronica F. Busa
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yoshinari Ando
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anthony K.L. Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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6
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Chuenchat J, Kardkarnklai S, Narkpuk J, Liwnaree B, Jongkaewwattana A, Jaru-Ampornpan P, Sungsuwan S. PEDV nucleocapsid antagonizes zinc-finger antiviral protein by disrupting the interaction with its obligate co-factor, TRIM25. Vet Microbiol 2024; 291:110033. [PMID: 38432077 DOI: 10.1016/j.vetmic.2024.110033] [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: 11/24/2023] [Revised: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
The genomes of many pathogens contain high-CpG content, which is less common in most vertebrate host genomes. Such a distinct di-nucleotide composition in a non-self invader constitutes a special feature recognized by its host's immune system. The zinc-finger antiviral protein (ZAP) is part of the pattern recognition receptors (PRRs) that recognize CpG-rich viral RNA and subsequently initiate RNA degradation as an antiviral defense measure. To counteract such ZAP-mediated restriction, some viruses evolve to either suppress the CpG content in their genome or produce an antagonistic factor to evade ZAP sensing. We have previously shown that a coronavirus, Porcine epidermic diarrhea virus (PEDV), employs its nucleocapsid protein (PEDV-N) to suppress the ZAP-dependent antiviral activity. Here, we propose a mechanism by which PEDV-N suppresses ZAP function by interfering with the interaction between ZAP and its essential cofactor, Tripartite motif-containing protein 25 (TRIM25). PEDV-N was found to interact with ZAP through its N-terminal domain and with TRIM25 through its C-terminal domain. We showed that PEDV-N and ZAP compete for binding to the SPla and the RYanodine Receptor (SPRY) domain of TRIM25, resulting in PEDV-N preventing TRIM25 from interacting with and promoting ZAP. Our result also showed that the presence of PEDV-N in the complex reduces the E3 ligase activity of TRIM25 on ZAP, which is required for the antiviral activity of ZAP. The host-pathogen interaction mechanism presented herein provides an insight into the new function of this abundant and versatile viral protein from a coronavirus which could be a key target for development of antiviral interventions.
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Affiliation(s)
- Jantakarn Chuenchat
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Pathum Thani 12120, Thailand
| | - Supasek Kardkarnklai
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Pathum Thani 12120, Thailand
| | - Jaraspim Narkpuk
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Pathum Thani 12120, Thailand
| | - Benjamas Liwnaree
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Pathum Thani 12120, Thailand
| | - Anan Jongkaewwattana
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Pathum Thani 12120, Thailand
| | - Peera Jaru-Ampornpan
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Pathum Thani 12120, Thailand
| | - Suttipun Sungsuwan
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Pathum Thani 12120, Thailand.
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7
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de Andrade KQ, Cirne-Santos CC. Antiviral Activity of Zinc Finger Antiviral Protein (ZAP) in Different Virus Families. Pathogens 2023; 12:1461. [PMID: 38133344 PMCID: PMC10747524 DOI: 10.3390/pathogens12121461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
The CCCH-type zinc finger antiviral protein (ZAP) in humans, specifically isoforms ZAP-L and ZAP-S, is a crucial component of the cell's intrinsic immune response. ZAP acts as a post-transcriptional RNA restriction factor, exhibiting its activity during infections caused by retroviruses and alphaviruses. Its function involves binding to CpG (cytosine-phosphate-guanine) dinucleotide sequences present in viral RNA, thereby directing it towards degradation. Since vertebrate cells have a suppressed frequency of CpG dinucleotides, ZAP is capable of distinguishing foreign genetic elements. The expression of ZAP leads to the reduction of viral replication and impedes the assembly of new virus particles. However, the specific mechanisms underlying these effects have yet to be fully understood. Several questions regarding ZAP's mechanism of action remain unanswered, including the impact of CpG dinucleotide quantity on ZAP's activity, whether this sequence is solely required for the binding between ZAP and viral RNA, and whether the recruitment of cofactors is dependent on cell type, among others. This review aims to integrate the findings from studies that elucidate ZAP's antiviral role in various viral infections, discuss gaps that need to be filled through further studies, and shed light on new potential targets for therapeutic intervention.
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Affiliation(s)
- Kívia Queiroz de Andrade
- Laboratory of Immunology of Infectious Disease, Immunology Department, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Claudio Cesar Cirne-Santos
- Laboratory of Molecular Virology and Marine Biotechnology, Department of Cellular and Molecular Biology, Institute of Biology, Federal Fluminense University, Niterói 24020-150, RJ, Brazil
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8
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Lytras S, Wickenhagen A, Sugrue E, Stewart DG, Swingler S, Sims A, Jackson Ireland H, Davies EL, Ludlam EM, Li Z, Hughes J, Wilson SJ. Resurrection of 2'-5'-oligoadenylate synthetase 1 (OAS1) from the ancestor of modern horseshoe bats blocks SARS-CoV-2 replication. PLoS Biol 2023; 21:e3002398. [PMID: 38015855 PMCID: PMC10683996 DOI: 10.1371/journal.pbio.3002398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
The prenylated form of the human 2'-5'-oligoadenylate synthetase 1 (OAS1) protein has been shown to potently inhibit the replication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. However, the OAS1 orthologue in the horseshoe bats (superfamily Rhinolophoidea), the reservoir host of SARS-related coronaviruses (SARSr-CoVs), has lost the prenylation signal required for this antiviral activity. Herein, we used an ancestral state reconstruction approach to predict and reconstitute in vitro, the most likely OAS1 protein sequence expressed by the Rhinolophoidea common ancestor prior to its prenylation loss (RhinoCA OAS1). We exogenously expressed the ancient bat protein in vitro to show that, unlike its non-prenylated horseshoe bat descendants, RhinoCA OAS1 successfully blocks SARS-CoV-2 replication. Using protein structure predictions in combination with evolutionary hypothesis testing methods, we highlight sites under unique diversifying selection specific to OAS1's evolution in the Rhinolophoidea. These sites are located near the RNA-binding region and the C-terminal end of the protein where the prenylation signal would have been. Our results confirm that OAS1 prenylation loss at the base of the Rhinolophoidea clade ablated the ability of OAS1 to restrict SARSr-CoV replication and that subsequent evolution of the gene in these bats likely favoured an alternative function. These findings can advance our understanding of the tightly linked association between SARSr-CoVs and horseshoe bats.
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Affiliation(s)
- Spyros Lytras
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Elena Sugrue
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Douglas G. Stewart
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Simon Swingler
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Anna Sims
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Hollie Jackson Ireland
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Emma L. Davies
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Eliza M. Ludlam
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Zhuonan Li
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC–University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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9
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Sharp CP, Thompson BH, Nash TJ, Diebold O, Pinto RM, Thorley L, Lin YT, Sives S, Wise H, Clohisey Hendry S, Grey F, Vervelde L, Simmonds P, Digard P, Gaunt ER. CpG dinucleotide enrichment in the influenza A virus genome as a live attenuated vaccine development strategy. PLoS Pathog 2023; 19:e1011357. [PMID: 37146066 PMCID: PMC10191365 DOI: 10.1371/journal.ppat.1011357] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/17/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023] Open
Abstract
Synonymous recoding of RNA virus genomes is a promising approach for generating attenuated viruses to use as vaccines. Problematically, recoding typically hinders virus growth, but this may be rectified using CpG dinucleotide enrichment. CpGs are recognised by cellular zinc-finger antiviral protein (ZAP), and so in principle, removing ZAP sensing from a virus propagation system will reverse attenuation of a CpG-enriched virus, enabling high titre yield of a vaccine virus. We tested this using a vaccine strain of influenza A virus (IAV) engineered for increased CpG content in genome segment 1. Virus attenuation was mediated by the short isoform of ZAP, correlated with the number of CpGs added, and was enacted via turnover of viral transcripts. The CpG-enriched virus was strongly attenuated in mice, yet conveyed protection from a potentially lethal challenge dose of wildtype virus. Importantly for vaccine development, CpG-enriched viruses were genetically stable during serial passage. Unexpectedly, in both MDCK cells and embryonated hens' eggs that are used to propagate live attenuated influenza vaccines, the ZAP-sensitive virus was fully replication competent. Thus, ZAP-sensitive CpG enriched viruses that are defective in human systems can yield high titre in vaccine propagation systems, providing a realistic, economically viable platform to augment existing live attenuated vaccines.
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Affiliation(s)
- Colin P. Sharp
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Beth H. Thompson
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Tessa J. Nash
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Ola Diebold
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Rute M. Pinto
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Luke Thorley
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Yao-Tang Lin
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Samantha Sives
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Helen Wise
- Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Sara Clohisey Hendry
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Finn Grey
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Lonneke Vervelde
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Paul Digard
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Eleanor R. Gaunt
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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10
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IFN-Induced PARPs—Sensors of Foreign Nucleic Acids? Pathogens 2023; 12:pathogens12030457. [PMID: 36986379 PMCID: PMC10057411 DOI: 10.3390/pathogens12030457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Cells have developed different strategies to cope with viral infections. Key to initiating a defense response against viruses is the ability to distinguish foreign molecules from their own. One central mechanism is the perception of foreign nucleic acids by host proteins which, in turn, initiate an efficient immune response. Nucleic acid sensing pattern recognition receptors have evolved, each targeting specific features to discriminate viral from host RNA. These are complemented by several RNA-binding proteins that assist in sensing of foreign RNAs. There is increasing evidence that the interferon-inducible ADP-ribosyltransferases (ARTs; PARP9—PARP15) contribute to immune defense and attenuation of viruses. However, their activation, subsequent targets, and precise mechanisms of interference with viruses and their propagation are still largely unknown. Best known for its antiviral activities and its role as RNA sensor is PARP13. In addition, PARP9 has been recently described as sensor for viral RNA. Here we will discuss recent findings suggesting that some PARPs function in antiviral innate immunity. We expand on these findings and integrate this information into a concept that outlines how the different PARPs might function as sensors of foreign RNA. We speculate about possible consequences of RNA binding with regard to the catalytic activities of PARPs, substrate specificity and signaling, which together result in antiviral activities.
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11
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Lista MJ, Ficarelli M, Wilson H, Kmiec D, Youle RL, Wanford J, Winstone H, Odendall C, Taylor IA, Neil SJD, Swanson CM. A Nuclear Export Signal in KHNYN Required for Its Antiviral Activity Evolved as ZAP Emerged in Tetrapods. J Virol 2023; 97:e0087222. [PMID: 36633408 PMCID: PMC9888277 DOI: 10.1128/jvi.00872-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
The zinc finger antiviral protein (ZAP) inhibits viral replication by directly binding CpG dinucleotides in cytoplasmic viral RNA to inhibit protein synthesis and target the RNA for degradation. ZAP evolved in tetrapods and there are clear orthologs in reptiles, birds, and mammals. When ZAP emerged, other proteins may have evolved to become cofactors for its antiviral activity. KHNYN is a putative endoribonuclease that is required for ZAP to restrict retroviruses. To determine its evolutionary path after ZAP emerged, we compared KHNYN orthologs in mammals and reptiles to those in fish, which do not encode ZAP. This identified residues in KHNYN that are highly conserved in species that encode ZAP, including several in the CUBAN domain. The CUBAN domain interacts with NEDD8 and Cullin-RING E3 ubiquitin ligases. Deletion of the CUBAN domain decreased KHNYN antiviral activity, increased protein expression and increased nuclear localization. However, mutation of residues required for the CUBAN domain-NEDD8 interaction increased KHNYN abundance but did not affect its antiviral activity or cytoplasmic localization, indicating that Cullin-mediated degradation may control its homeostasis and regulation of protein turnover is separable from its antiviral activity. By contrast, the C-terminal residues in the CUBAN domain form a CRM1-dependent nuclear export signal (NES) that is required for its antiviral activity. Deletion or mutation of the NES increased KHNYN nuclear localization and decreased its interaction with ZAP. The final 2 positions of this NES are not present in fish KHNYN orthologs and we hypothesize their evolution allowed KHNYN to act as a ZAP cofactor. IMPORTANCE The interferon system is part of the innate immune response that inhibits viruses and other pathogens. This system emerged approximately 500 million years ago in early vertebrates. Since then, some genes have evolved to become antiviral interferon-stimulated genes (ISGs) while others evolved so their encoded protein could interact with proteins encoded by ISGs and contribute to their activity. However, this remains poorly characterized. ZAP is an ISG that arose during tetrapod evolution and inhibits viral replication. Because KHNYN interacts with ZAP and is required for its antiviral activity against retroviruses, we conducted an evolutionary analysis to determine how specific amino acids in KHNYN evolved after ZAP emerged. This identified a nuclear export signal that evolved in tetrapods and is required for KHNYN to traffic in the cell and interact with ZAP. Overall, specific residues in KHNYN evolved to allow it to act as a cofactor for ZAP antiviral activity.
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Affiliation(s)
- Maria J. Lista
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Mattia Ficarelli
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Harry Wilson
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Dorota Kmiec
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Rebecca L. Youle
- King’s College London, Department of Infectious Diseases, London, United Kingdom
- The Francis Crick Institute, Macromolecular Structure Laboratory, London, United Kingdom
| | - Joseph Wanford
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Helena Winstone
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Charlotte Odendall
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Ian A. Taylor
- The Francis Crick Institute, Macromolecular Structure Laboratory, London, United Kingdom
| | - Stuart J. D. Neil
- King’s College London, Department of Infectious Diseases, London, United Kingdom
| | - Chad M. Swanson
- King’s College London, Department of Infectious Diseases, London, United Kingdom
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12
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Yuan Y, Fang A, Wang Z, Tian B, Zhang Y, Sui B, Luo Z, Li Y, Zhou M, Chen H, Fu ZF, Zhao L. Trim25 restricts rabies virus replication by destabilizing phosphoprotein. CELL INSIGHT 2022; 1:100057. [PMID: 37193556 PMCID: PMC10120326 DOI: 10.1016/j.cellin.2022.100057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 05/18/2023]
Abstract
Tripartite motif-containing protein 25 (Trim25) is an E3 ubiquitin ligase that activates retinoid acid-inducible gene I (RIG-I) and promotes the antiviral interferon response. Recent studies have shown that Trim25 can bind and degrade viral proteins, suggesting a different mechanism of Trim25 on its antiviral effects. In this study, Trim25 expression was upregulated in cells and mouse brains after rabies virus (RABV) infection. Moreover, expression of Trim25 limited RABV replication in cultured cells. Overexpression of Trim25 caused attenuated viral pathogenicity in a mouse model that was intramuscularly injected with RABV. Further experiments confirmed that Trim25 inhibited RABV replication via two different mechanisms: an E3 ubiquitin ligase-dependent mechanism and an E3 ubiquitin ligase-independent mechanism. Specifically, the CCD domain of Trim25 interacted with RABV phosphoprotein (RABV-P) at amino acid (AA) position at 72 and impaired the stability of RABV-P via complete autophagy. This study reveals a novel mechanism by which Trim25 restricts RABV replication by destabilizing RABV-P, which is independent of its E3 ubiquitin ligase activity.
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Affiliation(s)
- Yueming Yuan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - An Fang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zongmei Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Tian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baokun Sui
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhaochen Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingying Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ming Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhen F. Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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13
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Sungsuwan S, Kadkanklai S, Mhuantong W, Jongkaewwattana A, Jaru-Ampornpan P. Zinc-finger antiviral protein-mediated inhibition of porcine epidemic diarrhea virus growth is antagonized by the coronaviral nucleocapsid protein. Front Microbiol 2022; 13:975632. [PMID: 36160209 PMCID: PMC9493364 DOI: 10.3389/fmicb.2022.975632] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Coronaviruses have long posed a major threat not only to human health but also to agriculture. Outbreaks of an animal coronavirus such as porcine epidemic diarrhea virus (PEDV) can cause up-to-100% mortality in suckling piglets, resulting in devastating effects on the livestock industry. Understanding how the virus evades its host's defense can help us better manage the infection. Zinc-finger antiviral protein (ZAP) is an important class of host antiviral factors against a variety of viruses, including the human coronavirus. In this study, we have shown that a representative porcine coronavirus, PEDV, can be suppressed by endogenous or porcine-cell-derived ZAP in VeroE6 cells. An uneven distribution pattern of CpG dinucleotides in the viral genome is one of the factors contributing to suppression, as an increase in CpG content in the nucleocapsid (N) gene renders the virus more susceptible to ZAP. Our study revealed that the virus uses its own nucleocapsid protein (pCoV-N) to interact with ZAP and counteract the activity of ZAP. The insights into coronavirus-host interactions shown in this work could be used in the design and development of modern vaccines and antiviral agents for the next pandemic.
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Affiliation(s)
- Suttipun Sungsuwan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
| | - Supasek Kadkanklai
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
| | - Anan Jongkaewwattana
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
| | - Peera Jaru-Ampornpan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
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14
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Yang E, Nguyen LP, Wisherop CA, Kan RL, Li MM. The Role of ZAP and TRIM25 RNA Binding in Restricting Viral Translation. Front Cell Infect Microbiol 2022; 12:886929. [PMID: 35800389 PMCID: PMC9253567 DOI: 10.3389/fcimb.2022.886929] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/23/2022] Open
Abstract
The innate immune response controls the acute phase of virus infections; critical to this response is the induction of type I interferon (IFN) and resultant IFN-stimulated genes to establish an antiviral environment. One such gene, zinc finger antiviral protein (ZAP), is a potent antiviral factor that inhibits replication of diverse RNA and DNA viruses by binding preferentially to CpG-rich viral RNA. ZAP restricts alphaviruses and the flavivirus Japanese encephalitis virus (JEV) by inhibiting translation of their positive-sense RNA genomes. While ZAP residues important for RNA binding and CpG specificity have been identified by recent structural studies, their role in viral translation inhibition has yet to be characterized. Additionally, the ubiquitin E3 ligase tripartite motif-containing protein 25 (TRIM25) has recently been uncovered as a critical co-factor for ZAP's suppression of alphavirus translation. While TRIM25 RNA binding is required for efficient TRIM25 ligase activity, its importance in the context of ZAP translation inhibition remains unclear. Here, we characterized the effects of ZAP and TRIM25 RNA binding on translation inhibition in the context of the prototype alphavirus Sindbis virus (SINV) and JEV. To do so, we generated a series of ZAP and TRIM25 RNA binding mutants, characterized loss of their binding to SINV genomic RNA, and assessed their ability to interact with each other and to suppress SINV replication, SINV translation, and JEV translation. We found that mutations compromising general RNA binding of ZAP and TRIM25 impact their ability to restrict SINV replication, but mutations specifically targeting ZAP CpG-mediated RNA binding have a greater effect on SINV and JEV translation inhibition. Interestingly, ZAP-TRIM25 interaction is a critical determinant of JEV translation inhibition. Taken together, these findings illuminate the contribution of RNA binding and co-factor interaction to the synergistic inhibition of viral translation by ZAP and TRIM25.
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Affiliation(s)
- Emily Yang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - LeAnn P. Nguyen
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Carlyn A. Wisherop
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ryan L. Kan
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Melody M.H. Li
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
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15
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The Evolutionary Dance between Innate Host Antiviral Pathways and SARS-CoV-2. Pathogens 2022; 11:pathogens11050538. [PMID: 35631059 PMCID: PMC9147806 DOI: 10.3390/pathogens11050538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 02/04/2023] Open
Abstract
Compared to what we knew at the start of the SARS-CoV-2 global pandemic, our understanding of the interplay between the interferon signaling pathway and SARS-CoV-2 infection has dramatically increased. Innate antiviral strategies range from the direct inhibition of viral components to reprograming the host’s own metabolic pathways to block viral infection. SARS-CoV-2 has also evolved to exploit diverse tactics to overcome immune barriers and successfully infect host cells. Herein, we review the current knowledge of the innate immune signaling pathways triggered by SARS-CoV-2 with a focus on the type I interferon response, as well as the mechanisms by which SARS-CoV-2 impairs those defenses.
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16
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Novak Kujundžić R. COVID-19: Are We Facing Secondary Pellagra Which Cannot Simply Be Cured by Vitamin B3? Int J Mol Sci 2022; 23:ijms23084309. [PMID: 35457123 PMCID: PMC9032523 DOI: 10.3390/ijms23084309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
Immune response to SARS-CoV-2 and ensuing inflammation pose a huge challenge to the host’s nicotinamide adenine dinucleotide (NAD+) metabolism. Humans depend on vitamin B3 for biosynthesis of NAD+, indispensable for many metabolic and NAD+-consuming signaling reactions. The balance between its utilization and resynthesis is vitally important. Many extra-pulmonary symptoms of COVID-19 strikingly resemble those of pellagra, vitamin B3 deficiency (e.g., diarrhoea, dermatitis, oral cavity and tongue manifestations, loss of smell and taste, mental confusion). In most developed countries, pellagra is successfully eradicated by vitamin B3 fortification programs. Thus, conceivably, it has not been suspected as a cause of COVID-19 symptoms. Here, the deregulation of the NAD+ metabolism in response to the SARS-CoV-2 infection is reviewed, with special emphasis on the differences in the NAD+ biosynthetic pathway’s efficiency in conditions predisposing for the development of serious COVID-19. SARS-CoV-2 infection-induced NAD+ depletion and the elevated levels of its metabolites contribute to the development of a systemic disease. Acute liberation of nicotinamide (NAM) in antiviral NAD+-consuming reactions potentiates “NAM drain”, cooperatively mediated by nicotinamide N-methyltransferase and aldehyde oxidase. “NAM drain” compromises the NAD+ salvage pathway’s fail-safe function. The robustness of the host’s NAD+ salvage pathway, prior to the SARS-CoV-2 infection, is an important determinant of COVID-19 severity and persistence of certain symptoms upon resolution of infection.
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Affiliation(s)
- Renata Novak Kujundžić
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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17
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Zhao X, Chen D, Li X, Griffith L, Chang J, An P, Guo JT. Interferon Control of Human Coronavirus Infection and Viral Evasion: Mechanistic Insights and Implications for Antiviral Drug and Vaccine Development. J Mol Biol 2022; 434:167438. [PMID: 34990653 PMCID: PMC8721920 DOI: 10.1016/j.jmb.2021.167438] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 12/16/2022]
Abstract
Recognition of viral infections by various pattern recognition receptors (PRRs) activates an inflammatory cytokine response that inhibits viral replication and orchestrates the activation of adaptive immune responses to control the viral infection. The broadly active innate immune response puts a strong selective pressure on viruses and drives the selection of variants with increased capabilities to subvert the induction and function of antiviral cytokines. This revolutionary process dynamically shapes the host ranges, cell tropism and pathogenesis of viruses. Recent studies on the innate immune responses to the infection of human coronaviruses (HCoV), particularly SARS-CoV-2, revealed that HCoV infections can be sensed by endosomal toll-like receptors and/or cytoplasmic RIG-I-like receptors in various cell types. However, the profiles of inflammatory cytokines and transcriptome response induced by a specific HCoV are usually cell type specific and determined by the virus-specific mechanisms of subverting the induction and function of interferons and inflammatory cytokines as well as the genetic trait of the host genes of innate immune pathways. We review herein the recent literatures on the innate immune responses and their roles in the pathogenesis of HCoV infections with emphasis on the pathobiological roles and therapeutic effects of type I interferons in HCoV infections and their antiviral mechanisms. The knowledge on the mechanism of innate immune control of HCoV infections and viral evasions should facilitate the development of therapeutics for induction of immune resolution of HCoV infections and vaccines for efficient control of COVID-19 pandemics and other HCoV infections.
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Affiliation(s)
- Xuesen Zhao
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
| | - Danying Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xinglin Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Lauren Griffith
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Jinhong Chang
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Ping An
- Basic Research Laboratory, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA.
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18
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Kumar A, Goyal N, Saranathan N, Dhamija S, Saraswat S, Menon MB, Vivekanandan P. The slowing rate of CpG depletion in SARS-CoV-2 genomes is consistent with adaptations to the human host. Mol Biol Evol 2022; 39:6521032. [PMID: 35134218 PMCID: PMC8892944 DOI: 10.1093/molbev/msac029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Depletion of CpG dinucleotides in SARS-CoV-2 genomes has been linked to virus evolution, host-switching, virus replication, and innate immune responses. Temporal variations, if any, in the rate of CpG depletion during virus evolution in the host remain poorly understood. Here, we analysed the CpG content of over 1.4 million full-length SARS-CoV-2 genomes representing over 170 million documented infections during the first 17 months of the pandemic. Our findings suggest that the extent of CpG depletion in SARS-CoV-2 genomes is modest. Interestingly, the rate of CpG depletion is highest during early evolution in humans and it gradually tapers off almost reaching an equilibrium; this is consistent with adaptations to the human host. Furthermore, within the coding regions, CpG depletion occurs predominantly at codon positions 2-3 and 3-1. Loss of ZAP-binding motifs in SARS-CoV-2 genomes is primarily driven by the loss of the terminal CpG in the motifs. Nonetheless, majority of the CpG depletion in SARS-CoV-2 genomes occurs outside ZAP-binding motifs. SARS-CoV-2 genomes selectively lose CpGs-motifs from a U-rich context; this may help avoid immune recognition by TLR7. SARS-CoV-2 alpha-, beta- and delta-variants of concern have reduced CpG content compared to sequences from the beginning of the pandemic. In sum, we provide evidence that the rate of CpG depletion in virus genomes is not uniform and it greatly varies over time and during adaptations to the host. This work highlights how temporal variations in selection pressures during virus adaption may impact the rate and the extent of CpG depletion in virus genomes.
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Affiliation(s)
- Akhil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Nishank Goyal
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Sonam Dhamija
- CSIR-Institute of Genomics and Integrative Biology, New Delhi-110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Saurabh Saraswat
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Manoj B Menon
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
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19
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Burgess HM, Vink EI, Mohr I. Minding the message: tactics controlling RNA decay, modification, and translation in virus-infected cells. Genes Dev 2022; 36:108-132. [PMID: 35193946 PMCID: PMC8887129 DOI: 10.1101/gad.349276.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
With their categorical requirement for host ribosomes to translate mRNA, viruses provide a wealth of genetically tractable models to investigate how gene expression is remodeled post-transcriptionally by infection-triggered biological stress. By co-opting and subverting cellular pathways that control mRNA decay, modification, and translation, the global landscape of post-transcriptional processes is swiftly reshaped by virus-encoded factors. Concurrent host cell-intrinsic countermeasures likewise conscript post-transcriptional strategies to mobilize critical innate immune defenses. Here we review strategies and mechanisms that control mRNA decay, modification, and translation in animal virus-infected cells. Besides settling infection outcomes, post-transcriptional gene regulation in virus-infected cells epitomizes fundamental physiological stress responses in health and disease.
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Affiliation(s)
- Hannah M Burgess
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Elizabeth I Vink
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
- Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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20
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Guillemin A, Kumar A, Wencker M, Ricci EP. Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. Front Immunol 2022; 12:796012. [PMID: 35087521 PMCID: PMC8787094 DOI: 10.3389/fimmu.2021.796012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Innate immunity is the frontline of defense against infections and tissue damage. It is a fast and semi-specific response involving a myriad of processes essential for protecting the organism. These reactions promote the clearance of danger by activating, among others, an inflammatory response, the complement cascade and by recruiting the adaptive immunity. Any disequilibrium in this functional balance can lead to either inflammation-mediated tissue damage or defense inefficiency. A dynamic and coordinated gene expression program lies at the heart of the innate immune response. This expression program varies depending on the cell-type and the specific danger signal encountered by the cell and involves multiple layers of regulation. While these are achieved mainly via transcriptional control of gene expression, numerous post-transcriptional regulatory pathways involving RNA-binding proteins (RBPs) and other effectors play a critical role in its fine-tuning. Alternative splicing, translational control and mRNA stability have been shown to be tightly regulated during the innate immune response and participate in modulating gene expression in a global or gene specific manner. More recently, microRNAs assisting RBPs and post-transcriptional modification of RNA bases are also emerging as essential players of the innate immune process. In this review, we highlight the numerous roles played by specific RNA-binding effectors in mediating post-transcriptional control of gene expression to shape innate immunity.
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Affiliation(s)
- Anissa Guillemin
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
| | - Anuj Kumar
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Mélanie Wencker
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, ENS de Lyon, CNRS, UMR 5308, INSERM, Lyon, France
| | - Emiliano P. Ricci
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
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