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Hardy K, Lutz M, Takimoto T. Human coronavirus NL63 nsp1 induces degradation of RNA polymerase II to inhibit host protein synthesis. PLoS Pathog 2024; 20:e1012329. [PMID: 38900816 DOI: 10.1371/journal.ppat.1012329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024] Open
Abstract
Coronavirus (CoV) nonstructural protein 1 (nsp1) is considered a pathogenic factor due to its ability to inhibit host antiviral responses by inducing general shutoff of host protein synthesis. Nsp1 is expressed by α- and β-CoVs, but its functions and strategies to induce host shutoff are not fully elucidated. We compared the nsp1s from two β-CoVs (SARS-CoV and SARS-CoV-2) and two α-CoVs (NL63 and 229E) and found that NL63 nsp1 has the strongest shutoff activity. Unlike SARS-CoV nsp1s, which bind to 40S ribosomes and block translation of cellular mRNA, NL63 nsp1 did not inhibit translation of mRNAs transfected into cells. Instead, NL63 nsp1 localized to the nucleus and specifically inhibited transcription of genes under an RNA polymerase II (RNAPII) promoter. Further analysis revealed that NL63 nsp1 induces degradation of the largest subunit of RNAPII, Rpb1. This degradation was detected regardless of the phosphorylation state of Rpb1 and was blocked by the proteasome inhibitor MG132. We also found that Rpb1 was ubiquitinated in NL63-infected cells, and inhibition of ubiquitination by a ubiquitin activating enzyme inhibitor (TAK243) prevented degradation of Rpb1 in virus-infected cells. These data reveal an unrecognized strategy of host shutoff by human α-CoV NL63: targeting host transcription by inducing Rpb1 degradation to prevent host protein expression. Our study indicates that viruses within the same family can use completely distinct mechanisms to regulate host antiviral responses.
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Affiliation(s)
- Kala Hardy
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Michael Lutz
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Toru Takimoto
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
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Drzeniek NM, Kahwaji N, Picht S, Dimitriou IM, Schlickeiser S, Moradian H, Geissler S, Schmueck-Henneresse M, Gossen M, Volk HD. In Vitro Transcribed mRNA Immunogenicity Induces Chemokine-Mediated Lymphocyte Recruitment and Can Be Gradually Tailored by Uridine Modification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308447. [PMID: 38491873 DOI: 10.1002/advs.202308447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/28/2024] [Indexed: 03/18/2024]
Abstract
Beyond SARS-CoV2 vaccines, mRNA drugs are being explored to overcome today's greatest healthcare burdens, including cancer and cardiovascular disease. Synthetic mRNA triggers immune responses in transfected cells, which can be reduced by chemically modified nucleotides. However, the side effects of mRNA-triggered immune activation on cell function and how different nucleotides, such as the N1-methylpseudouridine (m1Ψ) used in SARS-CoV2 vaccines, can modulate cellular responses is not fully understood. Here, cellular responses toward a library of uridine-modified mRNAs are investigated in primary human cells. Targeted proteomics analyses reveal that unmodified mRNA induces a pro-inflammatory paracrine pattern marked by the secretion of chemokines, which recruit T and B lymphocytes toward transfected cells. Importantly, the magnitude of mRNA-induced changes in cell function varies quantitatively between unmodified, Ψ-, m1Ψ-, and 5moU-modified mRNA and can be gradually tailored, with implications for deliberately exploiting this effect in mRNA drug design. Indeed, both the immunosuppressive effect of stromal cells on T-cell proliferation, and the anti-inflammatory effect of IL-10 mRNA are enhanced by appropriate uridine modification. The results provide new insights into the effects of mRNA drugs on cell function and cell-cell communication and open new possibilities to tailor mRNA-triggered immune activation to the desired pro- or anti-inflammatory application.
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Affiliation(s)
- Norman M Drzeniek
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Institute of Medical Immunology, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
| | - Nourhan Kahwaji
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
| | - Samira Picht
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies (BSRT; graduate school 203 of the German Excellence Initiative), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Ioanna Maria Dimitriou
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies (BSRT; graduate school 203 of the German Excellence Initiative), Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Stephan Schlickeiser
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Institute of Medical Immunology, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
- CheckImmune GmbH, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Hanieh Moradian
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Sven Geissler
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin Center for Advanced Therapies (BeCAT), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Michael Schmueck-Henneresse
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin Center for Advanced Therapies (BeCAT), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Hans-Dieter Volk
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Institute of Medical Immunology, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
- CheckImmune GmbH, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin Center for Advanced Therapies (BeCAT), Augustenburger Platz 1, 13353, Berlin, Germany
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King CR, Dodge MJ, MacNeil KM, Tessier TM, Mymryk JS, Mehle A. Expanding the adenovirus toolbox: reporter viruses for studying the dynamics of human adenovirus replication. J Virol 2024; 98:e0020724. [PMID: 38639487 PMCID: PMC11092356 DOI: 10.1128/jvi.00207-24] [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] [Received: 01/30/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
To streamline standard virological assays, we developed a suite of nine fluorescent or bioluminescent replication competent human species C5 adenovirus reporter viruses that mimic their parental wild-type counterpart. These reporter viruses provide a rapid and quantitative readout of various aspects of viral infection and replication based on EGFP, mCherry, or NanoLuc measurement. Moreover, they permit real-time non-invasive measures of viral load, replication dynamics, and infection kinetics over the entire course of infection, allowing measurements that were not previously possible. This suite of replication competent reporter viruses increases the ease, speed, and adaptability of standard assays and has the potential to accelerate multiple areas of human adenovirus research.IMPORTANCEIn this work, we developed a versatile toolbox of nine HAdV-C5 reporter viruses and validated their functions in cell culture. These reporter viruses provide a rapid and quantitative readout of various aspects of viral infection and replication based on EGFP, mCherry, or NanoLuc measurement. The utility of these reporter viruses could also be extended for use in 3D cell culture, organoids, live cell imaging, or animal models, and provides a conceptual framework for the development of new reporter viruses representing other clinically relevant HAdV species.
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Affiliation(s)
- Cason R. King
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mackenzie J. Dodge
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Katelyn M. MacNeil
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Tanner M. Tessier
- Division of Protective Immunity, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
- Department of Oncology, University of Western Ontario, London, Ontario, Canada
- Department of Otolaryngology, University of Western Ontario, London, Ontario, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, Ontario, Canada
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Chen S, Jiang Z, Li Q, Pan W, Chen Y, Liu J. Viral RNA capping: Mechanisms and antiviral therapy. J Med Virol 2024; 96:e29622. [PMID: 38682614 DOI: 10.1002/jmv.29622] [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] [Received: 12/19/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
RNA capping is an essential trigger for protein translation in eukaryotic cells. Many viruses have evolved various strategies for initiating the translation of viral genes and generating progeny virions in infected cells via synthesizing cap structure or stealing the RNA cap from nascent host messenger ribonucleotide acid (mRNA). In addition to protein translation, a new understanding of the role of the RNA cap in antiviral innate immunity has advanced the field of mRNA synthesis in vitro and therapeutic applications. Recent studies on these viral RNA capping systems have revealed startlingly diverse ways and molecular machinery. A comprehensive understanding of how viruses accomplish the RNA capping in infected cells is pivotal for designing effective broad-spectrum antiviral therapies. Here we systematically review the contemporary insights into the RNA-capping mechanisms employed by viruses causing human and animal infectious diseases, while also highlighting its impact on host antiviral innate immune response. The therapeutic applications of targeting RNA capping against viral infections and the development of RNA-capping inhibitors are also summarized.
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Affiliation(s)
- Saini Chen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhimin Jiang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qiuchen Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenliang Pan
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Chen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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You T, Wang M, Zhang H, Wang X, Gao X, Yin X, Sun Y, Wang G, Chen HT, Ren S. Identification of the murine osteoblastic cell MC3T3-E1 as a permissive cell line in response to lumpy skin disease virus. J Virol Methods 2024; 326:114916. [PMID: 38479589 DOI: 10.1016/j.jviromet.2024.114916] [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: 01/14/2024] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Lumpy skin disease virus (LSDV) is a rapidly emerging pathogen in China. Screening suitable cells for LSDV replication is vital for future research on pathogenic mechanisms and vaccine development. Previous comparative studies have identified that the rodent-derived BHK21 is a highly susceptible cell model to LSDV infection. Using western blot, indirect immune-fluorescence assay, flow cytometry, and transmission electron microscopy methods, this study is the first to identify the murine osteoblastic cell line MC3T3-E1 as a novel permissive cell model for LSDV infection. The establishment of MC3T3-E1 as a suitable infectious cell model enhances our understanding of the species range and cell types of the permissive cells and nonpermissive that support LSDV replication. It is helpful to accelerate future research on the pathogenesis, clinical application, and vaccine development of LSDV.
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Affiliation(s)
- Ting You
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China; Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Meng Wang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Hongqiang Zhang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Xiangwei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Xiaolong Gao
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, PR China
| | - Xiangping Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Yuefeng Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China
| | - Guirong Wang
- Laboratory of Veterinary Microbiology, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Hao-Tai Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
| | - Shanhui Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China.
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6
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Xia C, Wang T, Hahm B. Triggering Degradation of Host Cellular Proteins for Robust Propagation of Influenza Viruses. Int J Mol Sci 2024; 25:4677. [PMID: 38731896 PMCID: PMC11083682 DOI: 10.3390/ijms25094677] [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] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Following infection, influenza viruses strive to establish a new host cellular environment optimized for efficient viral replication and propagation. Influenza viruses use or hijack numerous host factors and machinery not only to fulfill their own replication process but also to constantly evade the host's antiviral and immune response. For this purpose, influenza viruses appear to have formulated diverse strategies to manipulate the host proteins or signaling pathways. One of the most effective tactics is to specifically induce the degradation of the cellular proteins that are detrimental to the virus life cycle. Here, we summarize the cellular factors that are deemed to have been purposefully degraded by influenza virus infection. The focus is laid on the mechanisms for the protein ubiquitination and degradation in association with facilitated viral amplification. The fate of influenza viral infection of hosts is heavily reliant on the outcomes of the interplay between the virus and the host antiviral immunity. Understanding the processes of how influenza viruses instigate the protein destruction pathways could provide a foundation for the development of advanced therapeutics to target host proteins and conquer influenza.
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Affiliation(s)
- Chuan Xia
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Ting Wang
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China;
| | - Bumsuk Hahm
- Departments of Surgery & Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212, USA
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Sinha S, Singh K, Ravi Kumar YS, Roy R, Phadnis S, Meena V, Bhattacharyya S, Verma B. Dengue virus pathogenesis and host molecular machineries. J Biomed Sci 2024; 31:43. [PMID: 38649998 PMCID: PMC11036733 DOI: 10.1186/s12929-024-01030-9] [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] [Received: 01/24/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024] Open
Abstract
Dengue viruses (DENV) are positive-stranded RNA viruses belonging to the Flaviviridae family. DENV is the causative agent of dengue, the most rapidly spreading viral disease transmitted by mosquitoes. Each year, millions of people contract the virus through bites from infected female mosquitoes of the Aedes species. In the majority of individuals, the infection is asymptomatic, and the immune system successfully manages to control virus replication within a few days. Symptomatic individuals may present with a mild fever (Dengue fever or DF) that may or may not progress to a more critical disease termed Dengue hemorrhagic fever (DHF) or the fatal Dengue shock syndrome (DSS). In the absence of a universally accepted prophylactic vaccine or therapeutic drug, treatment is mostly restricted to supportive measures. Similar to many other viruses that induce acute illness, DENV has developed several ways to modulate host metabolism to create an environment conducive to genome replication and the dissemination of viral progeny. To search for new therapeutic options, understanding the underlying host-virus regulatory system involved in various biological processes of the viral life cycle is essential. This review aims to summarize the complex interaction between DENV and the host cellular machinery, comprising regulatory mechanisms at various molecular levels such as epigenetic modulation of the host genome, transcription of host genes, translation of viral and host mRNAs, post-transcriptional regulation of the host transcriptome, post-translational regulation of viral proteins, and pathways involved in protein degradation.
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Affiliation(s)
- Saumya Sinha
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Kinjal Singh
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Y S Ravi Kumar
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, MSR Nagar, Bengaluru, India
| | - Riya Roy
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sushant Phadnis
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Varsha Meena
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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Yin Q, Liu W, Jiang Y, Feng Q, Wang X, Dou H, Liu Z, He F, Fan Y, Jiao B, Jiao B. Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022. BMC Genomics 2024; 25:378. [PMID: 38632523 PMCID: PMC11022347 DOI: 10.1186/s12864-024-10246-w] [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] [Received: 12/03/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China. METHODS Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites. RESULTS All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites. CONCLUSION SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.
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Affiliation(s)
- Qiang Yin
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Wei Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Yajuan Jiang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Qiang Feng
- Department of Laboratory, Rencheng Center for Disease Control and Prevention, Jining, China
| | - Xiaoyu Wang
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Huixin Dou
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Zanzan Liu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China
| | - Feifei He
- Computer Information Technology, Northern Arizona University, Arizona, USA
| | - Yingying Fan
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
| | - Baihai Jiao
- Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT, USA.
| | - Boyan Jiao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
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Li XQ, Cai MP, Wang MY, Shi BW, Yang GY, Wang J, Chu BB, Ming SL. Pseudorabies virus manipulates mitochondrial tryptophanyl-tRNA synthetase 2 for viral replication. Virol Sin 2024:S1995-820X(24)00039-7. [PMID: 38636706 DOI: 10.1016/j.virs.2024.04.003] [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: 10/10/2023] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
The pseudorabies virus (PRV) is identified as a double-helical DNA virus responsible for causing Aujeszky's disease, which results in considerable economic impacts globally. The enzyme tryptophanyl-tRNA synthetase 2 (WARS2), a mitochondrial protein involved in protein synthesis, is recognized for its broad expression and vital role in the translation process. The findings of our study showed an increase in both mRNA and protein levels of WARS2 following PRV infection in both cell cultures and animal models. Suppressing WARS2 expression via RNA interference in PK-15 cells led to a reduction in PRV infection rates, whereas enhancing WARS2 expression resulted in increased infection rates. Furthermore, the activation of WARS2 in response to PRV was found to be reliant on the cGAS/STING/TBK1/IRF3 signaling pathway and the interferon-alpha receptor-1, highlighting its regulation via the type I interferon signaling pathway. Further analysis revealed that reducing WARS2 levels hindered PRV's ability to promote protein and lipid synthesis. Our research provides novel evidence that WARS2 facilitates PRV infection through its management of protein and lipid levels, presenting new avenues for developing preventative and therapeutic measures against PRV infections.
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Affiliation(s)
- Xiu-Qing Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Meng-Pan Cai
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Ming-Yang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Bo-Wen Shi
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Guo-Yu Yang
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China; International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450046, China.
| | - Bei-Bei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China; Longhu Advanced Immunization Laboratory, Zhengzhou 450046, China; International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450046, China.
| | - Sheng-Li Ming
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
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Yuan S, Zhou G, Xu G. Translation machinery: the basis of translational control. J Genet Genomics 2024; 51:367-378. [PMID: 37536497 DOI: 10.1016/j.jgg.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
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Affiliation(s)
- Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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11
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Zhang Q, Ye H, Liu C, Zhou H, He M, Liang X, Zhou Y, Wang K, Qin Y, Li Z, Chen M. PABP-driven secondary condensed phase within RSV inclusion bodies activates viral mRNAs for ribosomal recruitment. Virol Sin 2024; 39:235-250. [PMID: 38072230 PMCID: PMC11074649 DOI: 10.1016/j.virs.2023.12.001] [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: 11/18/2023] [Accepted: 12/03/2023] [Indexed: 01/12/2024] Open
Abstract
Inclusion bodies (IBs) of respiratory syncytial virus (RSV) are formed by liquid-liquid phase separation (LLPS) and contain internal structures termed "IB-associated granules" (IBAGs), where anti-termination factor M2-1 and viral mRNAs are concentrated. However, the mechanism of IBAG formation and the physiological function of IBAGs are unclear. Here, we found that the internal structures of RSV IBs are actual M2-1-free viral messenger ribonucleoprotein (mRNP) condensates formed by secondary LLPS. Mechanistically, the RSV nucleoprotein (N) and M2-1 interact with and recruit PABP to IBs, promoting PABP to bind viral mRNAs transcribed in IBs by RNA-recognition motif and drive secondary phase separation. Furthermore, PABP-eIF4G1 interaction regulates viral mRNP condensate composition, thereby recruiting specific translation initiation factors (eIF4G1, eIF4E, eIF4A, eIF4B and eIF4H) into the secondary condensed phase to activate viral mRNAs for ribosomal recruitment. Our study proposes a novel LLPS-regulated translation mechanism during viral infection and a novel antiviral strategy via targeting on secondary condensed phase.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hanzhe Ye
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Cong Liu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haiwu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mingbin He
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaodong Liang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Wang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Zhifei Li
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China; Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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12
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Breunig K, Lei X, Montalbano M, Guardia GDA, Ostadrahimi S, Alers V, Kosti A, Chiou J, Klein N, Vinarov C, Wang L, Li M, Song W, Kraus WL, Libich DS, Tiziani S, Weintraub ST, Galante PAF, Penalva LOF. SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586270. [PMID: 38585848 PMCID: PMC10996453 DOI: 10.1101/2024.03.22.586270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. Using a proteomics approach followed by functional analysis, we defined SERBP1's interactome. We uncovered novel SERBP1 roles in splicing, cell division, and ribosomal biogenesis and showed its participation in pathological stress granules and Tau aggregates in Alzheimer's disease brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
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13
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Jobe F, Kelly JT, Simpson J, Wells J, Armstrong SD, Spick M, Lacey E, Logan L, Geifman N, Hawes P, Bailey D. Viral PIC-pocketing: RSV sequestration of translational preinitiation complexes into bi-phasic biomolecular condensates. J Virol 2024; 98:e0015324. [PMID: 38421168 PMCID: PMC10949503 DOI: 10.1128/jvi.00153-24] [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] [Received: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Orthopneumoviruses characteristically form membrane-less cytoplasmic inclusion bodies (IBs) wherein RNA replication and transcription occur. Here, we report a strategy whereby the orthopneumoviruses sequester various components of the translational preinitiation complex machinery into viral inclusion bodies to facilitate translation of their own mRNAs-PIC-pocketing. Electron microscopy of respiratory syncytial virus (RSV)-infected cells revealed bi-phasic organization of IBs, specifically, spherical "droplets" nested within the larger inclusion. Using correlative light and electron microscopy, combined with fluorescence in situ hybridization, we showed that the observed bi-phasic morphology represents functional compartmentalization of the inclusion body and that these domains are synonymous with the previously reported inclusion body-associated granules (IBAGs). Detailed analysis demonstrated that IBAGs concentrate nascent viral mRNA, the viral M2-1 protein as well as components of eukaryotic translation initiation factors (eIF), eIF4F and eIF3, and 40S complexes involved in translation initiation. Interestingly, although ribopuromycylation-based imaging indicates that the majority of viral mRNA translation occurs in the cytoplasm, there was some evidence for intra-IBAG translation, consistent with the likely presence of ribosomes in a subset of IBAGs imaged by electron microscopy. Mass spectrometry analysis of sub-cellular fractions from RSV-infected cells identified significant modification of the cellular translation machinery; however, interestingly, ribopuromycylation assays showed no changes to global levels of translation. The mechanistic basis for this pathway was subsequently determined to involve the viral M2-1 protein interacting with eIF4G, likely to facilitate its transport between the cytoplasm and the separate phases of the viral inclusion body. In summary, our data show that these viral organelles function to spatially regulate early steps in viral translation within a highly selective bi-phasic biomolecular condensate. IMPORTANCE Respiratory syncytial viruses (RSVs) of cows and humans are a significant cause of morbidity and mortality in their respective populations. These RNA viruses replicate in the infected cells by compartmentalizing the cell's cytoplasm into distinct viral microdomains called inclusion bodies (IBs). In this paper, we show that these IBs are further compartmentalized into smaller structures that have significantly different density, as observed by electron microscopy. Within smaller intra-IB structures, we observed ribosomal components and evidence for active translation. These findings highlight that RSV may additionally compartmentalize translation to favor its own replication in the cell. These data contribute to our understanding of how RNA viruses hijack the cell to favor replication of their own genomes and may provide new targets for antiviral therapeutics in vivo.
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Affiliation(s)
| | | | | | - Joanna Wells
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Stuart D. Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Matt Spick
- School of Health Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Emily Lacey
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Leanne Logan
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Nophar Geifman
- School of Health Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | | | - Dalan Bailey
- The Pirbright Institute, Woking, Surrey, United Kingdom
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14
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Dopkins N, Nixon DF. Activation of human endogenous retroviruses and its physiological consequences. Nat Rev Mol Cell Biol 2024; 25:212-222. [PMID: 37872387 DOI: 10.1038/s41580-023-00674-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Human endogenous retroviruses (HERVs) are abundant sequences that persist within the human genome as remnants of ancient retroviral infections. These sequences became fixed and accumulate mutations or deletions over time. HERVs have affected human evolution and physiology by providing a unique repertoire of coding and non-coding sequences to the genome. In healthy individuals, HERVs participate in immune responses, formation of syncytiotrophoblasts and cell-fate specification. In this Review, we discuss how endogenized retroviral motifs and regulatory sequences have been co-opted into human physiology and how they are tightly regulated. Infections and mutations can derail this regulation, leading to differential HERV expression, which may contribute to pathologies including neurodegeneration, pathological inflammation and oncogenesis. Emerging evidence demonstrates that HERVs are crucial to human health and represent an understudied facet of many diseases, and we therefore argue that investigating their fundamental properties could improve existing therapies and help develop novel therapeutic strategies.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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15
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Shehata SI, Watkins JM, Burke JM, Parker R. Mechanisms and consequences of mRNA destabilization during viral infections. Virol J 2024; 21:38. [PMID: 38321453 PMCID: PMC10848536 DOI: 10.1186/s12985-024-02305-1] [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] [Received: 07/13/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
During viral infection there is dynamic interplay between the virus and the host to regulate gene expression. In many cases, the host induces the expression of antiviral genes to combat infection, while the virus uses "host shut-off" systems to better compete for cellular resources and to limit the induction of the host antiviral response. Viral mechanisms for host shut-off involve targeting translation, altering host RNA processing, and/or inducing the degradation of host mRNAs. In this review, we discuss the diverse mechanisms viruses use to degrade host mRNAs. In addition, the widespread degradation of host mRNAs can have common consequences including the accumulation of RNA binding proteins in the nucleus, which leads to altered RNA processing, mRNA export, and changes to transcription.
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Affiliation(s)
- Soraya I Shehata
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Monty Watkins
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
| | - James M Burke
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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16
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Tidu A, Martin F. The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes. Biochimie 2024; 217:20-30. [PMID: 37741547 DOI: 10.1016/j.biochi.2023.09.017] [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: 05/04/2023] [Revised: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.
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Affiliation(s)
- Antonin Tidu
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France.
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17
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Liao T, Chen Y, Guo L, Zhu S, Zhan T, Lu X, Xu H, Hu Z, Hu J, Gu M, Liu X, Wang X, Hu S, Liu X. The NP protein of Newcastle disease virus dictates its oncolytic activity by regulating viral mRNA translation efficiency. PLoS Pathog 2024; 20:e1012027. [PMID: 38377149 PMCID: PMC10906838 DOI: 10.1371/journal.ppat.1012027] [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: 06/05/2023] [Revised: 03/01/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Newcastle disease virus (NDV) has been extensively studied as a promising oncolytic virus for killing tumor cells in vitro and in vivo in clinical trials. However, the viral components that regulate the oncolytic activity of NDV remain incompletely understood. In this study, we systematically compared the replication ability of different NDV genotypes in various tumor cells and identified NP protein determines the oncolytic activity of NDV. On the one hand, NDV strains with phenylalanine (F) at the 450th amino acid position of the NP protein (450th-F-NP) exhibit a loss of oncolytic activity. This phenotype is predominantly associated with genotype VII NDVs. In contrast, the NP protein with a leucine amino acid at this site in other genotypes (450th-L-NP) can facilitate the loading of viral mRNA onto ribosomes more effectively than 450th-F-NP. On the other hand, the NP protein from NDV strains that exhibit strong oncogenicity interacts with eIF4A1 within its 366-489 amino acid region, leading to the inhibition of cellular mRNA translation with a complex 5' UTR structure. Our study provide mechanistic insights into how highly oncolytic NDV strains selectively promote the translation of viral mRNA and will also facilitate the screening of oncolytic strains for oncolytic therapy.
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Affiliation(s)
- Tianxing Liao
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yu Chen
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Lili Guo
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Shanshan Zhu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Tiansong Zhan
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiaolong Lu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Haixu Xu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zenglei Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Jiao Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Min Gu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infections Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, China
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18
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Li C, Zhang P, Hong PP, Niu GJ, Wang XP, Zhao XF, Wang JX. White spot syndrome virus hijacks host PP2A-FOXO axes to promote its propagation. Int J Biol Macromol 2024; 256:128333. [PMID: 38007022 DOI: 10.1016/j.ijbiomac.2023.128333] [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: 06/23/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023]
Abstract
Viruses have developed superior strategies to escape host defenses or exploit host components and enable their infection. The forkhead box transcription factor O family proteins (FOXOs) are reportedly utilized by human cytomegalovirus during their reactivation in mammals, but if FOXOs are exploited by viruses during their infection remains unclear. In the present study, we found that the FOXO of kuruma shrimp (Marsupenaeus japonicus) was hijacked by white spot syndrome virus (WSSV) during infection. Mechanistically, the expression of leucine carboxyl methyl transferase 1 (LCMT1) was up-regulated during the early stages of WSSV infection, which activated the protein phosphatase 2A (PP2A) by methylation, leading to dephosphorylation of FOXO and translocation into the nucleus. The FOXO directly promoted transcription of the immediate early gene, wsv079 of WSSV, which functioned as a transcriptional activator to initiate the expression of viral early and late genes. Thus, WSSV utilized the host LCMT1-PP2A-FOXO axis to promote its replication during the early infection stage. We also found that, during the late stages of WSSV infection, the envelope protein of WSSV (VP26) promoted PP2A activity by directly binding to FOXO and the regulatory subunit of PP2A (B55), which further facilitated FOXO dephosphorylation and WSSV replication via the VP26-PP2A-FOXO axis in shrimp. Overall, this study reveals novel viral strategies by which WSSV hijacks host LCMT1-PP2A-FOXO or VP26-PP2A-FOXO axes to promote its propagation, and provides clinical targets for WSSV control in shrimp aquaculture.
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Affiliation(s)
- Cang Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Peng Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Pan-Pan Hong
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Guo-Juan Niu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Xiao-Pei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Xiao-Fan Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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19
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Krishnan D, Babu S, Raju R, Veettil MV, Prasad TSK, Abhinand CS. Epstein-Barr Virus: Human Interactome Reveals New Molecular Insights into Viral Pathogenesis for Potential Therapeutics and Antiviral Drug Discovery. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:32-44. [PMID: 38190109 DOI: 10.1089/omi.2023.0241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Host-virus Protein-Protein Interactions (PPIs) play pivotal roles in biological processes crucial for viral pathogenesis and by extension, inform antiviral drug discovery and therapeutics innovations. Despite efforts to develop the Epstein-Barr virus (EBV)-host PPI network, there remain significant knowledge gaps and a limited number of interacting human proteins deciphered. Furthermore, understanding the dynamics of the EBV-host PPI network in the distinct lytic and latent viral stages remains elusive. In this study, we report a comprehensive map of the EBV-human protein interactions, encompassing 1752 human and 61 EBV proteins by integrating data from the public repository HPIDB (v3.0) as well as curated high-throughput proteomic data from the literature. To address the stage-specific nature of EBV infection, we generated two detailed subset networks representing the latent and lytic stages, comprising 747 and 481 human proteins, respectively. Functional and pathway enrichment analysis of these subsets uncovered the profound impact of EBV proteins on cancer. The identification of highly connected proteins and the characterization of intrinsically disordered and cancer-related proteins provide valuable insights into potential therapeutic targets. Moreover, the exploration of drug-protein interactions revealed notable associations between hub proteins and anticancer drugs, offering novel perspectives for controlling EBV pathogenesis. This study represents, to the best of our knowledge, the first comprehensive investigation of the two distinct stages of EBV infection using high-throughput datasets. This makes a contribution to our understanding of EBV-host interactions and provides a foundation for future drug discovery and therapeutic interventions.
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Affiliation(s)
- Deepak Krishnan
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, India
| | - Sreeranjini Babu
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore, India
| | | | | | - Chandran S Abhinand
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, India
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20
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Karousis ED, Schubert K, Ban N. Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective. EMBO J 2024; 43:151-167. [PMID: 38200146 PMCID: PMC10897431 DOI: 10.1038/s44318-023-00019-8] [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] [Received: 06/01/2023] [Revised: 11/01/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
Coronaviruses are a group of related RNA viruses that cause respiratory diseases in humans and animals. Understanding the mechanisms of translation regulation during coronaviral infections is critical for developing antiviral therapies and preventing viral spread. Translation of the viral single-stranded RNA genome in the host cell cytoplasm is an essential step in the life cycle of coronaviruses, which affects the cellular mRNA translation landscape in many ways. Here we discuss various viral strategies of translation control, including how members of the Betacoronavirus genus shut down host cell translation and suppress host innate immune functions, as well as the role of the viral non-structural protein 1 (Nsp1) in the process. We also outline the fate of viral RNA, considering stress response mechanisms triggered in infected cells, and describe how unique viral RNA features contribute to programmed ribosomal -1 frameshifting, RNA editing, and translation shutdown evasion.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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21
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Daskou M, Fotooh Abadi L, Gain C, Wong M, Sharma E, Kombe Kombe AJ, Nanduri R, Kelesidis T. The Role of the NRF2 Pathway in the Pathogenesis of Viral Respiratory Infections. Pathogens 2023; 13:39. [PMID: 38251346 PMCID: PMC10819673 DOI: 10.3390/pathogens13010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
In humans, acute and chronic respiratory infections caused by viruses are associated with considerable morbidity and mortality. Respiratory viruses infect airway epithelial cells and induce oxidative stress, yet the exact pathogenesis remains unclear. Oxidative stress activates the transcription factor NRF2, which plays a key role in alleviating redox-induced cellular injury. The transcriptional activation of NRF2 has been reported to affect both viral replication and associated inflammation pathways. There is complex bidirectional crosstalk between virus replication and the NRF2 pathway because virus replication directly or indirectly regulates NRF2 expression, and NRF2 activation can reversely hamper viral replication and viral spread across cells and tissues. In this review, we discuss the complex role of the NRF2 pathway in the regulation of the pathogenesis of the main respiratory viruses, including coronaviruses, influenza viruses, respiratory syncytial virus (RSV), and rhinoviruses. We also summarize the scientific evidence regarding the effects of the known NRF2 agonists that can be utilized to alter the NRF2 pathway.
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Affiliation(s)
- Maria Daskou
- Department of Medicine, Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Leila Fotooh Abadi
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.F.A.); (R.N.)
| | - Chandrima Gain
- Department of Medicine, Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Wong
- Department of Medicine, Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Eashan Sharma
- Department of Medicine, Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Arnaud John Kombe Kombe
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.F.A.); (R.N.)
| | - Ravikanth Nanduri
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.F.A.); (R.N.)
| | - Theodoros Kelesidis
- Department of Medicine, Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (L.F.A.); (R.N.)
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22
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Bello AJ, Popoola A, Okpuzor J, Ihekwaba-Ndibe AE, Olorunniji FJ. A Genetic Circuit Design for Targeted Viral RNA Degradation. Bioengineering (Basel) 2023; 11:22. [PMID: 38247899 PMCID: PMC10813695 DOI: 10.3390/bioengineering11010022] [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: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Advances in synthetic biology have led to the design of biological parts that can be assembled in different ways to perform specific functions. For example, genetic circuits can be designed to execute specific therapeutic functions, including gene therapy or targeted detection and the destruction of invading viruses. Viral infections are difficult to manage through drug treatment. Due to their high mutation rates and their ability to hijack the host's ribosomes to make viral proteins, very few therapeutic options are available. One approach to addressing this problem is to disrupt the process of converting viral RNA into proteins, thereby disrupting the mechanism for assembling new viral particles that could infect other cells. This can be done by ensuring precise control over the abundance of viral RNA (vRNA) inside host cells by designing biological circuits to target vRNA for degradation. RNA-binding proteins (RBPs) have become important biological devices in regulating RNA processing. Incorporating naturally upregulated RBPs into a gene circuit could be advantageous because such a circuit could mimic the natural pathway for RNA degradation. This review highlights the process of viral RNA degradation and different approaches to designing genetic circuits. We also provide a customizable template for designing genetic circuits that utilize RBPs as transcription activators for viral RNA degradation, with the overall goal of taking advantage of the natural functions of RBPs in host cells to activate targeted viral RNA degradation.
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Affiliation(s)
- Adebayo J. Bello
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
- Department of Biological Sciences, Redeemer’s University, Ede 232101, Osun State, Nigeria
| | - Abdulgafar Popoola
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
- Department of Medical Laboratory Science, Kwara State University, Malete, Ilorin 241102, Kwara State, Nigeria
| | - Joy Okpuzor
- Department of Cell Biology & Genetics, University of Lagos, Akoka, Lagos 101017, Lagos State, Nigeria;
| | | | - Femi J. Olorunniji
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (A.J.B.); (A.P.)
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23
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Kim J, Youn D, Choi S, Lee YW, Sumberzul D, Yoon J, Lee H, Bae JW, Noh H, On D, Hong SM, An SH, Jang HJ, Kim SY, Kim YB, Hwang JY, Lee HJ, Bin Kim H, Park JW, Yun JW, Shin JS, Seo JY, Nam KT, Choi KS, Lee HY, Chang H, Seong JK, Cho J. SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs. Exp Mol Med 2023; 55:2541-2552. [PMID: 37907741 PMCID: PMC10767024 DOI: 10.1038/s12276-023-01110-0] [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] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 11/02/2023] Open
Abstract
Translational regulation in tissue environments during in vivo viral pathogenesis has rarely been studied due to the lack of translatomes from virus-infected tissues, although a series of translatome studies using in vitro cultured cells with viral infection have been reported. In this study, we exploited tissue-optimized ribosome profiling (Ribo-seq) and severe-COVID-19 model mice to establish the first temporal translation profiles of virus and host genes in the lungs during SARS-CoV-2 pathogenesis. Our datasets revealed not only previously unknown targets of translation regulation in infected tissues but also hitherto unreported molecular signatures that contribute to tissue pathology after SARS-CoV-2 infection. Specifically, we observed gradual increases in pseudoribosomal ribonucleoprotein (RNP) interactions that partially overlapped the trails of ribosomes, being likely involved in impeding translation elongation. Contemporaneously developed ribosome heterogeneity with predominantly dysregulated 5 S rRNP association supported the malfunction of elongating ribosomes. Analyses of canonical Ribo-seq reads (ribosome footprints) highlighted two obstructive characteristics to host gene expression: ribosome stalling on codons within transmembrane domain-coding regions and compromised translation of immunity- and metabolism-related genes with upregulated transcription. Our findings collectively demonstrate that the abrogation of translation integrity may be one of the most critical factors contributing to pathogenesis after SARS-CoV-2 infection of tissues.
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Affiliation(s)
- Junsoo Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Daehwa Youn
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Seunghoon Choi
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Youn Woo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Dulguun Sumberzul
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jeongeun Yoon
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hanju Lee
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Jong Woo Bae
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyuna Noh
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea
| | - Dain On
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Seung-Min Hong
- Laboratory of Avian Diseases, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Se-Hee An
- Laboratory of Avian Diseases, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Seo Yeon Kim
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Young Been Kim
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Ji-Yeon Hwang
- Preclinical Research Center, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, ChunCheon, Republic of Korea
| | - Jun-Won Yun
- Laboratory of Veterinary Toxicology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jeon-Soo Shin
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jun-Young Seo
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University, College of Medicine, Seoul, Republic of Korea.
| | - Hyeshik Chang
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, Republic of Korea.
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Je Kyung Seong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, Republic of Korea.
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
- Interdisciplinary Program and BIO MAX Institute, Seoul National University, Seoul, Republic of Korea.
| | - Jun Cho
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
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24
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Macauslane KL, Pegg CL, Short KR, Schulz BL. Modulation of endoplasmic reticulum stress response pathways by respiratory viruses. Crit Rev Microbiol 2023:1-19. [PMID: 37934111 DOI: 10.1080/1040841x.2023.2274840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/15/2023] [Indexed: 11/08/2023]
Abstract
Acute respiratory infections (ARIs) are amongst the leading causes of death and disability, and the greatest burden of disease impacts children, pregnant women, and the elderly. Respiratory viruses account for the majority of ARIs. The unfolded protein response (UPR) is a host homeostatic defence mechanism primarily activated in response to aberrant endoplasmic reticulum (ER) resident protein accumulation in cell stresses including viral infection. The UPR has been implicated in the pathogenesis of several respiratory diseases, as the respiratory system is particularly vulnerable to chronic and acute activation of the ER stress response pathway. Many respiratory viruses therefore employ strategies to modulate the UPR during infection, with varying effects on the host and the pathogens. Here, we review the specific means by which respiratory viruses affect the host UPR, particularly in association with the high production of viral glycoproteins, and the impact of UPR activation and subversion on viral replication and disease pathogenesis. We further review the activation of UPR in common co-morbidities of ARIs and discuss the therapeutic potential of modulating the UPR in virally induced respiratory diseases.
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Affiliation(s)
- Kyle L Macauslane
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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25
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Tian YF, Zhang YP, Wu QM, Pang DW, Liu SL, Wang ZG. Real-Time Imaging of Single Viral mRNA Translation in Live Cells Using CRISPR/dCas13. Anal Chem 2023; 95:16298-16304. [PMID: 37874254 DOI: 10.1021/acs.analchem.3c03365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Translation is one of the many critical cellular activities regulated by viruses following host-cell invasion, and studies of viral mRNA translation kinetics and subcellular localization require techniques for the dynamic, real-time visualization of translation. However, conventional tools for imaging mRNA translation often require coding region modifications that may affect native translation. Here, we achieve dynamic imaging of translation with a tool that labels target mRNAs with unmodified coding regions using a CRISPR/dCas13 system with specific complementary paired guide RNAs. This system enables a real-time dynamic visualization of the translation process and is a promising tool for further investigations of the mechanisms of translation.
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Affiliation(s)
- Yi-Fan Tian
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Yu-Peng Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Qiu-Mei Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, 1 Xue Fu North Road, Fuzhou 350122, P. R. China
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
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26
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Barrero-Canosa J, Wang L, Oyugi A, Klaes S, Fischer P, Adrian L, Szewzyk U, Cooper M. Characterization of phage vB_EcoS-EE09 infecting E. coli DSM613 Isolated from Wastewater Treatment Plant Effluent and Comparative Proteomics of the Infected and Non-Infected Host. Microorganisms 2023; 11:2688. [PMID: 38004701 PMCID: PMC10673088 DOI: 10.3390/microorganisms11112688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Phages influence microbial communities, can be applied in phage therapy, or may serve as bioindicators, e.g., in (waste)water management. We here characterized the Escherichia phage vB_EcoS-EE09 isolated from an urban wastewater treatment plant effluent. Phage vB_EcoS-EE09 belongs to the genus Dhillonvirus, class Caudoviricetes. It has an icosahedral capsid with a long non-contractile tail and a dsDNA genome with an approximate size of 44 kb and a 54.6% GC content. Phage vB_EcoS-EE09 infected 12 out of the 17 E. coli strains tested. We identified 16 structural phage proteins, including the major capsid protein, in cell-free lysates by protein mass spectrometry. Comparative proteomics of protein extracts of infected E. coli cells revealed that proteins involved in amino acid and protein metabolism were more abundant in infected compared to non-infected cells. Among the proteins involved in the stress response, 74% were less abundant in the infected cultures compared to the non-infected controls, with six proteins showing significant less abundance. Repressing the expression of these proteins may be a phage strategy to evade host defense mechanisms. Our results contribute to diversifying phage collections, identifying structural proteins to enable better reliability in annotating taxonomically related phage genomes, and understanding phage-host interactions at the protein level.
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Affiliation(s)
- Jimena Barrero-Canosa
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Luyao Wang
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Angelah Oyugi
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Simon Klaes
- Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (S.K.)
- Helmholtz Centre for Environmental Research GmbH—UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Pascal Fischer
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Lorenz Adrian
- Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (S.K.)
- Helmholtz Centre for Environmental Research GmbH—UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Ulrich Szewzyk
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Myriel Cooper
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
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27
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Uematsu S, Qian SB. Hijacking host ribosomes via tRNA mimicry. Nat Cell Biol 2023; 25:1562-1563. [PMID: 37857832 DOI: 10.1038/s41556-023-01249-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Affiliation(s)
- Saori Uematsu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA.
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28
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Zafirov D, Giovinazzo N, Lecampion C, Field B, Ducassou JN, Couté Y, Browning KS, Robaglia C, Gallois JL. Arabidopsis eIF4E1 protects the translational machinery during TuMV infection and restricts virus accumulation. PLoS Pathog 2023; 19:e1011417. [PMID: 37983287 PMCID: PMC10721207 DOI: 10.1371/journal.ppat.1011417] [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: 05/12/2023] [Revised: 12/14/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023] Open
Abstract
Successful subversion of translation initiation factors eIF4E determines the infection success of potyviruses, the largest group of viruses affecting plants. In the natural variability of many plant species, resistance to potyvirus infection is provided by polymorphisms at eIF4E that renders them inadequate for virus hijacking but still functional in translation initiation. In crops where such natural resistance alleles are limited, the genetic inactivation of eIF4E has been proposed for the engineering of potyvirus resistance. However, recent findings indicate that knockout eIF4E alleles may be deleterious for plant health and could jeopardize resistance efficiency in comparison to functional resistance proteins. Here, we explored the cause of these adverse effects by studying the role of the Arabidopsis eIF4E1, whose inactivation was previously reported as conferring resistance to the potyvirus clover yellow vein virus (ClYVV) while also promoting susceptibility to another potyvirus turnip mosaic virus (TuMV). We report that eIF4E1 is required to maintain global plant translation and to restrict TuMV accumulation during infection, and its absence is associated with a favoured virus multiplication over host translation. Furthermore, our findings show that, in the absence of eIF4E1, infection with TuMV results in the production of a truncated eIFiso4G1 protein. Finally, we demonstrate a role for eIFiso4G1 in TuMV accumulation and in supporting plant fitness during infection. These findings suggest that eIF4E1 counteracts the hijacking of the plant translational apparatus during TuMV infection and underscore the importance of preserving the functionality of translation initiation factors eIF4E when implementing potyvirus resistance strategies.
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Affiliation(s)
- Delyan Zafirov
- GAFL, INRAE, Montfavet, France
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
| | | | - Cécile Lecampion
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
| | - Ben Field
- Aix-Marseille Univ, CEA, CNRS, BIAM, LGBP Team, Marseille, France
| | | | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, Grenoble, France
| | - Karen S. Browning
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
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29
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Lantican DV, Nocum JDL, Manohar ANC, Mendoza JVS, Gardoce RR, Lachica GC, Gueco LS, Dela Cueva FM. Comparative RNA-seq analysis of resistant and susceptible banana genotypes reveals molecular mechanisms in response to banana bunchy top virus (BBTV) infection. Sci Rep 2023; 13:18719. [PMID: 37907581 PMCID: PMC10618458 DOI: 10.1038/s41598-023-45937-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023] Open
Abstract
Bananas hold significant economic importance as an agricultural commodity, serving as a primary livelihood source, a favorite fruit, and a staple crop in various regions across the world. However, Banana bunchy top disease (BBTD), which is caused by banana bunchy top virus (BBTV), poses a considerable threat to banana cultivation. To understand the resistance mechanism and the interplay of host suitability factors in the presence of BBTV, we conducted RNA-seq-based comparative transcriptomics analysis on mock-inoculated and BBTV-inoculated samples from resistant (wild Musa balbisiana) and susceptible (Musa acuminata 'Lakatan') genotypes. We observed common patterns of expression for 62 differentially expressed genes (DEGs) in both genotypes, which represent the typical defense response of bananas to BBTV. Furthermore, we identified 99 DEGs exclusive to the 'Lakatan' banana cultivar, offering insights into the host factors and susceptibility mechanisms that facilitate successful BBTV infection. In parallel, we identified 151 DEGs unique to the wild M. balbisiana, shedding light on the multifaceted mechanisms of BBTV resistance, involving processes such as secondary metabolite biosynthesis, cell wall modification, and pathogen perception. Notably, our validation efforts via RT-qPCR confirmed the up-regulation of the glucuronoxylan 4-O-methyltransferase gene (14.28 fold-change increase), implicated in xylan modification and degradation. Furthermore, our experiments highlighted the potential recruitment of host's substrate adaptor ADO (30.31 fold-change increase) by BBTV, which may play a role in enhancing banana susceptibility to the viral pathogen. The DEGs identified in this work can be used as basis in designing associated gene markers for the precise integration of resistance genes in marker-assisted breeding programs. Furthermore, the findings can be applied to develop genome-edited banana cultivars targeting the resistance and susceptibility genes, thus developing novel cultivars that are resilient to important diseases.
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Affiliation(s)
- Darlon V Lantican
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines.
| | - Jen Daine L Nocum
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Anand Noel C Manohar
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Jay-Vee S Mendoza
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Roanne R Gardoce
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Grace C Lachica
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
- Philippine Genome Center - Program for Agriculture, Livestock, Fisheries, Forestry, Office of the Vice Chancellor for Research and Extension, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Lavernee S Gueco
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Fe M Dela Cueva
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
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30
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Maurina SF, O'Sullivan JP, Sharma G, Pineda Rodriguez DC, MacFadden A, Cendali F, Henen MA, Vögeli B, Kieft JS, Glasgow A, Steckelberg AL. An Evolutionarily Conserved Strategy for Ribosome Binding and Host Translation Inhibition by β-coronavirus Non-structural Protein 1. J Mol Biol 2023; 435:168259. [PMID: 37660941 PMCID: PMC10543557 DOI: 10.1016/j.jmb.2023.168259] [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] [Received: 06/12/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
An important pathogenicity factor of SARS-CoV-2 and related coronaviruses is Non-structural protein 1 (Nsp1), which suppresses host gene expression and stunts antiviral signaling. SARS-CoV-2 Nsp1 binds the ribosome to inhibit translation through mRNA displacement and induces degradation of host mRNAs. Here we show that Nsp1-dependent host shutoff is conserved in diverse coronaviruses, but only Nsp1 from β-Coronaviruses (β-CoV) inhibits translation through ribosome binding. The C-terminal domain (CTD) of all β-CoV Nsp1s confers high-affinity ribosome binding despite low sequence conservation. Modeling of interactions of four Nsp1s with the ribosome identified the few absolutely conserved amino acids that, together with an overall conservation in surface charge, form the β-CoV Nsp1 ribosome-binding domain. Contrary to previous models, the Nsp1 ribosome-binding domain is an inefficient translation inhibitor. Instead, the Nsp1-CTD likely functions by recruiting Nsp1's N-terminal "effector" domain. Finally, we show that a cis-acting viral RNA element has co-evolved to fine-tune SARS-CoV-2 Nsp1 function, but does not provide similar protection against Nsp1 from related viruses. Together, our work provides new insight into the diversity and conservation of ribosome-dependent host-shutoff functions of Nsp1, knowledge that could aid future efforts in pharmacological targeting of Nsp1 from SARS-CoV-2 and related human-pathogenic β-CoVs. Our study also exemplifies how comparing highly divergent Nsp1 variants can help to dissect the different modalities of this multi-functional viral protein.
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Affiliation(s)
- Stephanie F Maurina
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - John P O'Sullivan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Geetika Sharma
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Anum Glasgow
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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31
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Kamzeeva P, Petushkov I, Knizhnik E, Snoeck R, Khodarovich Y, Ryabukhina E, Alferova V, Eshtukov-Shcheglov A, Belyaev E, Svetlova J, Vedekhina T, Kulbachinskiy A, Varizhuk A, Andrei G, Aralov A. Phenotypic Test of Benzo[4,5]imidazo[1,2-c]pyrimidinone-Based Nucleoside and Non-Nucleoside Derivatives against DNA and RNA Viruses, Including Coronaviruses. Int J Mol Sci 2023; 24:14540. [PMID: 37834006 PMCID: PMC10572855 DOI: 10.3390/ijms241914540] [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] [Received: 08/20/2023] [Revised: 09/16/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Emerging and re-emerging viruses periodically cause outbreaks and epidemics around the world, which ultimately lead to global events such as the COVID-19 pandemic. Thus, the urgent need for new antiviral drugs is obvious. Over more than a century of antiviral development, nucleoside analogs have proven to be promising agents against diversified DNA and RNA viruses. Here, we present the synthesis and evaluation of the antiviral activity of nucleoside analogs and their deglycosylated derivatives based on a hydroxybenzo[4,5]imidazo[1,2-c]pyrimidin-1(2H)-one scaffold. The antiviral activity was evaluated against a panel of structurally and phylogenetically diverse RNA and DNA viruses. The leader compound showed micromolar activity against representatives of the family Coronaviridae, including SARS-CoV-2, as well as against respiratory syncytial virus in a submicromolar range without noticeable toxicity for the host cells. Surprisingly, methylation of the aromatic hydroxyl group of the leader compound resulted in micromolar activity against the varicella-zoster virus without any significant impact on cell viability. The leader compound was shown to be a weak inhibitor of the SARS-CoV-2 RNA-dependent RNA polymerase. It also inhibited biocondensate formation important for SARS-CoV-2 replication. The active compounds may be considered as a good starting point for further structure optimization and mechanistic and preclinical studies.
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Affiliation(s)
- Polina Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Ivan Petushkov
- Institute of Molecular Genetics, National Research Centre ‘Kurchatov Institute’, 123182 Moscow, Russia; (I.P.); (A.K.)
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ekaterina Knizhnik
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (T.V.); (A.V.)
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (R.S.); (G.A.)
| | - Yuri Khodarovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Ekaterina Ryabukhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Vera Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Artur Eshtukov-Shcheglov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Evgeny Belyaev
- Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, 119071 Moscow, Russia;
| | - Julia Svetlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (T.V.); (A.V.)
| | - Tatiana Vedekhina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (T.V.); (A.V.)
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Centre ‘Kurchatov Institute’, 123182 Moscow, Russia; (I.P.); (A.K.)
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (T.V.); (A.V.)
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (R.S.); (G.A.)
| | - Andrey Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
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32
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D′Oliviera A, Dai X, Mottaghinia S, Geissler EP, Etienne L, Zhang Y, Mugridge JS. Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529306. [PMID: 36865253 PMCID: PMC9980103 DOI: 10.1101/2023.02.20.529306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) is critical for the production of functional viral proteins during infection and, like many viral proteases, can also target host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes global protein synthesis and cellular redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain required for tRNA modification activity in cells. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 may be resistant to cleavage. In primates, regions outside the cleavage site with rapid evolution could indicate adaptation to ancient viral pathogens. We determined the structure of a TRMT1 peptide in complex with Mpro, revealing a substrate binding conformation distinct from the majority of available Mpro-peptide complexes. Kinetic parameters for peptide cleavage showed that the TRMT1(526-536) sequence is cleaved with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage that could help inform future therapeutic design and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection suppresses protein translation and oxidative stress response to impact viral pathogenesis.
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Affiliation(s)
- Angel D′Oliviera
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Xuhang Dai
- Department of Chemistry, New York University, New York, NY 10003
| | - Saba Mottaghinia
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Evan P. Geissler
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
| | - Lucie Etienne
- CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY 10003
- Simons Center for Computational Physical Chemistry at New York University, New York, NY 10003
| | - Jeffrey S. Mugridge
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
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33
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Kamzeeva PN, Aralov AV, Alferova VA, Korshun VA. Recent Advances in Molecular Mechanisms of Nucleoside Antivirals. Curr Issues Mol Biol 2023; 45:6851-6879. [PMID: 37623252 PMCID: PMC10453654 DOI: 10.3390/cimb45080433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
The search for new drugs has been greatly accelerated by the emergence of new viruses and drug-resistant strains of known pathogens. Nucleoside analogues (NAs) are a prospective class of antivirals due to known safety profiles, which are important for rapid repurposing in the fight against emerging pathogens. Recent improvements in research methods have revealed new unexpected details in the mechanisms of action of NAs that can pave the way for new approaches for the further development of effective drugs. This review accounts advanced techniques in viral polymerase targeting, new viral and host enzyme targeting approaches, and prodrug-based strategies for the development of antiviral NAs.
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Affiliation(s)
| | | | | | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (P.N.K.); (A.V.A.); (V.A.A.)
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34
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Xu T, Zhao J, Xiong M. Graphical Learning and Causal Inference for Drug Repurposing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.29.23293346. [PMID: 37577650 PMCID: PMC10418581 DOI: 10.1101/2023.07.29.23293346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Gene expression profiles that connect drug perturbations, disease gene expression signatures, and clinical data are important for discovering potential drug repurposing indications. However, the current approach to gene expression reversal has several limitations. First, most methods focus on validating the reversal expression of individual genes. Second, there is a lack of causal approaches for identifying drug repurposing candidates. Third, few methods for passing and summarizing information on a graph have been used for drug repurposing analysis, with classical network propagation and gene set enrichment analysis being the most common. Fourth, there is a lack of graph-valued association analysis, with current approaches using real-valued association analysis one gene at a time to reverse abnormal gene expressions to normal gene expressions. To overcome these limitations, we propose a novel causal inference and graph neural network (GNN)-based framework for identifying drug repurposing candidates. We formulated a causal network as a continuous constrained optimization problem and developed a new algorithm for reconstructing large-scale causal networks of up to 1,000 nodes. We conducted large-scale simulations that demonstrated good false positive and false negative rates. To aggregate and summarize information on both nodes and structure from the spatial domain of the causal network, we used directed acyclic graph neural networks (DAGNN). We also developed a new method for graph regression in which both dependent and independent variables are graphs. We used graph regression to measure the degree to which drugs reverse altered gene expressions of disease to normal levels and to select potential drug repurposing candidates. To illustrate the application of our proposed methods for drug repurposing, we applied them to phase I and II L1000 connectivity map perturbational profiles from the Broad Institute LINCS, which consist of gene-expression profiles for thousands of perturbagens at a variety of time points, doses, and cell lines, as well as disease gene expression data under-expressed and over-expressed in response to SARS-CoV-2.
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Affiliation(s)
- Tao Xu
- Department of Epidemiology, University of Florida, Gainesville, FL 32611, USA
| | - Jinying Zhao
- Department of Epidemiology, University of Florida, Gainesville, FL 32611, USA
| | - Momiao Xiong
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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35
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Kim IJ, Lee YH, Khalid MM, Chen IP, Zhang Y, Ott M, Verdin E. SARS-CoV-2 protein ORF8 limits expression levels of Spike antigen and facilitates immune evasion of infected host cells. J Biol Chem 2023; 299:104955. [PMID: 37354973 PMCID: PMC10289268 DOI: 10.1016/j.jbc.2023.104955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
Recovery from COVID-19 depends on the ability of the host to effectively neutralize virions and infected cells, a process largely driven by antibody-mediated immunity. However, with the newly emerging variants that evade Spike-targeting antibodies, re-infections and breakthrough infections are increasingly common. A full characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mechanisms counteracting antibody-mediated immunity is therefore needed. Here, we report that ORF8 is a virally encoded SARS-CoV-2 factor that controls cellular Spike antigen levels. We show that ORF8 limits the availability of mature Spike by inhibiting host protein synthesis and retaining Spike at the endoplasmic reticulum, reducing cell-surface Spike levels and recognition by anti-SARS-CoV-2 antibodies. In conditions of limited Spike availability, we found ORF8 restricts Spike incorporation during viral assembly, reducing Spike levels in virions. Cell entry of these virions then leaves fewer Spike molecules at the cell surface, limiting antibody recognition of infected cells. Based on these findings, we propose that SARS-CoV-2 variants may adopt an ORF8-dependent strategy that facilitates immune evasion of infected cells for extended viral production.
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Affiliation(s)
- Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, California, United States.
| | - Yong-Ho Lee
- Buck Institute for Research on Aging, Novato, California, United States; Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Irene P Chen
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Yini Zhang
- Buck Institute for Research on Aging, Novato, California, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States; Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, United States.
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36
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Rainey SM, Geoghegan V, Lefteri DA, Ant TH, Martinez J, McNamara CJ, Kamel W, de Laurent ZR, Castello A, Sinkins SP. Differences in proteome perturbations caused by the Wolbachia strain wAu suggest multiple mechanisms of Wolbachia-mediated antiviral activity. Sci Rep 2023; 13:11737. [PMID: 37474590 PMCID: PMC10359319 DOI: 10.1038/s41598-023-38127-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023] Open
Abstract
Some strains of the inherited bacterium Wolbachia have been shown to be effective at reducing the transmission of dengue virus (DENV) and other RNA viruses by Aedes aegypti in both laboratory and field settings and are being deployed for DENV control. The degree of virus inhibition varies between Wolbachia strains. Density and tissue tropism can contribute to these differences but there are also indications that this is not the only factor involved: for example, strains wAu and wAlbA are maintained at similar intracellular densities but only wAu produces strong DENV inhibition. We previously reported perturbations in lipid transport dynamics, including sequestration of cholesterol in lipid droplets, with strains wMel/wMelPop in Ae. aegypti. To further investigate the cellular basis underlying these differences, proteomic analysis of midguts was carried out on Ae. aegypti lines carrying strains wAu and wAlbA: with the hypothesis that differences in perturbations may underline Wolbachia-mediated antiviral activity. Surprisingly, wAu-carrying midguts not only showed distinct proteome perturbations when compared to non-Wolbachia carrying and wAlbA-carrying midguts but also wMel-carrying midguts. There are changes in RNA processing pathways and upregulation of a specific set of RNA-binding proteins in the wAu-carrying line, including genes with known antiviral activity. Lipid transport and metabolism proteome changes also differ between strains, and we show that strain wAu does not produce the same cholesterol sequestration phenotype as wMel. Moreover, in contrast to wMel, wAu antiviral activity was not rescued by cyclodextrin treatment. Together these results suggest that wAu could show unique features in its inhibition of arboviruses compared to previously characterized Wolbachia strains.
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Affiliation(s)
| | - Vincent Geoghegan
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
- The University of York, York, UK
| | | | - Thomas H Ant
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | - Julien Martinez
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | | | - Wael Kamel
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | | | - Alfredo Castello
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK
| | - Steven P Sinkins
- MRC-University of Glasgow-Centre for Virus Research, Glasgow, UK.
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37
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Lidsky PV, Yuan J, Lashkevich KA, Dmitriev SE, Andino R. Monitoring integrated stress response in live Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548942. [PMID: 37502856 PMCID: PMC10369977 DOI: 10.1101/2023.07.13.548942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cells exhibit stress responses to various environmental changes. Among these responses, the integrated stress response (ISR) plays a pivotal role as a crucial stress signaling pathway. While extensive ISR research has been conducted on cultured cells, our understanding of its implications in multicellular organisms remains limited, largely due to the constraints of current techniques that hinder our ability to track and manipulate the ISR in vivo. To overcome these limitations, we have successfully developed an internal ribosome entry site (IRES)-based fluorescent reporter system. This innovative reporter enables us to label Drosophila cells, within the context of a living organism, that exhibit eIF2 phosphorylation-dependent translational shutoff - a characteristic feature of the ISR and viral infections. Through this methodology, we have unveiled tissue- and cell-specific regulation of stress response in Drosophila flies and have even been able to detect stressed tissues in vivo during virus and bacterial infections. To further validate the specificity of our reporter, we have engineered ISR-null eIF2αS50A mutant flies for stress response analysis. Our results shed light on the tremendous potential of this technique for investigating a broad range of developmental, stress, and infection-related experimental conditions. Combining the reporter tool with ISR-null mutants establishes Drosophila as an exceptionally powerful model for studying the ISR in the context of multicellular organisms.
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Affiliation(s)
- Peter V Lidsky
- University of California San Francisco, San Francisco, CA, 94158
| | - Jing Yuan
- University of California San Francisco, San Francisco, CA, 94158
| | - Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Raul Andino
- University of California San Francisco, San Francisco, CA, 94158
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38
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Zhao N, Ho JSY, Meng F, Zheng S, Kurland AP, Tian L, Rea-Moreno M, Song X, Seo JS, Kaniskan HÜ, Te Velthuis AJW, Tortorella D, Chen YW, Johnson JR, Jin J, Marazzi I. Generation of host-directed and virus-specific antivirals using targeted protein degradation promoted by small molecules and viral RNA mimics. Cell Host Microbe 2023; 31:1154-1169.e10. [PMID: 37339625 PMCID: PMC10528416 DOI: 10.1016/j.chom.2023.05.030] [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] [Received: 08/01/2022] [Revised: 04/24/2023] [Accepted: 05/30/2023] [Indexed: 06/22/2023]
Abstract
Targeted protein degradation (TPD), as exemplified by proteolysis-targeting chimera (PROTAC), is an emerging drug discovery platform. PROTAC molecules, which typically contain a target protein ligand linked to an E3 ligase ligand, recruit a target protein to the E3 ligase to induce its ubiquitination and degradation. Here, we applied PROTAC approaches to develop broad-spectrum antivirals targeting key host factors for many viruses and virus-specific antivirals targeting unique viral proteins. For host-directed antivirals, we identified a small-molecule degrader, FM-74-103, that elicits selective degradation of human GSPT1, a translation termination factor. FM-74-103-mediated GSPT1 degradation inhibits both RNA and DNA viruses. Among virus-specific antivirals, we developed viral RNA oligonucleotide-based bifunctional molecules (Destroyers). As a proof of principle, RNA mimics of viral promoter sequences were used as heterobifunctional molecules to recruit and target influenza viral polymerase for degradation. This work highlights the broad utility of TPD to rationally design and develop next-generation antivirals.
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Affiliation(s)
- Nan Zhao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fanye Meng
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lu Tian
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martha Rea-Moreno
- Department of Otolaryngology, Master of Science in Biomedical Science Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiangyang Song
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ji-Seon Seo
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aartjan J W Te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Domenico Tortorella
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ya-Wen Chen
- Department of Otolaryngology, Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Institute for Airway Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
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39
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Hardy A, Bakshi S, Furnon W, MacLean O, Gu Q, Varjak M, Varela M, Aziz MA, Shaw AE, Pinto RM, Cameron Ruiz N, Mullan C, Taggart AE, Da Silva Filipe A, Randall RE, Wilson SJ, Stewart ME, Palmarini M. The Timing and Magnitude of the Type I Interferon Response Are Correlated with Disease Tolerance in Arbovirus Infection. mBio 2023; 14:e0010123. [PMID: 37097030 PMCID: PMC10294695 DOI: 10.1128/mbio.00101-23] [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] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 04/26/2023] Open
Abstract
Infected hosts possess two alternative strategies to protect themselves against the negative impact of virus infections: resistance, used to abrogate virus replication, and disease tolerance, used to avoid tissue damage without controlling viral burden. The principles governing pathogen resistance are well understood, while less is known about those involved in disease tolerance. Here, we studied bluetongue virus (BTV), the cause of bluetongue disease of ruminants, as a model system to investigate the mechanisms of virus-host interactions correlating with disease tolerance. BTV induces clinical disease mainly in sheep, while cattle are considered reservoirs of infection, rarely exhibiting clinical symptoms despite sustained viremia. Using primary cells from multiple donors, we show that BTV consistently reaches higher titers in ovine cells than cells from cattle. The variable replication kinetics of BTV in sheep and cow cells were mostly abolished by abrogating the cell type I interferon (IFN) response. We identified restriction factors blocking BTV replication, but both the sheep and cow orthologues of these antiviral genes possess anti-BTV properties. Importantly, we demonstrate that BTV induces a faster host cell protein synthesis shutoff in primary sheep cells than cow cells, which results in an earlier downregulation of antiviral proteins. Moreover, by using RNA sequencing (RNA-seq), we also show a more pronounced expression of interferon-stimulated genes (ISGs) in BTV-infected cow cells than sheep cells. Our data provide a new perspective on how the type I IFN response in reservoir species can have overall positive effects on both virus and host evolution. IMPORTANCE The host immune response usually aims to inhibit virus replication in order to avoid cell damage and disease. In some cases, however, the infected host avoids the deleterious effects of infection despite high levels of viral replication. This strategy is known as disease tolerance, and it is used by animal reservoirs of some zoonotic viruses. Here, using a virus of ruminants (bluetongue virus [BTV]) as an experimental system, we dissected virus-host interactions in cells collected from species that are susceptible (sheep) or tolerant (cow) to disease. We show that (i) virus modulation of the host antiviral type I interferon (IFN) responses, (ii) viral replication kinetics, and (iii) virus-induced cell damage differ in tolerant and susceptible BTV-infected cells. Understanding the complex virus-host interactions in disease tolerance can allow us to disentangle the critical balance between protective and damaging host immune responses.
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Affiliation(s)
- Alexandra Hardy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Siddharth Bakshi
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Oscar MacLean
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Mariana Varela
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Muhamad Afiq Aziz
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Andrew E. Shaw
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Natalia Cameron Ruiz
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Catrina Mullan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Aislynn E. Taggart
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Richard E. Randall
- School of Biology, Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Fife, United Kingdom
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Meredith E. Stewart
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
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40
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Zhu J, Chiang C, Gack MU. Viral evasion of the interferon response at a glance. J Cell Sci 2023; 136:jcs260682. [PMID: 37341132 PMCID: PMC10411950 DOI: 10.1242/jcs.260682] [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: 06/22/2023] Open
Abstract
Re-emerging and new viral pathogens have caused significant morbidity and mortality around the world, as evidenced by the recent monkeypox, Ebola and Zika virus outbreaks and the ongoing COVID-19 pandemic. Successful viral infection relies on tactical viral strategies to derail or antagonize host innate immune defenses, in particular the production of type I interferons (IFNs) by infected cells. Viruses can thwart intracellular sensing systems that elicit IFN gene expression (that is, RIG-I-like receptors and the cGAS-STING axis) or obstruct signaling elicited by IFNs. In this Cell Science at a Glance article and the accompanying poster, we review the current knowledge about the major mechanisms employed by viruses to inhibit the activity of intracellular pattern-recognition receptors and their downstream signaling cascades leading to IFN-based antiviral host defenses. Advancing our understanding of viral immune evasion might spur unprecedented opportunities to develop new antiviral compounds or vaccines to prevent viral infectious diseases.
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Affiliation(s)
- Junji Zhu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
| | - Cindy Chiang
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
| | - Michaela U. Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
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41
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De Luca C, Gupta A, Bortvin A. Retrotransposon LINE-1 bodies in the cytoplasm of piRNA-deficient mouse spermatocytes: Ribonucleoproteins overcoming the integrated stress response. PLoS Genet 2023; 19:e1010797. [PMID: 37307272 DOI: 10.1371/journal.pgen.1010797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/23/2023] [Indexed: 06/14/2023] Open
Abstract
Transposable elements (TE) are mobile DNA sequences whose excessive proliferation endangers the host. Although animals have evolved robust TE-targeting defenses, including Piwi-interacting (pi)RNAs, retrotransposon LINE-1 (L1) still thrives in humans and mice. To gain insights into L1 endurance, we characterized L1 Bodies (LBs) and ORF1p complexes in germ cells of piRNA-deficient Maelstrom null mice. We report that ORF1p interacts with TE RNAs, genic mRNAs, and stress granule proteins, consistent with earlier studies. We also show that ORF1p associates with the CCR4-NOT deadenylation complex and PRKRA, a Protein Kinase R factor. Despite ORF1p interactions with these negative regulators of RNA expression, the stability and translation of LB-localized mRNAs remain unchanged. To scrutinize these findings, we studied the effects of PRKRA on L1 in cultured cells and showed that it elevates ORF1p levels and L1 retrotransposition. These results suggest that ORF1p-driven condensates promote L1 propagation, without affecting the metabolism of endogenous RNAs.
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Affiliation(s)
- Chiara De Luca
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, United States of Americ
| | - Anuj Gupta
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, United States of Americ
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42
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Maurina SF, O’Sullivan JP, Sharma G, Pineda Rodriguez DC, MacFadden A, Cendali F, Henen MA, Kieft JS, Glasgow A, Steckelberg AL. An evolutionarily conserved strategy for ribosome binding and inhibition by β-coronavirus non-structural protein 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544141. [PMID: 37333070 PMCID: PMC10274807 DOI: 10.1101/2023.06.07.544141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
An important pathogenicity factor of SARS-CoV-2 and related coronaviruses is Nsp1, which suppresses host gene expression and stunts antiviral signaling. SARS-CoV-2 Nsp1 binds the ribosome to inhibit translation through mRNA displacement and induces degradation of host mRNAs through an unknown mechanism. Here we show that Nsp1-dependent host shutoff is conserved in diverse coronaviruses, but only Nsp1 from β-CoV inhibits translation through ribosome binding. The C-terminal domain of all β-CoV Nsp1s confers high-affinity ribosome-binding despite low sequence conservation. Modeling of interactions of four Nsp1s to the ribosome identified few absolutely conserved amino acids that, together with an overall conservation in surface charge, form the β-CoV Nsp1 ribosome-binding domain. Contrary to previous models, the Nsp1 ribosome-binding domain is an inefficient translation inhibitor. Instead, the Nsp1-CTD likely functions by recruiting Nsp1's N-terminal "effector" domain. Finally, we show that a viral cis -acting RNA element has co-evolved to fine-tune SARS-CoV-2 Nsp1 function, but does not provide similar protection against Nsp1 from related viruses. Together, our work provides new insight into the diversity and conservation of ribosome-dependent host-shutoff functions of Nsp1, knowledge that could aide future efforts in pharmacological targeting of Nsp1 from SARS-CoV-2, but also related human-pathogenic β-coronaviruses. Our study also exemplifies how comparing highly divergent Nsp1 variants can help to dissect the different modalities of this multi-functional viral protein.
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Affiliation(s)
- Stephanie F. Maurina
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - John P. O’Sullivan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Geetika Sharma
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey S. Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
- Current address: New York Structural Biology Center, New York, NY, USA
| | - Anum Glasgow
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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43
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Wöhnke E, Klupp BG, Blome S, Mettenleiter TC, Karger A. Mass-Spectrometric Evaluation of the African Swine Fever Virus-Induced Host Shutoff Using Dynamic Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC). Viruses 2023; 15:1283. [PMID: 37376583 DOI: 10.3390/v15061283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
African swine fever is a viral disease of swine caused by the African swine fever virus (ASFV). Currently, ASFV is spreading over the Eurasian continent and threatening global pig husbandry. One viral strategy to undermine an efficient host cell response is to establish a global shutoff of host protein synthesis. This shutoff has been observed in ASFV-infected cultured cells using two-dimensional electrophoresis combined with metabolic radioactive labeling. However, it remained unclear if this shutoff was selective for certain host proteins. Here, we characterized ASFV-induced shutoff in porcine macrophages by measurement of relative protein synthesis rates using a mass spectrometric approach based on stable isotope labeling with amino acids in cell culture (SILAC). The impact of ASFV infection on the synthesis of >2000 individual host proteins showed a high degree of variability, ranging from complete shutoff to a strong induction of proteins that are absent from naïve cells. GO-term enrichment analysis revealed that the most effective shutoff was observed for proteins related to RNA metabolism, while typical representatives of the innate immune system were strongly induced after infection. This experimental setup is suitable to quantify a virion-induced host shutoff (vhs) after infection with different viruses.
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Affiliation(s)
- Elisabeth Wöhnke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Barbara G Klupp
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
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Uchida N. Design of supramolecular nanosheets for drug delivery applications. Polym J 2023; 55:1-8. [PMID: 37359988 PMCID: PMC10169173 DOI: 10.1038/s41428-023-00788-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 06/28/2023]
Abstract
Two specific concepts have emerged in the field of materials science over the last several decades: nanosheets and supramolecular polymers. More recently, supramolecular nanosheets, in which these two concepts are integrated, have attracted particular attention, and they exhibit many fascinating characteristics. This review focuses on the design and applications of supramolecular nanosheets consisting of tubulin proteins and phospholipid membranes.
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Affiliation(s)
- Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588 Japan
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
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45
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Ahmadi S, Bazargan M, Elahi R, Esmaeilzadeh A. Immune evasion of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); molecular approaches. Mol Immunol 2023; 156:10-19. [PMID: 36857806 PMCID: PMC9684099 DOI: 10.1016/j.molimm.2022.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
In December 2019, a new betacoronavirus, known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), caused an outbreak at the Wuhan seafood market in China. The disease was further named coronavirus disease 2019 (COVID-19). In March 2020, the World Health Organization (WHO) announced the disease to be a pandemic, as more cases were reported globally. SARS-CoV-2, like many other viruses, employs diverse strategies to elude the host immune response and/or counter immune responses. The infection outcome mainly depends on interactions between the virus and the host immune system. Inhibiting IFN production, blocking IFN signaling, enhancing IFN resistance, and hijacking the host's translation machinery to expedite the production of viral proteins are among the main immune evasion mechanisms of SARS-CoV-2. SARS-CoV-2 also downregulates the expression of MHC-I on infected cells, which is an additional immune-evasion mechanism of this virus. Moreover, antigenic modifications to the spike (S) protein, such as deletions, insertions, and also substitutions are essential for resistance to SARS-CoV-2 neutralizing antibodies. This review assesses the interaction between SARS-CoV-2 and host immune response and cellular and molecular approaches used by SARS-CoV-2 for immune evasion. Understanding the mechanisms of SARS-CoV-2 immune evasion is essential since it can improve the development of novel antiviral treatment options as well as vaccination methods.
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Affiliation(s)
- Shahrzad Ahmadi
- Virology Research Center, The National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Allergy and Immunology Subspecialty Lab, Tehran, Iran
| | - Mahsa Bazargan
- Virology Research Center, The National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Allergy and Immunology Subspecialty Lab, Tehran, Iran,Department of Immunology, School of Medicine, Sahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Elahi
- M.D., School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Abdolreza Esmaeilzadeh
- Department of Immunology, Zanjan University of Medical Sciences, Zanjan, Iran; Cancer Gene Therapy Research Center (CGRC), Zanjan University of Medical Sciences, Zanjan, Iran.
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46
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Roa-Linares VC, Escudero-Flórez M, Vicente-Manzanares M, Gallego-Gómez JC. Host Cell Targets for Unconventional Antivirals against RNA Viruses. Viruses 2023; 15:v15030776. [PMID: 36992484 PMCID: PMC10058429 DOI: 10.3390/v15030776] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/12/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
The recent COVID-19 crisis has highlighted the importance of RNA-based viruses. The most prominent members of this group are SARS-CoV-2 (coronavirus), HIV (human immunodeficiency virus), EBOV (Ebola virus), DENV (dengue virus), HCV (hepatitis C virus), ZIKV (Zika virus), CHIKV (chikungunya virus), and influenza A virus. With the exception of retroviruses which produce reverse transcriptase, the majority of RNA viruses encode RNA-dependent RNA polymerases which do not include molecular proofreading tools, underlying the high mutation capacity of these viruses as they multiply in the host cells. Together with their ability to manipulate the immune system of the host in different ways, their high mutation frequency poses a challenge to develop effective and durable vaccination and/or treatments. Consequently, the use of antiviral targeting agents, while an important part of the therapeutic strategy against infection, may lead to the selection of drug-resistant variants. The crucial role of the host cell replicative and processing machinery is essential for the replicative cycle of the viruses and has driven attention to the potential use of drugs directed to the host machinery as therapeutic alternatives to treat viral infections. In this review, we discuss small molecules with antiviral effects that target cellular factors in different steps of the infectious cycle of many RNA viruses. We emphasize the repurposing of FDA-approved drugs with broad-spectrum antiviral activity. Finally, we postulate that the ferruginol analog (18-(phthalimide-2-yl) ferruginol) is a potential host-targeted antiviral.
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Affiliation(s)
- Vicky C Roa-Linares
- Molecular and Translation Medicine Group, University of Antioquia, Medellin 050010, Colombia
| | - Manuela Escudero-Flórez
- Molecular and Translation Medicine Group, University of Antioquia, Medellin 050010, Colombia
| | - Miguel Vicente-Manzanares
- Molecular Mechanisms Program, Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, 37007 Salamanca, Spain
| | - Juan C Gallego-Gómez
- Molecular and Translation Medicine Group, University of Antioquia, Medellin 050010, Colombia
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47
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Hoang HD, Said A, Vaidya N, Gilchrist VH, Malone K, Kabilan U, Topshee S, Xiang X, Yang AD, Olagnier D, Mossman K, Beug ST, Jafarnejad SM, Workenhe ST, Graber TE, Alain T. Adaptation of transgene mRNA translation boosts the anticancer efficacy of oncolytic HSV1. J Immunother Cancer 2023; 11:jitc-2022-006408. [PMID: 36958764 PMCID: PMC10040010 DOI: 10.1136/jitc-2022-006408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Transgenes deliver therapeutic payloads to improve oncolytic virus immunotherapy. Transgenes encoded within oncolytic viruses are designed to be highly transcribed, but protein synthesis is often negatively affected by viral infection, compromising the amount of therapeutic protein expressed. Studying the oncolytic herpes simplex virus-1 (HSV1), we found standard transgene mRNAs to be suboptimally translated in infected cells. METHODS Using RNA-Seq reads, we determined the transcription start sites and 5'leaders of HSV1 genes and uncovered the US11 5'leader to confer superior activity in translation reporter assays. We then incorporated this 5'leader into GM-CSF expression cassette in oncolytic HSV1 and compared the translationally adapted oncolytic virus with the conventional, leaderless, virus in vitro and in mice. RESULTS Inclusion of the US11 5'leader in the GM-CSF transgene incorporated into HSV1 boosted translation in vitro and in vivo. Importantly, treatment with US11 5'leader-GM-CSF oncolytic HSV1 showed superior antitumor immune activity and improved survival in a syngeneic mouse model of colorectal cancer as compared with leaderless-GM-CSF HSV1. CONCLUSIONS Our study demonstrates the therapeutic value of identifying and integrating platform-specific cis-acting sequences that confer increased protein synthesis on transgene expression.
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Affiliation(s)
- Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Aida Said
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Nasana Vaidya
- Department Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Victoria H Gilchrist
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Kyle Malone
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Usha Kabilan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Serena Topshee
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - Xiao Xiang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | - An-Dao Yang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - David Olagnier
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Shawn T Beug
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
| | | | - Samuel T Workenhe
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa Faculty of Medicine, Ottawa, Ontario, Canada
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48
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Berber E, Sumbria D, Kokkaya S. A metabolic blueprint of COVID-19 and long-term vaccine efficacy. Drug Metab Pers Ther 2023; 38:15-29. [PMID: 36166711 DOI: 10.1515/dmpt-2022-0148] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Viruses are obligatory protein-coated units and often utilize the metabolic functions of the cells they infect. Viruses hijack cellular metabolic functions and cause consequences that can range from minor to devastating, as we have all witnessed during the COVID-19 pandemic. For understanding the virus-driven pathogenesis and its implications on the host, the cellular metabolism needs to be elucidated. How SARS-CoV-2 triggers metabolic functions and rewires the metabolism remains unidentified but the implications of the metabolic patterns are under investigation by several researchers. In this review, we have described the SARS-CoV-2-mediated metabolic alterations from in vitro studies to metabolic changes reported in victims of COVID-19. We have also discussed potential therapeutic targets to diminish the viral infection and suppress the inflammatory response, with respect to evidenced studies based on COVID-19 research. Finally, we aimed to explain how we could extend vaccine-induced immunity in people by targeting the immunometabolism.
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Affiliation(s)
- Engin Berber
- College of Veterinary Medicine, University of Tennessee, Knoxville, TN, USA
| | - Deepak Sumbria
- College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Rampura Phul, Bathinda, India
| | - Serkan Kokkaya
- Faculty of Veterinary Medicine, Bozok University, Yozgat, Turkey
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49
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Drzeniek NM, Kahwaji N, Schlickeiser S, Reinke P, Geißler S, Volk HD, Gossen M. Immuno-engineered mRNA combined with cell adhesive niche for synergistic modulation of the MSC secretome. Biomaterials 2023; 294:121971. [PMID: 36634491 DOI: 10.1016/j.biomaterials.2022.121971] [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: 07/14/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022]
Abstract
In vitro transcribed (IVT-)mRNA has entered center stage for vaccine development due to its immune co-stimulating properties. Given the widely demonstrated safety of IVT-mRNA-based vaccines, we aimed to adopt IVT-mRNA encoding VEGF for secretory phenotype modulation of therapeutic cells. However, we observed that the immunogenicity of IVT-mRNA impairs the endogenous secretion of pro-angiogenic mediators from transfected mesenchymal stromal cells, instead inducing anti-angiogenic chemokines. This inflammatory secretome modulation limits the application potential of unmodified IVT-mRNA for cell therapy manufacturing, pro-angiogenic therapy and regenerative medicine. To uncouple immunogenicity from the protein expression functionality, we immuno-engineered IVT-mRNA with different chemically modified ribonucleotides. 5-Methoxy-uridine-modification of IVT-mRNA rescued the endogenous secretome pattern of transfected cells and prolonged secretion of IVT-mRNA-encoded VEGF. We found that high secretion of IVT-mRNA-encoded protein further depends on optimized cell adhesion. Cell encapsulation in a collagen-hyaluronic acid hydrogel increased secretion of IVT-mRNA-encoded VEGF and augmented the endogenous secretion of supporting pro-angiogenic mediators, such as HGF. Integrating minimally immunogenic mRNA technology with predesigned matrix-derived cues allows for the synergistic combination of multiple dimensions of cell manipulation and opens routes for biomaterial-based delivery of mRNA-engineered cell products. Such multimodal systems could present a more biologically relevant way to therapeutically address complex multifactorial processes such as tissue ischemia, angiogenesis, and regeneration.
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Affiliation(s)
- Norman Michael Drzeniek
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Augustenburger Platz 1, 13353, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies (BSRT; Graduate School 203 of the German Excellence Initiative), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Nourhan Kahwaji
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Augustenburger Platz 1, 13353, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
| | - Stephan Schlickeiser
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Augustenburger Platz 1, 13353, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany
| | - Petra Reinke
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin Center for Advanced Therapies (BeCAT), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Sven Geißler
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin Center for Advanced Therapies (BeCAT), Augustenburger Platz 1, 13353, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Julius Wolff Institute (JWI), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Hans-Dieter Volk
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Augustenburger Platz 1, 13353, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Föhrer Straße 15, 13353, Berlin, Germany.
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513, Teltow, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Augustenburger Platz 1, 13353, Berlin, Germany.
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Multiple Regulations of Parasitic Protozoan Viruses: A Double-Edged Sword for Protozoa. mBio 2023; 14:e0264222. [PMID: 36633419 PMCID: PMC9973342 DOI: 10.1128/mbio.02642-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Parasite infections affect human and animal health significantly and contribute to a major burden on the global economy. Parasitic protozoan viruses (PPVs) affect the protozoan parasites' morphology, phenotypes, pathogenicity, and growth rates. This discovery provides an opportunity to develop a novel preventive and therapeutic strategy for parasitic protozoan diseases (PPDs). Currently, there is greater awareness regarding PPVs; however, knowledge of viruses and their associations with host diseases remains limited. Parasite-host interactions become more complex owing to PPVs; however, few studies have investigated underlying viral regulatory mechanisms in parasites. In this study, we reviewed relevant studies to identify studies that investigated PPV development and life cycles, the triangular association between viruses, parasites, and hosts, and the effects of viruses on protozoan pathogenicity. This study highlights that viruses can alter parasite biology, and viral infection of parasites may exacerbate the adverse effects of virus-containing parasites on hosts or reduce parasite virulence. PPVs should be considered in the prevention of parasitic epidemics and outbreaks, although their effects on the host and the complexity of the triangular association between PPVs, protozoans, and hosts remain unclear. IMPORTANCE PPVs-based regulation of parasitic protozoa can provide a theoretical basis and direction for PPD prevention and control, although PPVs and PPV regulatory mechanisms remain unclear. In this review, we investigated the differences between PPVs and the unique properties of each virus regarding virus discovery, structures, and life cycles, focused on the Trichomonas vaginalis virus, Giardia lamblia virus, Leishmania RNA virus, and the Cryptosporidium parvum virus 1. The triangular association between PPVs, parasitic protozoa, and hosts reveals the "double-edged sword" property of PPVs, which maintains a balance between parasitic protozoa and hosts in both positive and negative respects. These studies discuss the complexity of parasitic protozoa and their co-existence with hosts and suggest novel pathways for using PPVs as tools to gain a deeper understanding of protozoal infection and treatment.
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