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Homma D, Limlingan SJM, Saito T, Ando K. SARS-CoV-2-derived protein Orf9b enhances MARK2 activity via interaction with the autoinhibitory KA1 domain. FEBS Lett 2024. [PMID: 38969617 DOI: 10.1002/1873-3468.14975] [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: 03/15/2024] [Revised: 06/01/2024] [Accepted: 06/12/2024] [Indexed: 07/07/2024]
Abstract
Microtubule affinity-regulating kinase 2 (MARK2) is a Ser/Thr protein kinase that regulates cell polarity and immune responses. Here, we report that Orf9b, one of the accessory proteins encoded in the SARS-CoV-2 genome, increases MARK2 activity via interaction with the autoinhibitory KAI domain. We found that co-expression of Orf9b enhances the kinase activity of MARK2 in HEK293 cells. Orf9b does not bind to or enhance the activity of the mutant form of MARK2 lacking the KA1 domain. Orf9b lowers inhibitory phosphorylation of MARK2 at T595 while mutation experiments indicate that this site is dispensable for Orf9b-mediated enhancement of MARK2 activity. Our results suggest that Orf9b enhances MARK2 activity by binding the autoinhibitory KA1 domain, which closely interacts with the kinase domain.
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Affiliation(s)
- Daiki Homma
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
| | | | - Taro Saito
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
- Department of Biological Sciences, School of Science, Tokyo Metropolitan University, Japan
| | - Kanae Ando
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
- Department of Biological Sciences, School of Science, Tokyo Metropolitan University, Japan
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2
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López-Ayllón BD, Marin S, Fernández MF, García-García T, Fernández-Rodríguez R, de Lucas-Rius A, Redondo N, Mendoza-García L, Foguet C, Grigas J, Calvet A, Villalba JM, Gómez MJR, Megías D, Mandracchia B, Luque D, Lozano JJ, Calvo C, Herrán UM, Thomson TM, Garrido JJ, Cascante M, Montoya M. Metabolic and mitochondria alterations induced by SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10. J Med Virol 2024; 96:e29752. [PMID: 38949191 DOI: 10.1002/jmv.29752] [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: 11/10/2023] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024]
Abstract
Antiviral signaling, immune response and cell metabolism are dysregulated by SARS-CoV-2, the causative agent of COVID-19. Here, we show that SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10 induce a significant mitochondrial and metabolic reprogramming in A549 lung epithelial cells. While ORF9b, ORF9c and ORF10 induced largely overlapping transcriptomes, ORF3a induced a distinct transcriptome, including the downregulation of numerous genes with critical roles in mitochondrial function and morphology. On the other hand, all four ORFs altered mitochondrial dynamics and function, but only ORF3a and ORF9c induced a marked alteration in mitochondrial cristae structure. Genome-Scale Metabolic Models identified both metabolic flux reprogramming features both shared across all accessory proteins and specific for each accessory protein. Notably, a downregulated amino acid metabolism was observed in ORF9b, ORF9c and ORF10, while an upregulated lipid metabolism was distinctly induced by ORF3a. These findings reveal metabolic dependencies and vulnerabilities prompted by SARS-CoV-2 accessory proteins that may be exploited to identify new targets for intervention.
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Affiliation(s)
- Blanca D López-Ayllón
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Marco Fariñas Fernández
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- Department of Biomedical Laboratory Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Tránsito García-García
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Ana de Lucas-Rius
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Natalia Redondo
- Unit of Infectious Diseases, University Hospital '12 de Octubre', Institute for Health Research Hospital '12 de Octubre' (imas12), Madrid, Spain
- Centre for Biomedical Research Network on Infectious Diseases (CIBERINFEC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Laura Mendoza-García
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Carles Foguet
- British Heart Foundation Cardiovascular Epidemiology Unit and Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Juozas Grigas
- Laboratory of Immunology, Department of Anatomy and Physiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alba Calvet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - José Manuel Villalba
- Department of Cell Biology, Physiology and Immunology, Agrifood Campus of International Excellence, University of Córdoba, Córdoba, Spain
| | - María Josefa Rodríguez Gómez
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Diego Megías
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
| | - Biagio Mandracchia
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- ETSI Telecommunication, University of Valladolid, Valladolid, Spain
| | - Daniel Luque
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Juan José Lozano
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Cristina Calvo
- Barcelona Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
| | - Unai Merino Herrán
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Timothy M Thomson
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Barcelona Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
- Translational Research and Computational Biology Laboratory, Faculty of Science and Engineering, Peruvian University Cayetano Heredia, Lima, Perú
| | - Juan J Garrido
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - María Montoya
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
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3
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Zhou Y, Chen Z, Liu S, Liu S, Liao Y, Du A, Dong Z, Zhang Y, Chen X, Tao S, Wu X, Razzaq A, Xu G, Tan DA, Li S, Deng Y, Peng J, Dai S, Deng X, Zhang X, Jiang T, Zhang Z, Cheng G, Zhao J, Xia Z. A Cullin 5-based complex serves as an essential modulator of ORF9b stability in SARS-CoV-2 replication. Signal Transduct Target Ther 2024; 9:159. [PMID: 38937432 PMCID: PMC11211426 DOI: 10.1038/s41392-024-01874-5] [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: 10/29/2023] [Revised: 04/12/2024] [Accepted: 05/15/2024] [Indexed: 06/29/2024] Open
Abstract
The ORF9b protein, derived from the nucleocapsid's open-reading frame in both SARS-CoV and SARS-CoV-2, serves as an accessory protein crucial for viral immune evasion by inhibiting the innate immune response. Despite its significance, the precise regulatory mechanisms underlying its function remain elusive. In the present study, we unveil that the ORF9b protein of SARS-CoV-2, including emerging mutant strains like Delta and Omicron, can undergo ubiquitination at the K67 site and subsequent degradation via the proteasome pathway, despite certain mutations present among these strains. Moreover, our investigation further uncovers the pivotal role of the translocase of the outer mitochondrial membrane 70 (TOM70) as a substrate receptor, bridging ORF9b with heat shock protein 90 alpha (HSP90α) and Cullin 5 (CUL5) to form a complex. Within this complex, CUL5 triggers the ubiquitination and degradation of ORF9b, acting as a host antiviral factor, while HSP90α functions to stabilize it. Notably, treatment with HSP90 inhibitors such as GA or 17-AAG accelerates the degradation of ORF9b, leading to a pronounced inhibition of SARS-CoV-2 replication. Single-cell sequencing data revealed an up-regulation of HSP90α in lung epithelial cells from COVID-19 patients, suggesting a potential mechanism by which SARS-CoV-2 may exploit HSP90α to evade the host immunity. Our study identifies the CUL5-TOM70-HSP90α complex as a critical regulator of ORF9b protein stability, shedding light on the intricate host-virus immune response dynamics and offering promising avenues for drug development against SARS-CoV-2 in clinical settings.
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Affiliation(s)
- Yuzheng Zhou
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
| | - Zongpeng Chen
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Sijie Liu
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Sixu Liu
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Yujie Liao
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Ashuai Du
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Zijun Dong
- Department of Basic Medicine, School of Medicine, Hunan Normal University, 410081, Changsha, China
| | - Yongxing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Xuan Chen
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Siyi Tao
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Xin Wu
- Department of spine surgery, The Third Xiangya Hospital, Central South University, 410013, Changsha, China
| | - Aroona Razzaq
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Gang Xu
- School of Basic Medical Sciences, Anhui Medical University, 230032, Hefei, China
| | - De-An Tan
- Hunan Key Laboratory of Neurorestoratology, 921 Hospital of Joint Logistics Support Force People's Liberation Army of China (The Second Affiliated Hospital of Hunan Normal University), 410003, Changsha, Hunan, China
| | - Shanni Li
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China
| | - Youwen Deng
- Department of spine surgery, The Third Xiangya Hospital, Central South University, 410013, Changsha, China
| | - Jian Peng
- Department of Geriatric Surgery, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Shuyan Dai
- Xiangya School of Pharmaceutical Sciences, Central South University, 410013, Changsha, China
| | - Xu Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, 410013, Changsha, China
| | - Xianwen Zhang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | | | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
| | - Gong Cheng
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, 518132, Shenzhen, China
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Jincun Zhao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, China
- Guangzhou Laboratory, 510005, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 510120, Guangzhou, China
| | - Zanxian Xia
- Department of Cell Biology, School of Life Sciences, Central South University, 410013, Changsha, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics & Center for Medical Genetics, School of Life Sciences, Central South University, 410008, Changsha, China.
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4
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Rurek M. Mitochondria in COVID-19: from cellular and molecular perspective. Front Physiol 2024; 15:1406635. [PMID: 38974521 PMCID: PMC11224649 DOI: 10.3389/fphys.2024.1406635] [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] [Received: 03/25/2024] [Accepted: 05/27/2024] [Indexed: 07/09/2024] Open
Abstract
The rapid development of the COVID-19 pandemic resulted in a closer analysis of cell functioning during β-coronavirus infection. This review will describe evidence for COVID-19 as a syndrome with a strong, albeit still underestimated, mitochondrial component. Due to the sensitivity of host mitochondria to coronavirus infection, SARS-CoV-2 affects mitochondrial signaling, modulates the immune response, modifies cellular energy metabolism, induces apoptosis and ageing, worsening COVID-19 symptoms which can sometimes be fatal. Various aberrations across human systems and tissues and their relationships with mitochondria were reported. In this review, particular attention is given to characterization of multiple alterations in gene expression pattern and mitochondrial metabolism in COVID-19; the complexity of interactions between SARS-CoV-2 and mitochondrial proteins is presented. The participation of mitogenome fragments in cell signaling and the occurrence of SARS-CoV-2 subgenomic RNA within membranous compartments, including mitochondria is widely discussed. As SARS-CoV-2 severely affects the quality system of mitochondria, the cellular background for aberrations in mitochondrial dynamics in COVID-19 is additionally characterized. Finally, perspectives on the mitigation of COVID-19 symptoms by affecting mitochondrial biogenesis by numerous compounds and therapeutic treatments are briefly outlined.
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Affiliation(s)
- Michał Rurek
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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5
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Waman VP, Ashford P, Lam SD, Sen N, Abbasian M, Woodridge L, Goldtzvik Y, Bordin N, Wu J, Sillitoe I, Orengo CA. Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics. Sci Rep 2024; 14:14208. [PMID: 38902252 PMCID: PMC11190248 DOI: 10.1038/s41598-024-61541-1] [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: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 06/22/2024] Open
Abstract
The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19. In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and their human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed the impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities for the human viral protein complexes. We predicted a total of 26 affinity-enhancing variants from 13 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed. Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.
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Affiliation(s)
- Vaishali P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Paul Ashford
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Neeladri Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Mahnaz Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Laurel Woodridge
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Yonathan Goldtzvik
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Jiaxin Wu
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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6
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Carvajal JJ, García-Castillo V, Cuellar SV, Campillay-Véliz CP, Salazar-Ardiles C, Avellaneda AM, Muñoz CA, Retamal-Díaz A, Bueno SM, González PA, Kalergis AM, Lay MK. New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic. Front Immunol 2024; 15:1363572. [PMID: 38911850 PMCID: PMC11190347 DOI: 10.3389/fimmu.2024.1363572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the respiratory distress condition known as COVID-19. This disease broadly affects several physiological systems, including the gastrointestinal, renal, and central nervous (CNS) systems, significantly influencing the patient's overall quality of life. Additionally, numerous risk factors have been suggested, including gender, body weight, age, metabolic status, renal health, preexisting cardiomyopathies, and inflammatory conditions. Despite advances in understanding the genome and pathophysiological ramifications of COVID-19, its precise origins remain elusive. SARS-CoV-2 interacts with a receptor-binding domain within angiotensin-converting enzyme 2 (ACE2). This receptor is expressed in various organs of different species, including humans, with different abundance. Although COVID-19 has multiorgan manifestations, the main pathologies occur in the lung, including pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. In the post-COVID-19 period, different sequelae may occur, which may have various causes, including the direct action of the virus, alteration of the immune response, and metabolic alterations during infection, among others. Recognizing the serious adverse health effects associated with COVID-19, it becomes imperative to comprehensively elucidate and discuss the existing evidence surrounding this viral infection, including those related to the pathophysiological effects of the disease and the subsequent consequences. This review aims to contribute to a comprehensive understanding of the impact of COVID-19 and its long-term effects on human health.
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Affiliation(s)
- Jonatan J. Carvajal
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Valeria García-Castillo
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Shelsy V. Cuellar
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | | | - Camila Salazar-Ardiles
- Center for Research in Physiology and Altitude Medicine (FIMEDALT), Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Andrea M. Avellaneda
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Antofagasta, Chile
| | - Christian A. Muñoz
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Angello Retamal-Díaz
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K. Lay
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
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7
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Caobi A, Saeed M. Upping the ante: enhanced expression of interferon-antagonizing ORF6 and ORF9b proteins by SARS-CoV-2 variants of concern. Curr Opin Microbiol 2024; 79:102454. [PMID: 38518551 PMCID: PMC11162932 DOI: 10.1016/j.mib.2024.102454] [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: 01/09/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024]
Abstract
SARS-CoV-2 exhibits a remarkable capability to subvert the host antiviral innate immune system. This adeptness is orchestrated by viral proteins, which initially attempt to obstruct the activation of the antiviral immune program and then act as a fail-safe mechanism to mitigate the downstream effects of the activated immune response. This dual strategy leads to delayed expression and enfeebled action of type-I and -III interferons at the infection site, enabling the virus to replicate extensively in the lungs and subsequently disseminate to other organs. Throughout the course of the COVID-19 pandemic, SARS-CoV-2 has undergone evolution, giving rise to several variants of concern, some with exceedingly higher transmission and virulence. These improved features have been linked, at least in part, to the heightened expression or activity of specific viral proteins involved in circumventing host defense mechanisms. In this review, we aim to provide a concise summary of two SARS-CoV-2 proteins, ORF6 and ORF9b, which provided selective advantage to certain variants, affecting their biology and pathogenesis.
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Affiliation(s)
- Allen Caobi
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Mohsan Saeed
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA.
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8
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Xiao X, Fu Y, You W, Huang C, Zeng F, Gu X, Sun X, Li J, Zhang Q, Du W, Cheng G, Liu Z, Liu L. Inhibition of the RLR signaling pathway by SARS-CoV-2 ORF7b is mediated by MAVS and abrogated by ORF7b-homologous interfering peptide. J Virol 2024; 98:e0157323. [PMID: 38572974 PMCID: PMC11092349 DOI: 10.1128/jvi.01573-23] [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: 10/09/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and characterized by dysregulated immune response. Studies have shown that the SARS-CoV-2 accessory protein ORF7b induces host cell apoptosis through the tumor necrosis factor alpha (TNF-α) pathway and blocks the production of interferon beta (IFN-β). The underlying mechanism remains to be investigated. In this study, we found that ORF7b facilitated viral infection and production, and inhibited the RIG-I-like receptor (RLR) signaling pathway through selectively interacting with mitochondrial antiviral-signaling protein (MAVS). MAVS439-466 region and MAVS Lys461 were essential for the physical association between MAVS and ORF7b, and the inhibition of the RLR signaling pathway by ORF7b. MAVSK461/K63 ubiquitination was essential for the RLR signaling regulated by the MAVS-ORF7b complex. ORF7b interfered with the recruitment of tumor necrosis factor receptor-related factor 6 (TRAF6) and the activation of the RLR signaling pathway by MAVS. Furthermore, interfering peptides targeting the ORF7b complex reversed the ORF7b-suppressed MAVS-RLR signaling pathway. The most potent interfering peptide V disrupts the formation of ORF7b tetramers, reverses the levels of the ORF7b-inhibited physical association between MAVS and TRAF6, leading to the suppression of viral growth and infection. Overall, this study provides a mechanism for the suppression of innate immunity by SARS-CoV-2 infection and the mechanism-based approach via interfering peptides to potentially prevent SARS-CoV-2 infection.IMPORTANCEThe pandemic coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and continues to be a threat to public health. It is imperative to understand the biology of SARS-CoV-2 infection and find approaches to prevent SARS-CoV-2 infection and ameliorate COVID-19. Multiple SARS-CoV-2 proteins are known to function on the innate immune response, but the underlying mechanism remains unknown. This study shows that ORF7b inhibits the RIG-I-like receptor (RLR) signaling pathway through the physical association between ORF7b and mitochondrial antiviral-signaling protein (MAVS), impairing the K63-linked MAVS polyubiquitination and its recruitment of tumor necrosis factor receptor-related factor 6 (TRAF6) to MAVS. The most potent interfering peptide V targeting the ORF7b-MAVS complex may reverse the suppression of the MAVS-mediated RLR signaling pathway by ORF7b and prevent viral infection and production. This study may provide new insights into the pathogenic mechanism of SARS-CoV-2 and a strategy to develop new drugs to prevent SARS-CoV-2 infection.
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Affiliation(s)
- Xiao Xiao
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Yanan Fu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Wanling You
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Feng Zeng
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Xinsheng Gu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xiaoguang Sun
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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9
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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10
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Outteridge M, Nunn CM, Devine K, Patel B, McLean GR. Antivirals for Broader Coverage against Human Coronaviruses. Viruses 2024; 16:156. [PMID: 38275966 PMCID: PMC10820748 DOI: 10.3390/v16010156] [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: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.
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Affiliation(s)
- Mia Outteridge
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Christine M. Nunn
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Kevin Devine
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Bhaven Patel
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
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11
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Arya R, Tripathi P, Nayak K, Ganesh J, Bihani SC, Ghosh B, Prashar V, Kumar M. Insights into the evolution of mutations in SARS-CoV-2 non-spike proteins. Microb Pathog 2023; 185:106460. [PMID: 37995880 DOI: 10.1016/j.micpath.2023.106460] [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: 06/12/2023] [Revised: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
The COVID-19 pandemic has been driven by the emergence of SARS-CoV-2 variants with mutations across all the viral proteins. Although mutations in the spike protein have received significant attention, understanding the prevalence and potential impact of mutations in other viral proteins is essential for comprehending the evolution of SARS-CoV-2. Here, we conducted a comprehensive analysis of approximately 14 million sequences of SARS-CoV-2 deposited in the GISAID database until December 2022 to identify prevalent mutations in the non-spike proteins at the global and country levels. Additionally, we evaluated the energetics of each mutation to better understand their impact on protein stability. While the consequences of many mutations remain unclear, we discuss potential structural and functional significance of some mutations. Our study highlights the ongoing evolutionary process of SARS-CoV-2 and underscores the importance of understanding changes in non-spike proteins.
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Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Preeti Tripathi
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Karthik Nayak
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; School of Chemical Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, 400098, India
| | - Janani Ganesh
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Biplab Ghosh
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India; Beamline Development & Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Vishal Prashar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| | - Mukesh Kumar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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12
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Oba T, Homma D, Limlingan SJM, Fukuchi A, Asada A, Saito T, Ando K. A cell-penetrating peptide derived from SARS-CoV-2 protein Orf9b allosterically inhibits MARK4 activity and mitigates tau toxicity. Neurobiol Dis 2023; 188:106334. [PMID: 37884211 DOI: 10.1016/j.nbd.2023.106334] [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: 09/04/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023] Open
Abstract
Abnormal activation of microtubule affinity-regulating kinase 4 (MARK4) and its phosphorylation of the microtubule-associated protein tau are believed to play a role in the pathogenesis of Alzheimer's disease, and MARK4 inhibition can be a strategy to develop disease-modifying therapy. Here we report the development of a membrane-permeable peptide that inhibits MARK4 activity in an allosteric manner. The SARS-CoV-2-derived protein Orf9b inhibited MARK4-mediated tau phosphorylation in primary neurons and Drosophila. Orf9b inhibited MARK4 activity in an allosteric manner and did not inhibit the activity of MARK2, which is another MARK family member and is closely related to MARK4. Co-expression of Orf9b in the fly retina expressing human tau and MARK4 suppressed phosphorylation of tau at the microtubule-binding repeats and tau-induced neurodegeneration. We identified the minimal sequence of Orf9b required to suppress MARK4 activity and fused it to a cell-permeable sequence (TAT-Orf9b10-18_78-95). Extracellular supplementation of TAT-Orf9b10-18_78-95 inhibited MARK4 activity in primary neurons, and feeding TAT-Orf9b10-18_78-95 to a fly model of tauopathy lowered phospho-tau levels and suppressed neurodegeneration. These results suggest that TAT-Orf9b10-18_78-95 is a unique class of MARK4 inhibitor and can be used to modify tau toxicity.
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Affiliation(s)
- Toshiya Oba
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Daiki Homma
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Sophia Jobien M Limlingan
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Aoi Fukuchi
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan
| | - Akiko Asada
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan; Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Japan
| | - Taro Saito
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan; Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Japan.
| | - Kanae Ando
- Laboratory of Molecular Neuroscience, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Japan; Department of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, Japan.
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13
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [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: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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14
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Wong LYR, Odle A, Luhmann E, Wu DC, Wang Y, Teo QW, Ptak C, Sariol A, Lowery S, Mack M, Meyerholz DK, Wu NC, Radoshevich L, Perlman S. Contrasting roles of MERS-CoV and SARS-CoV-2 internal proteins in pathogenesis in mice. mBio 2023; 14:e0247623. [PMID: 37882568 PMCID: PMC10746224 DOI: 10.1128/mbio.02476-23] [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: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
Betacoronaviruses encode an internal (I) gene via an alternative reading frame within the nucleocapsid gene, called ORF8b for Middle-East respiratory syndrome coronavirus (MERS-CoV) and ORF9b for severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Previous reports suggested that proteins 8b and 9b are involved in evading multiple innate immune signaling pathways. However, their roles in mediating pathogenesis in infected animals have not been determined. In this study, we abrogated the expression of protein 8b in MERS-CoV and protein 9b in SARS-CoV-2. Using mouse models of MERS-CoV and SARS-CoV-2 infection, we found that MERS-CoV lacking protein 8b expression was more virulent, while SARS-CoV-2 lacking protein 9b expression was attenuated compared with the respective wild-type viruses. Upon further analysis, we detected increased levels of type I interferon and enhanced infiltration of immune cells to the lungs of mice infected with MERS-CoV lacking protein 8b expression. These data suggest that the I protein of MERS-CoV plays a role in limiting pathogenesis while that of SARS-CoV-2 enhances disease severity. IMPORTANCE The function of betacoronavirus internal protein has been relatively understudied. The earliest report on the internal protein of mouse hepatitis virus suggested that the internal protein is a structural protein without significant functions in virus replication and virulence. However, the internal proteins of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle-East respiratory syndrome coronavirus, and SARS-CoV-2 have been shown to evade immune responses. Despite the reported functions of the internal protein in these highly pathogenic human coronaviruses, its role in mediating pathogenesis in experimentally infected animals has not been characterized. Our data indicated that despite the similar genomic location and expression strategy of these internal proteins, their effects on virulence are vastly different and virus specific, highlighting the complexity between host-virus interaction and disease outcome.
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Affiliation(s)
- Lok-Yin Roy Wong
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Abby Odle
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Emma Luhmann
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Douglas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Qi Wen Teo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Celeste Ptak
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Alan Sariol
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Shea Lowery
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Matthias Mack
- Department of Internal Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lilliana Radoshevich
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
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15
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Lenhard S, Gerlich S, Khan A, Rödl S, Bökenkamp JE, Peker E, Zarges C, Faust J, Storchova Z, Räschle M, Riemer J, Herrmann JM. The Orf9b protein of SARS-CoV-2 modulates mitochondrial protein biogenesis. J Cell Biol 2023; 222:e202303002. [PMID: 37682539 PMCID: PMC10491932 DOI: 10.1083/jcb.202303002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/06/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) expresses high amounts of the protein Orf9b to target the mitochondrial outer membrane protein Tom70. Tom70 serves as an import receptor for mitochondrial precursors and, independently of this function, is critical for the cellular antiviral response. Previous studies suggested that Orf9b interferes with Tom70-mediated antiviral signaling, but its implication for mitochondrial biogenesis is unknown. In this study, we expressed Orf9b in human HEK293 cells and observed an Orf9b-mediated depletion of mitochondrial proteins, particularly in respiring cells. To exclude that the observed depletion was caused by the antiviral response, we generated a yeast system in which the function of human Tom70 could be recapitulated. Upon expression of Orf9b in these cells, we again observed a specific decline of a subset of mitochondrial proteins and a general reduction of mitochondrial volume. Thus, the SARS-CoV-2 virus is able to modulate the mitochondrial proteome by a direct effect of Orf9b on mitochondrial Tom70-dependent protein import.
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Affiliation(s)
- Svenja Lenhard
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sarah Gerlich
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Azkia Khan
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jan-Eric Bökenkamp
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Esra Peker
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Christine Zarges
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Janina Faust
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Zuzana Storchova
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jan Riemer
- Biochemistry, University of Cologne, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
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16
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Mihalič F, Benz C, Kassa E, Lindqvist R, Simonetti L, Inturi R, Aronsson H, Andersson E, Chi CN, Davey NE, Överby AK, Jemth P, Ivarsson Y. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nat Commun 2023; 14:5636. [PMID: 37704626 PMCID: PMC10499821 DOI: 10.1038/s41467-023-41312-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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17
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Schafer JW, Porter LL. Evolutionary selection of proteins with two folds. Nat Commun 2023; 14:5478. [PMID: 37673981 PMCID: PMC10482954 DOI: 10.1038/s41467-023-41237-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Although most globular proteins fold into a single stable structure, an increasing number have been shown to remodel their secondary and tertiary structures in response to cellular stimuli. State-of-the-art algorithms predict that these fold-switching proteins adopt only one stable structure, missing their functionally critical alternative folds. Why these algorithms predict a single fold is unclear, but all of them infer protein structure from coevolved amino acid pairs. Here, we hypothesize that coevolutionary signatures are being missed. Suspecting that single-fold variants could be masking these signatures, we developed an approach, called Alternative Contact Enhancement (ACE), to search both highly diverse protein superfamilies-composed of single-fold and fold-switching variants-and protein subfamilies with more fold-switching variants. ACE successfully revealed coevolution of amino acid pairs uniquely corresponding to both conformations of 56/56 fold-switching proteins from distinct families. Then, we used ACE-derived contacts to (1) predict two experimentally consistent conformations of a candidate protein with unsolved structure and (2) develop a blind prediction pipeline for fold-switching proteins. The discovery of widespread dual-fold coevolution indicates that fold-switching sequences have been preserved by natural selection, implying that their functionalities provide evolutionary advantage and paving the way for predictions of diverse protein structures from single sequences.
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Affiliation(s)
- Joseph W Schafer
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Lauren L Porter
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA.
- National Heart, Lung, and Blood Institute, Biochemistry and Biophysics Center, National Institutes of Health, Bethesda, MD, 20892, USA.
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18
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Sharma A, Kaur M, Yadav P, Singh G, Barnwal RP. Expediting the drug discovery for ideal leads against SARS-CoV-2 via molecular docking of repurposed drugs. J Biomol Struct Dyn 2023; 41:7949-7965. [PMID: 36165445 DOI: 10.1080/07391102.2022.2127903] [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: 08/19/2021] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
Abstract
SARS-CoV-2, the novel coronavirus spreading worldwide urges the need to repurpose drugs that can quickly enter clinical trials to combat the on-going global pandemic. A cluster of proteins are encoded for by the viral genome, each assuming a critical role in pathogen endurance inside the host. To handle the adverse circumstances, robust virtual strategies such as repurposing are coming to the fore due to being economical, efficient and rapid. Five FDA approved repurposed drugs proposed to act as inhibitors by targeting SARS-CoV-2 were used for initial evaluation via molecular docking. Moreover, a comparative analysis of the selected SARS-CoV-2 proteins against five ligands (Clemizole hydrochloride, Exemestane, Nafamostat, Pregnenolone and Umifenovir) was designed. In this regard, non-structural proteins (nsp3, nsp5, nsp10, nsp12 and nsp15), structural proteins (Spike, Nucleocapsid protein) and accessory proteins (ORF 3a, ORF 7a and ORF 9 b) were selected. Here, we aim to expedite the search for a potential drug from the five FDA approved repurposing drugs already in use for treatment of multiple diseases. Based on docking analysis, Umifenovir and Pregnenolone are suggested to show potential inhibitory effects against most of the SARS-CoV-2 proteins. These drugs are noteworthy since they exhibit high binding towards target proteins and should be used as lead compounds towards in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Mandeep Kaur
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Priya Yadav
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
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19
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Porter LL. Fluid protein fold space and its implications. Bioessays 2023; 45:e2300057. [PMID: 37431685 PMCID: PMC10529699 DOI: 10.1002/bies.202300057] [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: 03/30/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Fold-switching proteins, which remodel their secondary and tertiary structures in response to cellular stimuli, suggest a new view of protein fold space. For decades, experimental evidence has indicated that protein fold space is discrete: dissimilar folds are encoded by dissimilar amino acid sequences. Challenging this assumption, fold-switching proteins interconnect discrete groups of dissimilar protein folds, making protein fold space fluid. Three recent observations support the concept of fluid fold space: (1) some amino acid sequences interconvert between folds with distinct secondary structures, (2) some naturally occurring sequences have switched folds by stepwise mutation, and (3) fold switching is evolutionarily selected and likely confers advantage. These observations indicate that minor amino acid sequence modifications can transform protein structure and function. Consequently, proteomic structural and functional diversity may be expanded by alternative splicing, small nucleotide polymorphisms, post-translational modifications, and modified translation rates.
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Affiliation(s)
- Lauren L. Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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20
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Zeng Z, Geng X, Wen X, Chen Y, Zhu Y, Dong Z, Hao L, Wang T, Yang J, Zhang R, Zheng K, Sun Z, Zhang Y. Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future. Front Microbiol 2023; 14:1232453. [PMID: 37645223 PMCID: PMC10461067 DOI: 10.3389/fmicb.2023.1232453] [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: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.
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Affiliation(s)
- Zhaomu Zeng
- Department of Neurosurgery, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- Department of Neurosurgery, Xiangya Hospital Jiangxi Hospital of Central South University, National Regional Medical Center for Nervous System Diseases, Nanchang, China
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiuchao Geng
- Department of Nursing, School of Medicine, Taizhou University, Taizhou, China
| | - Xichao Wen
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yueyue Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yixi Zhu
- Department of Pharmacy, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zishu Dong
- Department of Zoology, Advanced Research Institute, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Liangchao Hao
- Department of Plastic Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Tingting Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Jifeng Yang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ruobing Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Kebin Zheng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yuhao Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
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21
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Bhowal C, Ghosh S, Ghatak D, De R. Pathophysiological involvement of host mitochondria in SARS-CoV-2 infection that causes COVID-19: a comprehensive evidential insight. Mol Cell Biochem 2023; 478:1325-1343. [PMID: 36308668 PMCID: PMC9617539 DOI: 10.1007/s11010-022-04593-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/13/2022] [Indexed: 10/31/2022]
Abstract
SARS-CoV-2 is a positive-strand RNA virus that infects humans through the nasopharyngeal and oral route causing COVID-19. Scientists left no stone unturned to explore a targetable key player in COVID-19 pathogenesis against which therapeutic interventions can be initiated. This article has attempted to review, coordinate and accumulate the most recent observations in support of the hypothesis predicting the altered state of mitochondria concerning mitochondrial redox homeostasis, inflammatory regulations, morphology, bioenergetics and antiviral signalling in SARS-CoV-2 infection. Mitochondria is extremely susceptible to physiological as well as pathological stimuli, including viral infections. Recent studies suggest that SARS-CoV-2 pathogeneses alter mitochondrial integrity, in turn mitochondria modulate cellular response against the infection. SARS-CoV-2 M protein inhibited mitochondrial antiviral signalling (MAVS) protein aggregation in turn hinders innate antiviral response. Viral open reading frames (ORFs) also play an instrumental role in altering mitochondrial regulation of immune response. Notably, ORF-9b and ORF-6 impair MAVS activation. In aged persons, the NLRP3 inflammasome is over-activated due to impaired mitochondrial function, increased mitochondrial reactive oxygen species (mtROS), and/or circulating free mitochondrial DNA, resulting in a hyper-response of classically activated macrophages. This article also tries to understand how mitochondrial fission-fusion dynamics is affected by the virus. This review comprehends the overall mitochondrial attribute in pathogenesis as well as prognosis in patients infected with COVID-19 taking into account pertinent in vitro, pre-clinical and clinical data encompassing subjects with a broad range of severity and morbidity. This endeavour may help in exploring novel non-canonical therapeutic strategies to COVID-19 disease and associated complications.
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Affiliation(s)
- Chandan Bhowal
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Sayak Ghosh
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Debapriya Ghatak
- Indian Association for the Cultivation of Science, Jadavpur, 700032, Kolkata, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India.
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22
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Sacchi A, Giannessi F, Sabatini A, Percario ZA, Affabris E. SARS-CoV-2 Evasion of the Interferon System: Can We Restore Its Effectiveness? Int J Mol Sci 2023; 24:ijms24119353. [PMID: 37298304 DOI: 10.3390/ijms24119353] [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: 03/31/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Type I and III Interferons (IFNs) are the first lines of defense in microbial infections. They critically block early animal virus infection, replication, spread, and tropism to promote the adaptive immune response. Type I IFNs induce a systemic response that impacts nearly every cell in the host, while type III IFNs' susceptibility is restricted to anatomic barriers and selected immune cells. Both IFN types are critical cytokines for the antiviral response against epithelium-tropic viruses being effectors of innate immunity and regulators of the development of the adaptive immune response. Indeed, the innate antiviral immune response is essential to limit virus replication at the early stages of infection, thus reducing viral spread and pathogenesis. However, many animal viruses have evolved strategies to evade the antiviral immune response. The Coronaviridae are viruses with the largest genome among the RNA viruses. Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) pandemic. The virus has evolved numerous strategies to contrast the IFN system immunity. We intend to describe the virus-mediated evasion of the IFN responses by going through the main phases: First, the molecular mechanisms involved; second, the role of the genetic background of IFN production during SARS-CoV-2 infection; and third, the potential novel approaches to contrast viral pathogenesis by restoring endogenous type I and III IFNs production and sensitivity at the sites of infection.
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Affiliation(s)
- Alessandra Sacchi
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Flavia Giannessi
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Andrea Sabatini
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Zulema Antonia Percario
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Elisabetta Affabris
- Laboratory of Molecular Virology and Antimicrobial Immunity, Department of Science, Roma Tre University, 00146 Rome, Italy
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23
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Popovic M. The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants. MICROBIAL RISK ANALYSIS 2023; 23:100249. [PMID: 36777924 PMCID: PMC9898946 DOI: 10.1016/j.mran.2023.100249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 06/01/2023]
Abstract
SARS-CoV-2 resembles the ancient mythical creature Hydra. Just like with the Hydra, when one head is cut, it is followed by appearance of two more heads, suppression of one SARS-CoV-2 variant causes appearance of newer variants. Unlike Hydra that grows identical heads, newer SARS-CoV-2 variants are usually more infective, which can be observed as time evolution of the virus at hand, which occurs through acquisition of mutations during time. The appearance of new variants is followed by appearance of new COVID-19 pandemic waves. With the appearance of new pandemic waves and determining of sequences, in the scientific community and general public the question is always raised of whether the new variant will be more virulent and more pathogenic. The two variants characterized in this paper, BA.5.2 and BF.7, have caused a pandemic wave during the late 2022. This paper gives full chemical and thermodynamic characterization of the BA.5.2 and BF.7 variants of SARS-CoV-2. Having in mind that Gibbs energy of binding and biosynthesis represent the driving forces for the viral life cycle, based on the calculated thermodynamic properties we can conclude that the newer variants are more infective than earlier ones, but that their pathogenicity has not changed.
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Affiliation(s)
- Marko Popovic
- School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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24
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Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has been associated with substantial global morbidity and mortality. Despite a tropism that is largely confined to the airways, COVID-19 is associated with multiorgan dysfunction and long-term cognitive pathologies. A major driver of this biology stems from the combined effects of virus-mediated interference with the host antiviral defences in infected cells and the sensing of pathogen-associated material by bystander cells. Such a dynamic results in delayed induction of type I and III interferons (IFN-I and IFN-III) at the site of infection, but systemic IFN-I and IFN-III priming in distal organs and barrier epithelial surfaces, respectively. In this Review, we examine the relationship between SARS-CoV-2 biology and the cellular response to infection, detailing how antagonism and dysregulation of host innate immune defences contribute to disease severity of COVID-19.
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Affiliation(s)
- Judith M Minkoff
- Department of Microbiology, New York University Langone Health, New York, NY, USA
| | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health, New York, NY, USA.
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25
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Chakravarty D, Schafer JW, Porter LL. Distinguishing features of fold-switching proteins. Protein Sci 2023; 32:e4596. [PMID: 36782353 PMCID: PMC9951197 DOI: 10.1002/pro.4596] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Though many folded proteins assume one stable structure that performs one function, a small-but-increasing number remodel their secondary and tertiary structures and change their functions in response to cellular stimuli. These fold-switching proteins regulate biological processes and are associated with autoimmune dysfunction, severe acute respiratory syndrome coronavirus-2 infection, and more. Despite their biological importance, it is difficult to computationally predict fold switching. With the aim of advancing computational prediction and experimental characterization of fold switchers, this review discusses several features that distinguish fold-switching proteins from their single-fold and intrinsically disordered counterparts. First, the isolated structures of fold switchers are less stable and more heterogeneous than single folders but more stable and less heterogeneous than intrinsically disordered proteins (IDPs). Second, the sequences of single fold, fold switching, and intrinsically disordered proteins can evolve at distinct rates. Third, proteins from these three classes are best predicted using different computational techniques. Finally, late-breaking results suggest that single folders, fold switchers, and IDPs have distinct patterns of residue-residue coevolution. The review closes by discussing high-throughput and medium-throughput experimental approaches that might be used to identify new fold-switching proteins.
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Affiliation(s)
- Devlina Chakravarty
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
| | - Joseph W. Schafer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
| | - Lauren L. Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMarylandUSA
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26
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Schafer JW, Porter LL. Evolutionary selection of proteins with two folds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524637. [PMID: 36789442 PMCID: PMC9928049 DOI: 10.1101/2023.01.18.524637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although most globular proteins fold into a single stable structure 1 , an increasing number have been shown to remodel their secondary and tertiary structures in response to cellular stimuli 2 . State-of-the-art algorithms 3-5 predict that these fold-switching proteins assume only one stable structure 6,7 , missing their functionally critical alternative folds. Why these algorithms predict a single fold is unclear, but all of them infer protein structure from coevolved amino acid pairs. Here, we hypothesize that coevolutionary signatures are being missed. Suspecting that over-represented single-fold sequences may be masking these signatures, we developed an approach to search both highly diverse protein superfamilies-composed of single-fold and fold-switching variants-and protein subfamilies with more fold-switching variants. This approach successfully revealed coevolution of amino acid pairs uniquely corresponding to both conformations of 56/58 fold-switching proteins from distinct families. Then, using a set of coevolved amino acid pairs predicted by our approach, we successfully biased AlphaFold2 5 to predict two experimentally consistent conformations of a candidate protein with unsolved structure. The discovery of widespread dual-fold coevolution indicates that fold-switching sequences have been preserved by natural selection, implying that their functionalities provide evolutionary advantage and paving the way for predictions of diverse protein structures from single sequences.
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Affiliation(s)
- Joseph W. Schafer
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lauren L. Porter
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
- National Heart, Lung, and Blood Institute, Biochemistry and Biophysics Center, National Institutes of Health, Bethesda, MD 20892, USA
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27
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Lanjanian H, Hosseini S, Narimani Z, Meknatkhah S, Riazi GH. A knowledge-based protein-protein interaction inhibition (KPI) pipeline: an insight from drug repositioning for COVID-19 inhibition. J Biomol Struct Dyn 2023; 41:11700-11713. [PMID: 36622367 DOI: 10.1080/07391102.2022.2163425] [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: 10/10/2022] [Accepted: 12/22/2022] [Indexed: 01/10/2023]
Abstract
The inhibition of protein-protein interactions (PPIs) by small molecules is an exciting drug discovery strategy. Here, we aimed to develop a pipeline to identify candidate small molecules to inhibit PPIs. Therefore, KPI, a Knowledge-based Protein-Protein Interaction Inhibition pipeline, was introduced to improve the discovery of PPI inhibitors. Then, phytochemicals from a collection of known Middle Eastern antiviral herbs were screened to identify potential inhibitors of key PPIs involved in COVID-19. Here, the following investigations were sequenced: 1) Finding the binding partner and the interface of the proteins in PPIs, 2) Performing the blind ligand-protein inhibition (LPI) simulations, 3) Performing the local LPI simulations, 4) Simulating the interactions of the proteins and their binding partner in the presence and absence of the ligands, and 5) Performing the molecular dynamics simulations. The pharmacophore groups involved in the LPI were also characterized. Aloin, Genistein, Neoglucobrassicin, and Rutin are our new pipeline candidates for inhibiting PPIs involved in COVID-19. We also propose KPI for drug repositioning studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hossein Lanjanian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shadi Hosseini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Zahra Narimani
- Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Sogol Meknatkhah
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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28
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Shan SO. Role of Hsp70 in Post-Translational Protein Targeting: Tail-Anchored Membrane Proteins and Beyond. Int J Mol Sci 2023; 24:1170. [PMID: 36674686 PMCID: PMC9866221 DOI: 10.3390/ijms24021170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The Hsp70 family of molecular chaperones acts as a central 'hub' in the cell that interacts with numerous newly synthesized proteins to assist in their biogenesis. Apart from its central and well-established role in facilitating protein folding, Hsp70s also act as key decision points in the cellular chaperone network that direct client proteins to distinct biogenesis and quality control pathways. In this paper, we review accumulating data that illustrate a new branch in the Hsp70 network: the post-translational targeting of nascent membrane and organellar proteins to diverse cellular organelles. Work in multiple pathways suggests that Hsp70, via its ability to interact with components of protein targeting and translocation machineries, can initiate elaborate substrate relays in a sophisticated cascade of chaperones, cochaperones, and receptor proteins, and thus provide a mechanism to safeguard and deliver nascent membrane proteins to the correct cellular membrane. We discuss the mechanistic principles gleaned from better-studied Hsp70-dependent targeting pathways and outline the observations and outstanding questions in less well-studied systems.
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Affiliation(s)
- Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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29
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Jin X, Sun X, Chai Y, Bai Y, Li Y, Hao T, Qi J, Song H, Wong CCL, Gao GF. Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism. SCIENCE CHINA. LIFE SCIENCES 2023; 66:152-164. [PMID: 36184694 PMCID: PMC9527070 DOI: 10.1007/s11427-022-2168-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/20/2022] [Indexed: 11/06/2022]
Abstract
The constant emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants indicates the evolution and adaptation of the virus. Enhanced innate immune evasion through increased expression of viral antagonist proteins, including ORF9b, contributes to the improved transmission of the Alpha variant; hence, more attention should be paid to these viral proteins. ORF9b is an accessory protein that suppresses innate immunity via a monomer conformation by binding to Tom70. Here, we solved the dimeric structure of SARS-CoV-2 ORF9b with a long hydrophobic tunnel containing a lipid molecule that is crucial for the dimeric conformation and determined the specific lipid ligands as monoglycerides by conducting a liquid chromatography with tandem mass spectrometry analysis, suggesting an important role in the viral life cycle. Notably, a long intertwined loop accessible for host factor binding was observed in the structure. Eight phosphorylated residues in ORF9b were identified, and residues S50 and S53 were found to contribute to the stabilization of dimeric ORF9b. Additionally, we proposed a model of multifunctional ORF9b with a distinct conformation, suggesting that ORF9b is a fold-switching protein, while both lipids and phosphorylation contribute to the switching. Specifically, the ORF9b monomer interacts with Tom70 to suppress the innate immune response, whereas the ORF9b dimer binds to the membrane involving mature virion assembly. Our results provide a better understanding of the multiple functions of ORF9b.
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Affiliation(s)
- Xiyue Jin
- grid.59053.3a0000000121679639School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027 China ,grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xue Sun
- grid.11135.370000 0001 2256 9319Peking University First Hospital, Peking University, Beijing, 100034 China ,grid.11135.370000 0001 2256 9319Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, 100191 China
| | - Yan Chai
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yu Bai
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Li
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tianjiao Hao
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jianxun Qi
- grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hao Song
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Catherine C. L. Wong
- grid.11135.370000 0001 2256 9319Peking University First Hospital, Peking University, Beijing, 100034 China ,grid.11135.370000 0001 2256 9319Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, 100191 China ,grid.11135.370000 0001 2256 9319Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China ,grid.11135.370000 0001 2256 9319School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, 100191 China
| | - George F. Gao
- grid.59053.3a0000000121679639School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027 China ,grid.9227.e0000000119573309CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
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30
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Wang BG, Wang ZC, Wu Y, Xiong Y, Zhang J, Ma Z. A mathematical model reveals the influence of NPIs and vaccination on SARS-CoV-2 Omicron Variant. NONLINEAR DYNAMICS 2023; 111:3937-3952. [PMID: 36339320 PMCID: PMC9628561 DOI: 10.1007/s11071-022-07985-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/19/2022] [Indexed: 05/10/2023]
Abstract
An SVEIR SARS-CoV-2 Omicron variant model is proposed to provide some insights to coordinate non-pharmaceutical interventions (NPIs) and vaccination. Mathematically, we define the basic reproduction number R 0 and the effective reproduction number R e to measure the infection potential of Omicron variant and formulate an optimal disease control strategy. Our inversion results imply that the sick period of Omicron variant in the United States is longer than that of Delta variant in India. The decrease in the infectious period of the infection with infectiousness implies that the risk of hospitalization is reduced; but the increasing period of the infection with non-infectiousness signifies that Omicron variant lengthens the period of nucleic acid test being negative. Optimistically, Omicron's death rate is only a quarter of Delta's. Moreover, we forecast that the cumulative cases will exceed 100 million in the United States on February 28, 2022, and the daily confirmed cases will reach a peak on February 2, 2022. The results of parameters sensitivity analysis imply that NPIs are helpful to reduce the number of confirmed cases. In particular, NPIs are indispensable even if all the people were vaccinated when the efficiency of vaccine is relatively low. By simulating the relationships of the effective reproduction number R e , the vaccination rate and the efficacy of vaccine, we find that it is impossible to achieve the herd immunity without NPIs while the efficiency of vaccine is lower than 88.7 % . Therefore, the herd immunity area is defined by the evolution of relationships between the vaccination rate and the efficacy of vaccine. Finally, we present that the disease-induced mortality rate demonstrates the periodic oscillation and an almost periodic function is deduced to match the curve. A discussion completes the paper.
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Affiliation(s)
- Bin-Guo Wang
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Zhi-Cheng Wang
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Yan Wu
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Yongping Xiong
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Jiangqian Zhang
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
| | - Zhuihui Ma
- School of Mathematics and Statistics, Lanzhou University, Lanzhou, Gansu 730000 People’s Republic of China
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31
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Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022). Vaccines (Basel) 2022; 10:vaccines10122112. [PMID: 36560522 PMCID: PMC9784531 DOI: 10.3390/vaccines10122112] [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: 11/11/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Biothermodynamics of viruses is among the youngest but most rapidly developing scientific disciplines. During the COVID-19 pandemic, it closely followed the results published by molecular biologists. Empirical formulas were published for 50 viruses and thermodynamic properties for multiple viruses and virus variants, including all variants of concern of SARS-CoV-2, SARS-CoV, MERS-CoV, Ebola virus, Vaccinia and Monkeypox virus. A review of the development of biothermodynamics of viruses during the last several decades and intense development during the last 3 years is described in this paper.
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32
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Wu Y, Zhang M, Yuan C, Ma Z, Li W, Zhang Y, Su L, Xu J, Liu W. Progress of cGAS-STING signaling in response to SARS-CoV-2 infection. Front Immunol 2022; 13:1010911. [PMID: 36569852 PMCID: PMC9767964 DOI: 10.3389/fimmu.2022.1010911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an epidemic respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can cause infections in millions of individuals, who can develop lung injury, organ failure, and subsequent death. As the first line of host defense, the innate immune system is involved in initiating the immune response to SARS-CoV-2 infection and the hyperinflammatory phenotype of COVID-19. However, the interplay between SARS-CoV-2 and host innate immunity is not yet well understood. It had become known that the cGAS-STING pathway is involved in the detection of cytosolic DNA, which elicits an innate immune response involving a robust type I interferon response against viral and bacterial infections. Nevertheless, several lines of evidence indicate that SARS-CoV-2, a single-stranded positive-sense RNA virus, triggered the cGAS-STING signaling pathway. Therefore, understanding the molecular and cellular details of cGAS-STING signaling upon SARS-CoV-2 infection is of considerable biomedical importance. In this review, we discuss the role of cGAS-STING signaling in SARS-CoV-2 infection and summarize the potential therapeutics of STING agonists as virus vaccine adjuvants.
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Affiliation(s)
- Yaru Wu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Min Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Cui Yuan
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhenling Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenqing Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yanyan Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Lijuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jun Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China,*Correspondence: Wei Liu,
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33
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Focus on Marine Animal Safety and Marine Bioresources in Response to the SARS-CoV-2 Crisis. Int J Mol Sci 2022; 23:ijms232315136. [PMID: 36499463 PMCID: PMC9737530 DOI: 10.3390/ijms232315136] [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] [Received: 10/18/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2 as a zoonotic virus has significantly affected daily life and social behavior since its outbreak in late 2019. The concerns over its transmission through different media directly or indirectly have evoked great attention about the survival of SARS-CoV-2 virions in the environment and its potential infection of other animals. To evaluate the risk of infection by SARS-CoV-2 and to counteract the COVID-19 disease, extensive studies have been performed to understand SARS-CoV-2 biogenesis and its pathogenesis. This review mainly focuses on the molecular architecture of SARS-CoV-2, its potential for infecting marine animals, and the prospect of drug discovery using marine natural products to combat SARS-CoV-2. The main purposes of this review are to piece together progress in SARS-CoV-2 functional genomic studies and antiviral drug development, and to raise our awareness of marine animal safety on exposure to SARS-CoV-2.
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34
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Zandi M, Shafaati M, Kalantar-Neyestanaki D, Pourghadamyari H, Fani M, Soltani S, Kaleji H, Abbasi S. The role of SARS-CoV-2 accessory proteins in immune evasion. Biomed Pharmacother 2022; 156:113889. [PMID: 36265309 PMCID: PMC9574935 DOI: 10.1016/j.biopha.2022.113889] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 01/11/2023] Open
Abstract
Many questions on the SARS-CoV-2 pathogenesis remain to answer. The SARS-CoV-2 genome encodes some accessory proteins that are essential for infection. Notably, accessory proteins of SARS-CoV-2 play significant roles in affecting immune escape and viral pathogenesis. Therefore SARS-CoV-2 accessory proteins could be considered putative drug targets. IFN-I and IFN-III responses are the primary mechanisms of innate antiviral immunity in infection clearance. Previous research has shown that SARS-CoV-2 suppresses IFN-β by infecting host cells via ORF3a, ORF3b, ORF6, ORF7a, ORF7b, ORF8, and ORF9b. Furthermore, ORF3a, ORF7a, and ORF7b have a role in blocking IFNα signaling, and ORF8 represses IFNβ signaling. The ORF3a, ORF7a, and ORF7b disrupt the STAT1/2 phosphorylation. ORF3a, ORF6, ORF7a, and ORF7b could prevent the ISRE promoter activity. The main SARS-CoV-2 accessory proteins involved in immune evasion are discussed here for comprehensive learning on viral entry, replication, and transmission in vaccines and antiviral development.
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Affiliation(s)
- Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Shafaati
- Department of Microbiology, Faculty Science, Jahrom Branch, Islamic Azad University, Jahrom, Iran,Occupational Sleep Research Center, Baharloo Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Kalantar-Neyestanaki
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran,Department of Medical Microbiology (Bacteriology & Virology), Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Pourghadamyari
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran,Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mona Fani
- Department of Pathobiology & Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Kaleji
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Abbasi
- Department of Microbiology, School of Medicine, Abadan University of Medical Sciences, Abadan, Iran,Corresponding author
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35
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Atlas of interactions between SARS-CoV-2 macromolecules and host proteins. CELL INSIGHT 2022; 2:100068. [PMID: 37192911 PMCID: PMC9670597 DOI: 10.1016/j.cellin.2022.100068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Abstract
The proteins and RNAs of viruses extensively interact with host proteins after infection. We collected and reanalyzed all available datasets of protein-protein and RNA-protein interactions related to SARS-CoV-2. We investigated the reproducibility of those interactions and made strict filters to identify highly confident interactions. We systematically analyzed the interaction network and identified preferred subcellular localizations of viral proteins, some of which such as ORF8 in ER and ORF7A/B in ER membrane were validated using dual fluorescence imaging. Moreover, we showed that viral proteins frequently interact with host machinery related to protein processing in ER and vesicle-associated processes. Integrating the protein- and RNA-interactomes, we found that SARS-CoV-2 RNA and its N protein closely interacted with stress granules including 40 core factors, of which we specifically validated G3BP1, IGF2BP1, and MOV10 using RIP and Co-IP assays. Combining CRISPR screening results, we further identified 86 antiviral and 62 proviral factors and associated drugs. Using network diffusion, we found additional 44 interacting proteins including two proviral factors previously validated. Furthermore, we showed that this atlas could be applied to identify the complications associated with COVID-19. All data are available in the AIMaP database (https://mvip.whu.edu.cn/aimap/) for users to easily explore the interaction map.
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36
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Lee SJ, Kim YJ, Ahn DG. Distinct Molecular Mechanisms Characterizing Pathogenesis of SARS-CoV-2. J Microbiol Biotechnol 2022; 32:1073-1085. [PMID: 36039385 PMCID: PMC9628960 DOI: 10.4014/jmb.2206.06064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has continued for over 2 years, following the outbreak of coronavirus-19 (COVID-19) in 2019. It has resulted in enormous casualties and severe economic crises. The rapid development of vaccines and therapeutics against SARS-CoV-2 has helped slow the spread. In the meantime, various mutations in the SARS-CoV-2 have emerged to evade current vaccines and therapeutics. A better understanding of SARS-CoV-2 pathogenesis is a prerequisite for developing efficient, advanced vaccines and therapeutics. Since the outbreak of COVID-19, a tremendous amount of research has been conducted to unveil SARSCoV-2 pathogenesis, from clinical observations to biochemical analysis at the molecular level upon viral infection. In this review, we discuss the molecular mechanisms of SARS-CoV-2 propagation and pathogenesis, with an update on recent advances.
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Affiliation(s)
- Su Jin Lee
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Yu-Jin Kim
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Dae-Gyun Ahn
- Department of Convergent Research of Emerging Virus Infection, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
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37
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Iacobucci I, Monaco V, Canè L, Bibbò F, Cioffi V, Cozzolino F, Guarino A, Zollo M, Monti M. Spike S1 domain interactome in non-pulmonary systems: A role beyond the receptor recognition. Front Mol Biosci 2022; 9:975570. [PMID: 36225252 PMCID: PMC9550266 DOI: 10.3389/fmolb.2022.975570] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/29/2022] [Indexed: 12/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which, since 2019 in China, has rapidly become a worldwide pandemic. The aggressiveness and global spread were enhanced by the many SARS-CoV-2 variants that have been isolated up to now. These mutations affect mostly the viral glycoprotein Spike (S), the capsid protein mainly involved in the early stages of viral entry processes, through the recognition of specific receptors on the host cell surface. In particular, the subunit S1 of the Spike glycoprotein contains the Receptor Binding Domain (RBD) and it is responsible for the interaction with the angiotensin-converting enzyme 2 (ACE2). Although ACE2 is the primary Spike host receptor currently studied, it has been demonstrated that SARS-CoV-2 is also able to infect cells expressing low levels of ACE2, indicating that the virus may have alternative receptors on the host cells. The identification of the alternative receptors can better elucidate the pathogenicity and the tropism of SARS-CoV-2. Therefore, we investigated the Spike S1 interactomes, starting from host membrane proteins of non-pulmonary cell lines, such as human kidney (HK-2), normal colon (NCM460D), and colorectal adenocarcinoma (Caco-2). We employed an affinity purification-mass spectrometry (AP-MS) to pull down, from the membrane protein extracts of all cell lines, the protein partners of the recombinant form of the Spike S1 domain. The purified interactors were identified by a shotgun proteomics approach. The lists of S1 potential interacting proteins were then clusterized according to cellular localization, biological processes, and pathways, highlighting new possible S1 intracellular functions, crucial not only for the entrance mechanisms but also for viral replication and propagation processes.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Vittoria Monaco
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Luisa Canè
- CEINGE Advanced Biotechnologies, Naples, Italy
- Department of Translational Medical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Francesca Bibbò
- CEINGE Advanced Biotechnologies, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies (DMMBM), University of Naples “Federico II”, Naples, Italy
| | - Valentina Cioffi
- Department of Translational Medical Science, Section of Pediatrics, University of Naples “Federico II”, Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Alfredo Guarino
- Department of Translational Medical Science, Section of Pediatrics, University of Naples “Federico II”, Naples, Italy
| | - Massimo Zollo
- CEINGE Advanced Biotechnologies, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies (DMMBM), University of Naples “Federico II”, Naples, Italy
| | - Maria Monti
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
- *Correspondence: Maria Monti,
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38
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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39
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Ayinde KS, Pinheiro GM, Ramos CH. Binding of SARS-CoV-2 protein ORF9b to mitochondrial translocase TOM70 prevents its interaction with chaperone HSP90. Biochimie 2022; 200:99-106. [PMID: 35643212 PMCID: PMC9132681 DOI: 10.1016/j.biochi.2022.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 01/17/2023]
Abstract
The emergence of the COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a great threat to global health. ORF9b, an important accessory protein of SARS-CoV-2, plays a critical role in the viral host interaction, targeting TOM70, a member of the mitochondrial translocase of the outer membrane complex. The assembly between ORF9b and TOM70 is implicated in disrupting mitochondrial antiviral signaling, leading to immune evasion. We describe the expression, purification, and characterization of ORF9b alone or coexpressed with the cytosolic domain of human TOM70 in E. coli. ORF9b has 97 residues and was purified as a homodimer with an molecular mass of 22 kDa as determined by SEC-MALS. Circular dichroism experiments showed that Orf9b alone exhibits a random conformation. The ORF9b-TOM70 complex characterized by CD and differential scanning calorimetry showed that the complex is folded and more thermally stable than free TOM70, indicating strong binding. Importantly, protein-protein interaction assays demonstrated that full-length human Hsp90 is capable of binding to free TOM70 but not to the ORF9b-TOM70 complex. To narrow down the nature of this inhibition, the isolated C-terminal domain of Hsp90 was also tested. These results were used to build a model of the mechanism of inhibition, in which ORF9b efficiently targets two sites of interaction between TOM70 and Hsp90. The findings showed that ORF9b complexed with TOM70 prevents the interaction with Hsp90, and this is one major explanation for SARS-CoV-2 evasion of host innate immunity via the inhibition of the interferon activation pathway.
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Affiliation(s)
- Kehinde S. Ayinde
- Institute of Chemistry, University of Campinas UNICAMP, 13083-970, Campinas, SP, Brazil,Institute of Biology, University of Campinas (UNICAMP), SP, Brazil
| | - Glaucia M.S. Pinheiro
- Institute of Chemistry, University of Campinas UNICAMP, 13083-970, Campinas, SP, Brazil
| | - Carlos H.I. Ramos
- Institute of Chemistry, University of Campinas UNICAMP, 13083-970, Campinas, SP, Brazil,Corresponding author
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40
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Alsafar H, Albreiki M, Mousa M, Azman SK, Vurivi H, Waasia F, Ruta D, Alhosani F, Almazrouei S, Abuyadek R, Selvaraj F, Chaves-Coira I, Zvereff V, Abdel-Malek MAY, Alkaabi N, Uddin M, Al Awadhi T, Al Marzouqi N, Al Attar F, Al Shamsi S, Al Shehhi F, Alteneiji H, Mohamed K, Al Muhairi N, AlRand H, Fikri A, Henschel A. Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates. Sci Rep 2022; 12:14669. [PMID: 36038563 PMCID: PMC9421632 DOI: 10.1038/s41598-022-16967-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Since the declaration of SARS-CoV-2 outbreak as a pandemic, the United Arab Emirates (UAE) public health authorities have adopted strict measures to reduce transmission as early as March 2020. As a result of these measures, flight suspension, nationwide RT-PCR and surveillance of viral sequences were extensively implemented. This study aims to characterize the epidemiology, transmission pattern, and emergence of variants of concerns (VOCs) and variants of interests (VOIs) of SARS-CoV-2 in the UAE, followed by the investigation of mutations associated with hospitalized cases. A total of 1274 samples were collected and sequenced from all seven emirates between the period of 25 April 2020 to 15 February 2021. Phylogenetic analysis demonstrated multiple introductions of SARS-CoV-2 into the UAE in the early pandemic, followed by a local spread of root clades (A, B, B.1 and B.1.1). As the international flight resumed, the frequencies of VOCs surged indicating the January peak of positive cases. We observed that the hospitalized cases were significantly associated with the presence of B.1.1.7 (p < 0.001), B.1.351 (p < 0.001) and A.23.1 (p = 0.009). Deceased cases are more likely to occur in the presence of B.1.351 (p < 0.001) and A.23.1 (p = 0.022). Logistic and ridge regression showed that 51 mutations are significantly associated with hospitalized cases with the highest proportion originated from S and ORF1a genes (31% and 29% respectively). Our study provides an epidemiological insight of the emergence of VOCs and VOIs following the borders reopening and worldwide travels. It provides reassurance that hospitalization is markedly more associated with the presence of VOCs. This study can contribute to understand the global transmission of SARS-CoV-2 variants.
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Affiliation(s)
- Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Mohammed Albreiki
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates.,Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, UK
| | - Syafiq Kamarul Azman
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hema Vurivi
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Fathimathuz Waasia
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Dymitr Ruta
- Emirates ICT Innovation Center (EBTIC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Farida Alhosani
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates
| | - Shereena Almazrouei
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates
| | - Rowan Abuyadek
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates.,High Institute of Public Health, Alexandria University, Alexandria, Egypt
| | - Francis Selvaraj
- Department Laboratory Medicine Services, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Irene Chaves-Coira
- Molecular and Genetics Department, UniLabs, Abu Dhabi, United Arab Emirates
| | - Val Zvereff
- Department of Molecular Diagnostics, National Reference Laboratory, Abu Dhabi, United Arab Emirates.,Department of Pathology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mohamed A Y Abdel-Malek
- Molecular Biology Laboratory, Mediclinic Alnoor Hospital, Abu Dhabi, United Arab Emirates.,Clinical Pathology Department, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Nawal Alkaabi
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Maimunah Uddin
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Tayba Al Awadhi
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | - Fatma Al Attar
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | | | - Hala Alteneiji
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | - Noor Al Muhairi
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Hussain AlRand
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Asma Fikri
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Andreas Henschel
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates. .,Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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41
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Gao X, Tian H, Zhu K, Li Q, Hao W, Wang L, Qin B, Deng H, Cui S. Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport. Nat Commun 2022; 13:4782. [PMID: 35970938 PMCID: PMC9376891 DOI: 10.1038/s41467-022-32489-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022] Open
Abstract
The emergence of heavily mutated SARS-CoV-2 variants of concern (VOCs) place the international community on high alert. In addition to numerous mutations that map in the spike protein of VOCs, expression of the viral accessory proteins ORF6 and ORF9b also elevate; both are potent interferon antagonists. Here, we present the crystal structures of Rae1-Nup98 in complex with the C-terminal tails (CTT) of SARS-CoV-2 and SARS-CoV ORF6 to 2.85 Å and 2.39 Å resolution, respectively. An invariant methionine (M) 58 residue of ORF6 CTT extends its side chain into a hydrophobic cavity in the Rae1 mRNA binding groove, resembling a bolt-fitting-hole; acidic residues flanking M58 form salt-bridges with Rae1. Our mutagenesis studies identify key residues of ORF6 important for its interaction with Rae1-Nup98 in vitro and in cells, of which M58 is irreplaceable. Furthermore, we show that ORF6-mediated blockade of mRNA and STAT1 nucleocytoplasmic transport correlate with the binding affinity between ORF6 and Rae1-Nup98. Finally, binding of ORF6 to Rae1-Nup98 is linked to ORF6-induced interferon antagonism. Taken together, this study reveals the molecular basis for the antagonistic function of Sarbecovirus ORF6, and implies a strategy of using ORF6 CTT-derived peptides for immunosuppressive drug development. Sarbecovirus ORF6 binds to the Rae1-Nup98 complex, a component of the cytoplasmic face of the nuclear pore complex, and has been shown to suppress interferon responses. Here, the authors provide structures of Rae1-Nup98 in complex with the C-terminal tails of SARS-CoV-2 and SARS-CoV ORF6 and provide insights into ORF6-mediated blockade of mRNA and STAT1 nucleocytoplasmic transport.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Huabin Tian
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Qing Li
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Hao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Hongyu Deng
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China. .,Sanming Project of Medicine in Shenzhen, National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China.
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42
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Chen H, Hu X, Hu Y, Zhou J, Chen M. CoVM2: Molecular Biological Data Integration of SARS-CoV-2 Proteins in a Macro-to-Micro Method. Biomolecules 2022; 12:biom12081067. [PMID: 36008961 PMCID: PMC9405999 DOI: 10.3390/biom12081067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023] Open
Abstract
The COVID-19 pandemic has been a major public health event since 2020. Multiple variant strains of SARS-CoV-2, the causative agent of COVID-19, were detected based on the mutation sites in their sequences. These sequence mutations may lead to changes in the protein structures and affect the binding states of SARS-CoV-2 and human proteins. Experimental research on SARS-CoV-2 has accumulated a large amount of structural data and protein-protein interactions (PPIs), but the studies on the SARS-CoV-2–human PPI networks lack integration of physical associations with possible protein docking information. In addition, the docking structures of variant viral proteins with human receptor proteins are still insufficient. This study constructed SARS-CoV-2–human protein–protein interaction network with data integration methods. Crystal structures were collected to map the interaction pairs. The pairs of direct interactions and physical associations were selected and analyzed for variant docking calculations. The study examined the structures of spike (S) glycoprotein of variants Delta B.1.617.2, Omicron BA.1, and Omicron BA.2. The calculated docking structures of S proteins and potential human receptors were obtained. The study integrated binary protein interactions with 3D docking structures to fulfill an extended view of SARS-CoV-2 proteins from a macro- to micro-scale.
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Affiliation(s)
- Hongjun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.C.); (X.H.); (Y.H.)
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.C.); (X.H.); (Y.H.)
| | - Yanshi Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.C.); (X.H.); (Y.H.)
| | - Jiawen Zhou
- Chu Kochen Honors College, Zhejiang University, Hangzhou 310058, China;
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.C.); (X.H.); (Y.H.)
- Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-(0)571-8820-6612
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43
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Hossain A, Akter S, Rashid AA, Khair S, Alam ASMRU. Unique mutations in SARS-CoV-2 omicron subvariants' non-spike proteins: Potential impact on viral pathogenesis and host immune evasion. Microb Pathog 2022; 170:105699. [PMID: 35944840 PMCID: PMC9356572 DOI: 10.1016/j.micpath.2022.105699] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/20/2022]
Affiliation(s)
- Anamica Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Shammi Akter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Alfi Anjum Rashid
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sabik Khair
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
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44
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Mekawy AS, Alaswad Z, Ibrahim AA, Mohamed AA, AlOkda A, Elserafy M. The consequences of viral infection on host DNA damage response: a focus on SARS-CoVs. J Genet Eng Biotechnol 2022; 20:104. [PMID: 35829826 PMCID: PMC9277982 DOI: 10.1186/s43141-022-00388-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022]
Abstract
DNA damage and genome instability in host cells are introduced by many viruses during their life cycles. Severe acute respiratory syndrome coronaviruses (SARS-CoVs) manipulation of DNA damage response (DDR) is an important area of research that is still understudied. Elucidation of the direct and indirect interactions between SARS-CoVs and DDR not only provides important insights into how the viruses exploit DDR pathways in host cells but also contributes to our understanding of their pathogenicity. Here, we present the known interactions of both SARS-CoV and SARS-CoV-2 with DDR pathways of the host cells, to further understand the consequences of infection on genome integrity. Since this area of research is in its early stages, we try to connect the unlinked dots to speculate and propose different consequences on DDR mechanisms. This review provides new research scopes that can be further investigated in vitro and in vivo, opening new avenues for the development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Asmaa S Mekawy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Zina Alaswad
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Aya A Ibrahim
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Ahmed A Mohamed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Abdelrahman AlOkda
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada.,Metabolic Disorders and Complications Program and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt. .,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt.
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45
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Eskandarzade N, Ghorbani A, Samarfard S, Diaz J, Guzzi PH, Fariborzi N, Tahmasebi A, Izadpanah K. Network for network concept offers new insights into host- SARS-CoV-2 protein interactions and potential novel targets for developing antiviral drugs. Comput Biol Med 2022; 146:105575. [PMID: 35533462 PMCID: PMC9055686 DOI: 10.1016/j.compbiomed.2022.105575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, the causal agent of COVID-19, is primarily a pulmonary virus that can directly or indirectly infect several organs. Despite many studies carried out during the current COVID-19 pandemic, some pathological features of SARS-CoV-2 have remained unclear. It has been recently attempted to address the current knowledge gaps on the viral pathogenicity and pathological mechanisms via cellular-level tropism of SARS-CoV-2 using human proteomics, visualization of virus-host protein-protein interactions (PPIs), and enrichment analysis of experimental results. The synergistic use of models and methods that rely on graph theory has enabled the visualization and analysis of the molecular context of virus/host PPIs. We review current knowledge on the SARS-COV-2/host interactome cascade involved in the viral pathogenicity through the graph theory concept and highlight the hub proteins in the intra-viral network that create a subnet with a small number of host central proteins, leading to cell disintegration and infectivity. Then we discuss the putative principle of the "gene-for-gene and "network for network" concepts as platforms for future directions toward designing efficient anti-viral therapies.
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Affiliation(s)
- Neda Eskandarzade
- Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran,Corresponding author
| | - Samira Samarfard
- Berrimah Veterinary Laboratory, Department of Primary Industry and Resources, Berrimah, NT, 0828, Australia
| | - Jose Diaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Pietro H. Guzzi
- Department of Medical and Surgical Sciences, Laboratory of Bioinformatics Unit, Italy
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Tahmasebi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
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46
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Abstract
Ubiquitin signaling is essential for immunity to restrict pathogen proliferation. Due to its enormous impact on human health and the global economy, intensive efforts have been invested in studying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its interactions with hosts. However, the role of the ubiquitin network in pathogenicity has not yet been explored. Here, we found that ORF9b of SARS-CoV-2 is ubiquitinated on Lys-4 and Lys-40 by unknown E3 ubiquitin ligases and is degraded by the ubiquitin proteasomal system. Importantly, we identified USP29 as a host factor that prevents ORF9b ubiquitination and subsequent degradation. USP29 interacts with the carboxyl end of ORF9b and removes ubiquitin chains from the protein, thereby inhibiting type I interferon (IFN) induction and NF-κB activation. We also found that ORF9b stabilization by USP29 enhanced the virulence of VSV-eGFP and transcription and replication-competent SARS-CoV-2 virus-like-particles (trVLP). Moreover, we observed that the mRNA level of USP29 in SARS-CoV-2 patients was higher than that in healthy people. Our findings provide important evidence indicating that targeting USP29 may effectively combat SARS-CoV-2 infection.
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47
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Moga E, Lynton-Pons E, Domingo P. The Robustness of Cellular Immunity Determines the Fate of SARS-CoV-2 Infection. Front Immunol 2022; 13:904686. [PMID: 35833134 PMCID: PMC9271749 DOI: 10.3389/fimmu.2022.904686] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/27/2022] [Indexed: 12/11/2022] Open
Abstract
Two years after the appearance of the SARS-CoV-2 virus, the causal agent of the current global pandemic, it is time to analyze the evolution of the immune protection that infection and vaccination provide. Cellular immunity plays an important role in limiting disease severity and the resolution of infection. The early appearance, breadth and magnitude of SARS-CoV-2 specific T cell response has been correlated with disease severity and it has been thought that T cell responses may be sufficient to clear infection with minimal disease in COVID-19 patients with X-linked or autosomal recessive agammaglobulinemia. However, our knowledge of the phenotypic and functional diversity of CD8+ cytotoxic lymphocytes, CD4+ T helper cells, mucosal-associated invariant T (MAIT) cells and CD4+ T follicular helper (Tfh), which play a critical role in infection control as well as long-term protection, is still evolving. It has been described how CD8+ cytotoxic lymphocytes interrupt viral replication by secreting antiviral cytokines (IFN-γ and TNF-α) and directly killing infected cells, negatively correlating with stages of disease progression. In addition, CD4+ T helper cells have been reported to be key pieces, leading, coordinating and ultimately regulating antiviral immunity. For instance, in some more severe COVID-19 cases a dysregulated CD4+ T cell signature may contribute to the greater production of pro-inflammatory cytokines responsible for pathogenic inflammation. Here we discuss how cellular immunity is the axis around which the rest of the immune system components revolve, since it orchestrates and leads antiviral response by regulating the inflammatory cascade and, as a consequence, the innate immune system, as well as promoting a correct humoral response through CD4+ Tfh cells. This review also analyses the critical role of cellular immunity in modulating the development of high-affinity neutralizing antibodies and germinal center B cell differentiation in memory and long-lived antibody secreting cells. Finally, since there is currently a high percentage of vaccinated population and, in some cases, vaccine booster doses are even being administered in certain countries, we have also summarized newer approaches to long-lasting protective immunity and the cross-protection of cellular immune response against SARS-CoV-2.
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Affiliation(s)
- Esther Moga
- Department of Immunology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Spain,*Correspondence: Esther Moga,
| | - Elionor Lynton-Pons
- Department of Immunology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Domingo
- Unidad de enfermedades infecciosas, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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48
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Wang Y, Wu M, Li Y, Yuen HH, He ML. The effects of SARS-CoV-2 infection on modulating innate immunity and strategies of combating inflammatory response for COVID-19 therapy. J Biomed Sci 2022; 29:27. [PMID: 35505345 PMCID: PMC9063252 DOI: 10.1186/s12929-022-00811-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/27/2022] [Indexed: 12/15/2022] Open
Abstract
The global pandemic of COVID-19 has caused huge causality and unquantifiable loss of social wealth. The innate immune response is the first line of defense against SARS-CoV-2 infection. However, strong inflammatory response associated with dysregulation of innate immunity causes severe acute respiratory syndrome (SARS) and death. In this review, we update the current knowledge on how SARS-CoV-2 modulates the host innate immune response for its evasion from host defense and its corresponding pathogenesis caused by cytokine storm. We emphasize Type I interferon response and the strategies of evading innate immune defense used by SARS-CoV-2. We also extensively discuss the cells and their function involved in the innate immune response and inflammatory response, as well as the promises and challenges of drugs targeting excessive inflammation for antiviral treatment. This review would help us to figure out the current challenge questions of SARS-CoV-2 infection on innate immunity and directions for future studies.
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Affiliation(s)
- Yiran Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Yichen Li
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Ho Him Yuen
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China. .,CityU Shenzhen Research Institute, Nanshan, Shenzhen, China.
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49
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Zhang R, Chen J, Wang D, Fu ZQ. Hijacking of host mitochondria by Toxoplasma gondii and SARS-CoV-2. Trends Parasitol 2022; 38:269-271. [PMID: 35165074 PMCID: PMC8823957 DOI: 10.1016/j.pt.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 11/20/2022]
Abstract
Mitochondria regulate energy production, cell cycle, and immune signaling. Li et al. recently reported that Toxoplasma gondii induces the shedding of mitochondrial outer membrane to promote its growth. Intriguingly, the hijacking of host mitochondria has been shown to play an essential role in the pathogenesis of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Ruize Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Longzi Lake Campus, Zhengzhou 450046, China.
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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50
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Beyer DK, Forero A. Mechanisms of Antiviral Immune Evasion of SARS-CoV-2. J Mol Biol 2022; 434:167265. [PMID: 34562466 PMCID: PMC8457632 DOI: 10.1016/j.jmb.2021.167265] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022]
Abstract
Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is characterized by a delayed interferon (IFN) response and high levels of proinflammatory cytokine expression. Type I and III IFNs serve as a first line of defense during acute viral infections and are readily antagonized by viruses to establish productive infection. A rapidly growing body of work has interrogated the mechanisms by which SARS-CoV-2 antagonizes both IFN induction and IFN signaling to establish productive infection. Here, we summarize these findings and discuss the molecular interactions that prevent viral RNA recognition, inhibit the induction of IFN gene expression, and block the response to IFN treatment. We also describe the mechanisms by which SARS-CoV-2 viral proteins promote host shutoff. A detailed understanding of the host-pathogen interactions that unbalance the IFN response is critical for the design and deployment of host-targeted therapeutics to manage COVID-19.
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Affiliation(s)
- Daniel K. Beyer
- Molecular Genetics, College of Arts and Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210, USA,Corresponding author
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