1
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Dutta M, Su Y, Plescia CB, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. J Biol Chem 2024:107456. [PMID: 38866325 DOI: 10.1016/j.jbc.2024.107456] [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: 09/27/2023] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Caroline B Plescia
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA.
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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2
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Wei X, Zhou Y, Shen X, Fan L, Liu D, Gao X, Zhou J, Wu Y, Li Y, Feng W, Zhang Z. Ciclopirox inhibits SARS-CoV-2 replication by promoting the degradation of the nucleocapsid protein. Acta Pharm Sin B 2024; 14:2505-2519. [PMID: 38828154 PMCID: PMC11143514 DOI: 10.1016/j.apsb.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/04/2024] [Accepted: 02/28/2024] [Indexed: 06/05/2024] Open
Abstract
The nucleocapsid protein (NP) plays a crucial role in SARS-CoV-2 replication and is the most abundant structural protein with a long half-life. Despite its vital role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assembly and host inflammatory response, it remains an unexplored target for drug development. In this study, we identified a small-molecule compound (ciclopirox) that promotes NP degradation using an FDA-approved library and a drug-screening cell model. Ciclopirox significantly inhibited SARS-CoV-2 replication both in vitro and in vivo by inducing NP degradation. Ciclopirox induced abnormal NP aggregation through indirect interaction, leading to the formation of condensates with higher viscosity and lower mobility. These condensates were subsequently degraded via the autophagy-lysosomal pathway, ultimately resulting in a shortened NP half-life and reduced NP expression. Our results suggest that NP is a potential drug target, and that ciclopirox holds substantial promise for further development to combat SARS-CoV-2 replication.
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Affiliation(s)
- Xiafei Wei
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Yuzheng Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Xiaotong Shen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Lujie Fan
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511495, China
| | - Donglan Liu
- 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, Guangzhou 510120, China
| | - Xiang Gao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Jian Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Yezi Wu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Yunfei Li
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Wei Feng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China
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3
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Andronov L, Han M, Zhu Y, Balaji A, Roy AR, Barentine AES, Patel P, Garhyan J, Qi LS, Moerner WE. Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. Nat Commun 2024; 15:4644. [PMID: 38821943 PMCID: PMC11143195 DOI: 10.1038/s41467-024-48991-x] [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: 11/21/2023] [Accepted: 05/13/2024] [Indexed: 06/02/2024] Open
Abstract
The SARS-CoV-2 viral infection transforms host cells and produces special organelles in many ways, and we focus on the replication organelles, the sites of replication of viral genomic RNA (vgRNA). To date, the precise cellular localization of key RNA molecules and replication intermediates has been elusive in electron microscopy studies. We use super-resolution fluorescence microscopy and specific labeling to reveal the nanoscopic organization of replication organelles that contain numerous vgRNA molecules along with the replication enzymes and clusters of viral double-stranded RNA (dsRNA). We show that the replication organelles are organized differently at early and late stages of infection. Surprisingly, vgRNA accumulates into distinct globular clusters in the cytoplasmic perinuclear region, which grow and accommodate more vgRNA molecules as infection time increases. The localization of endoplasmic reticulum (ER) markers and nsp3 (a component of the double-membrane vesicle, DMV) at the periphery of the vgRNA clusters suggests that replication organelles are encapsulated into DMVs, which have membranes derived from the host ER. These organelles merge into larger vesicle packets as infection advances. Precise co-imaging of the nanoscale cellular organization of vgRNA, dsRNA, and viral proteins in replication organelles of SARS-CoV-2 may inform therapeutic approaches that target viral replication and associated processes.
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Affiliation(s)
- Leonid Andronov
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Mengting Han
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Yanyu Zhu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Ashwin Balaji
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Biophysics PhD Program; Stanford University, Stanford, CA, 94305, USA
| | - Anish R Roy
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | | | - Puja Patel
- In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine; Stanford University, Stanford, CA, 94305, USA
| | - Jaishree Garhyan
- In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine; Stanford University, Stanford, CA, 94305, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Sarafan ChEM-H; Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, 94158, USA.
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
- Sarafan ChEM-H; Stanford University, Stanford, CA, 94305, USA.
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4
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Zhang Y, Chen S, Tian Y, Fu X. Host factors of SARS-CoV-2 in infection, pathogenesis, and long-term effects. Front Cell Infect Microbiol 2024; 14:1407261. [PMID: 38846354 PMCID: PMC11155306 DOI: 10.3389/fcimb.2024.1407261] [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: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
SARS-CoV-2 is the causative virus of the devastating COVID-19 pandemic that results in an unparalleled global health and economic crisis. Despite unprecedented scientific efforts and therapeutic interventions, the fight against COVID-19 continues as the rapid emergence of different SARS-CoV-2 variants of concern and the increasing challenge of long COVID-19, raising a vast demand to understand the pathomechanisms of COVID-19 and its long-term sequelae and develop therapeutic strategies beyond the virus per se. Notably, in addition to the virus itself, the replication cycle of SARS-CoV-2 and clinical severity of COVID-19 is also governed by host factors. In this review, we therefore comprehensively overview the replication cycle and pathogenesis of SARS-CoV-2 from the perspective of host factors and host-virus interactions. We sequentially outline the pathological implications of molecular interactions between host factors and SARS-CoV-2 in multi-organ and multi-system long COVID-19, and summarize current therapeutic strategies and agents targeting host factors for treating these diseases. This knowledge would be key for the identification of new pathophysiological aspects and mechanisms, and the development of actionable therapeutic targets and strategies for tackling COVID-19 and its sequelae.
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Affiliation(s)
| | | | - Yan Tian
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital and Cancer Center, Sichuan University and Collaborative Innovation Center of Biotherapy, Sichuan, Chengdu, China
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5
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Hartmann S, Radochonski L, Ye C, Martinez-Sobrido L, Chen J. SARS-CoV-2 ORF3a drives dynamic dense body formation for optimal viral infectivity. RESEARCH SQUARE 2024:rs.3.rs-4292014. [PMID: 38798602 PMCID: PMC11118709 DOI: 10.21203/rs.3.rs-4292014/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
SARS-CoV-2 uses the double-membrane vesicles as replication organelles. However, how virion assembly occurs has not been fully understood. Here we identified a SARS-CoV-2-driven membrane structure named the 3a dense body (3DB). 3DBs have unusual electron-dense and dynamic inner structures, and their formation is driven by the accessory protein ORF3a via hijacking a specific subset of the trans-Golgi network (TGN) and early endosomal membranes. 3DB formation is conserved in related bat and pangolin coronaviruses yet lost during the evolution to SARS-CoV. 3DBs recruit the viral structural proteins spike (S) and membrane (M) and undergo dynamic fusion/fission to facilitate efficient virion assembly. A recombinant SARS-CoV-2 virus with an ORF3a mutant specifically defective in 3DB formation showed dramatically reduced infectivity for both extracellular and cell-associated virions. Our study uncovers the crucial role of 3DB in optimal SARS-CoV-2 infectivity and highlights its potential as a target for COVID-19 prophylactics and therapeutics.
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Affiliation(s)
- Stella Hartmann
- Department of Microbiology, University of Chicago, Chicago, IL, USA 60637
- Howard Taylor Ricketts Laboratory, University of Chicago, Lemont, IL, USA 60439
| | - Lisa Radochonski
- Department of Microbiology, University of Chicago, Chicago, IL, USA 60637
- Howard Taylor Ricketts Laboratory, University of Chicago, Lemont, IL, USA 60439
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, USA 78227
| | | | - Jueqi Chen
- Department of Microbiology, University of Chicago, Chicago, IL, USA 60637
- Howard Taylor Ricketts Laboratory, University of Chicago, Lemont, IL, USA 60439
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6
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Klevanski M, Kim H, Heilemann M, Kuner T, Bartenschlager R. Glycan-directed SARS-CoV-2 inhibition by leek extract and lectins with insights into the mode-of-action of Concanavalin A. Antiviral Res 2024; 225:105856. [PMID: 38447646 DOI: 10.1016/j.antiviral.2024.105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Four years after its outbreak, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a global challenge for human health. At its surface, SARS-CoV-2 features numerous extensively glycosylated spike proteins. This glycan coat supports virion docking and entry into host cells and at the same time renders the virus less susceptible to neutralizing antibodies. Given the high genetic plasticity of SARS-CoV-2 and the rapid emergence of immune escape variants, targeting the glycan shield by carbohydrate-binding agents emerges as a promising strategy. However, the potential of carbohydrate-targeting reagents as viral inhibitors remains underexplored. Here, we tested seven plant-derived carbohydrate-binding proteins, called lectins, and one crude plant extract for their antiviral activity against SARS-CoV-2 in two types of human lung cells: A549 cells ectopically expressing the ACE2 receptor and Calu-3 cells. We identified three lectins and an Allium porrum (leek) extract inhibiting SARS-CoV-2 infection in both cell systems with selectivity indices (SI) ranging between >2 and >299. Amongst these, the lectin Concanavalin A (Con A) exerted the most potent and broad activity against a panel of SARS-CoV-2 variants. We used multiplex super-resolution microscopy to address lectin interactions with SARS-CoV-2 and its host cells. Notably, we discovered that Con A not only binds to SARS-CoV-2 virions and their host cells, but also causes SARS-CoV-2 aggregation. Thus, Con A exerts a dual mode-of-action comprising both, antiviral and virucidal, mechanisms. These results establish Con A and other plant lectins as candidates for COVID-19 prevention and basis for further drug development.
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Affiliation(s)
- Maja Klevanski
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany.
| | - Heeyoung Kim
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120, Heidelberg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Thomas Kuner
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120, Heidelberg, Germany; German Center for Lung Research (DZL), Partner Site Heidelberg (TLRC), Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120, Heidelberg, Germany; Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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7
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Ray P, Ledgerwood-Lee M, Brickner H, Clark AE, Garretson A, Graham R, Van Zant W, Carlin AF, Aronoff-Spencer ES. Design and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein to Validate the Viral Quality Assurance Panels. Viruses 2024; 16:662. [PMID: 38793544 PMCID: PMC11125937 DOI: 10.3390/v16050662] [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: 03/30/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 05/26/2024] Open
Abstract
The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for the calibration and quality assurance of inactivated SARS-CoV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. A heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)-C-terminal domain (CTD) across all SARS-CoV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprised of UV-inactivated SARS-CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (limit of detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a 20 amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust 'pan-variant' antigen-based assays for viruses prone to high mutational rates.
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Affiliation(s)
- Partha Ray
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Melissa Ledgerwood-Lee
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Howard Brickner
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Alex E. Clark
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron Garretson
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Rishi Graham
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Westley Van Zant
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Eliah S. Aronoff-Spencer
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
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8
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Du L, Deiter F, Bouzidi MS, Billaud JN, Simmons G, Dabral P, Selvarajah S, Lingappa AF, Michon M, Yu SF, Paulvannan K, Manicassamy B, Lingappa VR, Boushey H, Greenland JR, Pillai SK. A viral assembly inhibitor blocks SARS-CoV-2 replication in airway epithelial cells. Commun Biol 2024; 7:486. [PMID: 38649430 PMCID: PMC11035691 DOI: 10.1038/s42003-024-06130-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
The ongoing evolution of SARS-CoV-2 to evade vaccines and therapeutics underlines the need for innovative therapies with high genetic barriers to resistance. Therefore, there is pronounced interest in identifying new pharmacological targets in the SARS-CoV-2 viral life cycle. The small molecule PAV-104, identified through a cell-free protein synthesis and assembly screen, was recently shown to target host protein assembly machinery in a manner specific to viral assembly. In this study, we investigate the capacity of PAV-104 to inhibit SARS-CoV-2 replication in human airway epithelial cells (AECs). We show that PAV-104 inhibits >99% of infection with diverse SARS-CoV-2 variants in immortalized AECs, and in primary human AECs cultured at the air-liquid interface (ALI) to represent the lung microenvironment in vivo. Our data demonstrate that PAV-104 inhibits SARS-CoV-2 production without affecting viral entry, mRNA transcription, or protein synthesis. PAV-104 interacts with SARS-CoV-2 nucleocapsid (N) and interferes with its oligomerization, blocking particle assembly. Transcriptomic analysis reveals that PAV-104 reverses SARS-CoV-2 induction of the type-I interferon response and the maturation of nucleoprotein signaling pathway known to support coronavirus replication. Our findings suggest that PAV-104 is a promising therapeutic candidate for COVID-19 with a mechanism of action that is distinct from existing clinical management approaches.
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Affiliation(s)
- Li Du
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA
- University of California, San Francisco, CA, 94143, USA
| | - Fred Deiter
- University of California, San Francisco, CA, 94143, USA
- Veterans Administration Health Care System, 4150 Clement St., San Francisco, CA, 94121, USA
| | - Mohamed S Bouzidi
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA
- University of California, San Francisco, CA, 94143, USA
| | | | - Graham Simmons
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA
- University of California, San Francisco, CA, 94143, USA
| | - Prerna Dabral
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA
- University of California, San Francisco, CA, 94143, USA
| | | | | | - Maya Michon
- Prosetta Biosciences Inc, 670 5th St., San Francisco, CA, 94107, USA
| | - Shao Feng Yu
- Prosetta Biosciences Inc, 670 5th St., San Francisco, CA, 94107, USA
| | - Kumar Paulvannan
- Prosetta Biosciences Inc, 670 5th St., San Francisco, CA, 94107, USA
| | | | | | - Homer Boushey
- University of California, San Francisco, CA, 94143, USA
| | - John R Greenland
- University of California, San Francisco, CA, 94143, USA
- Veterans Administration Health Care System, 4150 Clement St., San Francisco, CA, 94121, USA
| | - Satish K Pillai
- Vitalant Research Institute, 360 Spear St., San Francisco, CA, 94105, USA.
- University of California, San Francisco, CA, 94143, USA.
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9
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Andronov L, Han M, Zhu Y, Balaji A, Roy AR, Barentine AES, Patel P, Garhyan J, Qi LS, Moerner W. Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.07.566110. [PMID: 37986994 PMCID: PMC10659379 DOI: 10.1101/2023.11.07.566110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The SARS-CoV-2 viral infection transforms host cells and produces special organelles in many ways, and we focus on the replication organelle where the replication of viral genomic RNA (vgRNA) occurs. To date, the precise cellular localization of key RNA molecules and replication intermediates has been elusive in electron microscopy studies. We use super-resolution fluorescence microscopy and specific labeling to reveal the nanoscopic organization of replication organelles that contain vgRNA clusters along with viral double-stranded RNA (dsRNA) clusters and the replication enzyme, encapsulated by membranes derived from the host endoplasmic reticulum (ER). We show that the replication organelles are organized differently at early and late stages of infection. Surprisingly, vgRNA accumulates into distinct globular clusters in the cytoplasmic perinuclear region, which grow and accommodate more vgRNA molecules as infection time increases. The localization of ER labels and nsp3 (a component of the double-membrane vesicle, DMV) at the periphery of the vgRNA clusters suggests that replication organelles are enclosed by DMVs at early infection stages which then merge into vesicle packets as infection progresses. Precise co-imaging of the nanoscale cellular organization of vgRNA, dsRNA, and viral proteins in replication organelles of SARS-CoV-2 may inform therapeutic approaches that target viral replication and associated processes.
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Affiliation(s)
- Leonid Andronov
- Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A
| | - Mengting Han
- Department of Bioengineering; Stanford University, Stanford, CA 94305 U.S.A
| | - Yanyu Zhu
- Department of Bioengineering; Stanford University, Stanford, CA 94305 U.S.A
| | - Ashwin Balaji
- Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A
- Biophysics PhD Program; Stanford University, Stanford, CA 94305 U.S.A
| | - Anish R. Roy
- Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A
| | | | - Puja Patel
- In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine; Stanford University, Stanford, CA 94305 U.S.A
| | - Jaishree Garhyan
- In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine; Stanford University, Stanford, CA 94305 U.S.A
| | - Lei S. Qi
- Department of Bioengineering; Stanford University, Stanford, CA 94305 U.S.A
- Sarafan ChEM-H; Stanford University, Stanford, CA 94305 U.S.A
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA 94158 U.S.A
| | - W.E. Moerner
- Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A
- Sarafan ChEM-H; Stanford University, Stanford, CA 94305 U.S.A
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10
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Ali YM, Carnell GW, Fumagalli S, Mercurio D, Seminara S, Lynch NJ, Khatri P, Arachchilage CH, Mascheroni L, Kaminski C, George CL, Stewart H, Yabuki M, Demopulos G, Heeney JL, Schwaeble W. Inhibition of the Lectin Pathway of Complement Activation Reduces Acute Respiratory Distress Syndrome Severity in a Mouse Model of SARS-CoV-2 Infection. J Infect Dis 2024; 229:680-690. [PMID: 37878754 PMCID: PMC10938221 DOI: 10.1093/infdis/jiad462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023] Open
Abstract
Most patients with COVID-19 in the intensive care unit develop an acute respiratory distress syndrome characterized by severe hypoxemia, decreased lung compliance, and high vascular permeability. Activation of the complement system is a hallmark of moderate and severe COVID-19, with abundant deposition of complement proteins in inflamed tissue and on the endothelium during COVID-19. Using a transgenic mouse model of SARS-CoV-2 infection, we assessed the therapeutic utility of an inhibitory antibody (HG4) targeting MASP-2, a key enzyme in the lectin pathway. Treatment of infected mice with HG4 reduced the disease severity score and improved survival vs mice that received an isotype control antibody. Administration of HG4 significantly reduced the lung injury score, including alveolar inflammatory cell infiltration, alveolar edema, and alveolar hemorrhage. The ameliorating effect of MASP-2 inhibition on the severity of COVID-19 pathology is reflected by a significant reduction in the proinflammatory activation of brain microglia in HG4-treated mice.
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Affiliation(s)
- Youssif M Ali
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - George W Carnell
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Stefano Fumagalli
- Department of Acute Brain and Cardiovascular Injury, Laboratory of Stroke and Vascular Dysfunctions, Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy
| | - Domenico Mercurio
- Department of Acute Brain and Cardiovascular Injury, Laboratory of Stroke and Vascular Dysfunctions, Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy
| | - Serena Seminara
- Department of Acute Brain and Cardiovascular Injury, Laboratory of Stroke and Vascular Dysfunctions, Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy
| | - Nicholas J Lynch
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Priyanka Khatri
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Chanuka H Arachchilage
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Luca Mascheroni
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Clemens Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Charlotte L George
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | | | | | - Jonathan L Heeney
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
| | - Wilhelm Schwaeble
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge CB3 0ES, UK
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11
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Zheng G, Qiu G, Qian H, Shu Q, Xu J. Multifaceted role of SARS-CoV-2 structural proteins in lung injury. Front Immunol 2024; 15:1332440. [PMID: 38375473 PMCID: PMC10875085 DOI: 10.3389/fimmu.2024.1332440] [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: 11/02/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human coronavirus to cause acute respiratory distress syndrome (ARDS) and contains four structural proteins: spike, envelope, membrane, and nucleocapsid. An increasing number of studies have demonstrated that all four structural proteins of SARS-CoV-2 are capable of causing lung injury, even without the presence of intact virus. Therefore, the topic of SARS-CoV-2 structural protein-evoked lung injury warrants more attention. In the current article, we first synopsize the structural features of SARS-CoV-2 structural proteins. Second, we discuss the mechanisms for structural protein-induced inflammatory responses in vitro. Finally, we list the findings that indicate structural proteins themselves are toxic and sufficient to induce lung injury in vivo. Recognizing mechanisms of lung injury triggered by SARS-CoV-2 structural proteins may facilitate the development of targeted modalities in treating COVID-19.
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Affiliation(s)
| | - Guanguan Qiu
- Shaoxing Second Hospital, Shaoxing, Zhejiang, China
| | - Huifeng Qian
- Shaoxing Second Hospital, Shaoxing, Zhejiang, China
| | - Qiang Shu
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Jianguo Xu
- Shaoxing Second Hospital, Shaoxing, Zhejiang, China
- The Children’s Hospital of Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
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12
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McCoy R, Oldroyd S, Yang W, Wang K, Hoven D, Bulmer D, Zilbauer M, Owens RM. In Vitro Models for Investigating Intestinal Host-Pathogen Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306727. [PMID: 38155358 PMCID: PMC10885678 DOI: 10.1002/advs.202306727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Indexed: 12/30/2023]
Abstract
Infectious diseases are increasingly recognized as a major threat worldwide due to the rise of antimicrobial resistance and the emergence of novel pathogens. In vitro models that can adequately mimic in vivo gastrointestinal physiology are in high demand to elucidate mechanisms behind pathogen infectivity, and to aid the design of effective preventive and therapeutic interventions. There exists a trade-off between simple and high throughput models and those that are more complex and physiologically relevant. The complexity of the model used shall be guided by the biological question to be addressed. This review provides an overview of the structure and function of the intestine and the models that are developed to emulate this. Conventional models are discussed in addition to emerging models which employ engineering principles to equip them with necessary advanced monitoring capabilities for intestinal host-pathogen interrogation. Limitations of current models and future perspectives on the field are presented.
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Affiliation(s)
- Reece McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Sophie Oldroyd
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Woojin Yang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Kaixin Wang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Darius Hoven
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - David Bulmer
- Department of PharmacologyUniversity of CambridgeCambridgeCB2 1PDUK
| | - Matthias Zilbauer
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Róisín M. Owens
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
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13
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Sergio MC, Ricciardi S, Guarino AM, Giaquinto L, De Matteis MA. Membrane remodeling and trafficking piloted by SARS-CoV-2. Trends Cell Biol 2024:S0962-8924(23)00256-8. [PMID: 38262893 DOI: 10.1016/j.tcb.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]
Abstract
The molecular mechanisms underlying SARS-CoV-2 host cell invasion and life cycle have been studied extensively in recent years, with a primary focus on viral entry and internalization with the aim of identifying antiviral therapies. By contrast, our understanding of the molecular mechanisms involved in the later steps of the coronavirus life cycle is relatively limited. In this review, we describe what is known about the host factors and viral proteins involved in the replication, assembly, and egress phases of SARS-CoV-2, which induce significant host membrane rearrangements. We also discuss the limits of the current approaches and the knowledge gaps still to be addressed.
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Affiliation(s)
- Maria Concetta Sergio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | | | - Andrea M Guarino
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | - Laura Giaquinto
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; University of Naples Federico II, Naples, Italy.
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14
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Murigneux E, Softic L, Aubé C, Grandi C, Judith D, Bruce J, Le Gall M, Guillonneau F, Schmitt A, Parissi V, Berlioz-Torrent C, Meertens L, Hansen MMK, Gallois-Montbrun S. Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly. Nat Commun 2024; 15:640. [PMID: 38245532 PMCID: PMC10799903 DOI: 10.1038/s41467-024-44958-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
Considerable progress has been made in understanding the molecular host-virus battlefield during SARS-CoV-2 infection. Nevertheless, the assembly and egress of newly formed virions are less understood. To identify host proteins involved in viral morphogenesis, we characterize the proteome of SARS-CoV-2 virions produced from A549-ACE2 and Calu-3 cells, isolated via ultracentrifugation on sucrose cushion or by ACE-2 affinity capture. Bioinformatic analysis unveils 92 SARS-CoV-2 virion-associated host factors, providing a valuable resource to better understand the molecular environment of virion production. We reveal that G3BP1 and G3BP2 (G3BP1/2), two major stress granule nucleators, are embedded within virions and unexpectedly favor virion production. Furthermore, we show that G3BP1/2 participate in the formation of cytoplasmic membrane vesicles, that are likely virion assembly sites, consistent with a proviral role of G3BP1/2 in SARS-CoV-2 dissemination. Altogether, these findings provide new insights into host factors required for SARS-CoV-2 assembly with potential implications for future therapeutic targeting.
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Affiliation(s)
- Emilie Murigneux
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Laurent Softic
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Corentin Aubé
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Carmen Grandi
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, the Netherlands
| | - Delphine Judith
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Johanna Bruce
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Morgane Le Gall
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - François Guillonneau
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
- Institut de Cancérologie de l'Ouest (ICO), CRCi2NA-Inserm UMR 1307, CNRS UMR 6075, Nantes Université, Angers, France
| | - Alain Schmitt
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Vincent Parissi
- Microbiologie Fondamentale et Pathogénicité Laboratory (MFP), UMR 5234, « Mobility of pathogenic genomes and chromatin dynamics » team (MobilVIR), CNRS-University of Bordeaux, DyNAVIR network, Bordeaux, France
| | | | - Laurent Meertens
- Université Paris Cité, Inserm U944, CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, the Netherlands
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15
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Caldas LA, Carneiro FA, Augusto I, Corrêa IA, da Costa LJ, Miranda K, Tanuri A, de Souza W. SARS-CoV-2 egress from Vero cells: a morphological approach. Histochem Cell Biol 2024; 161:59-67. [PMID: 37736815 DOI: 10.1007/s00418-023-02239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Despite being extensively studied because of the current coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interactions with mammalian cells are still poorly understood. Furthermore, little is known about this coronavirus cycle within the host cells, particularly the steps that lead to viral egress. This study aimed to shed light on the morphological features of SARS-CoV-2 egress by utilizing transmission and high-resolution scanning electron microscopy, along with serial electron tomography, to describe the route of nascent virions towards the extracellular medium. Electron microscopy revealed that the clusters of viruses in the paracellular space did not seem to result from collective virus release. Instead, virus accumulation was observed on incurved areas of the cell surface, with egress primarily occurring through individual vesicles. Additionally, our findings showed that the emission of long membrane projections, which could facilitate virus surfing in Vero cells infected with SARS-CoV-2, was also observed in non-infected cultures, suggesting that these are constitutive events in this cell lineage.
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Affiliation(s)
- Lucio Ayres Caldas
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil.
- Núcleo Multidisciplinar de Pesquisas em Biologia - NUMPEX-BIO, Campus Duque de Caxias Geraldo Cidade, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Duque de Caxias, RJ, Brazil.
| | - Fabiana Avila Carneiro
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil
- Núcleo Multidisciplinar de Pesquisas em Biologia - NUMPEX-BIO, Campus Duque de Caxias Geraldo Cidade, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Duque de Caxias, RJ, Brazil
| | - Ingrid Augusto
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil
| | - Isadora Alonso Corrêa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana Jesus da Costa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kildare Miranda
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem (INBEB) and Centro Nacional de Biologia Estutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem (INBEB) and Centro Nacional de Biologia Estutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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16
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Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO. Assembly of SARS-CoV-2 ribonucleosomes by truncated N ∗ variant of the nucleocapsid protein. J Biol Chem 2023; 299:105362. [PMID: 37863261 PMCID: PMC10665939 DOI: 10.1016/j.jbc.2023.105362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein serine/arginine (SR) region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N∗ or Δ(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we use mass photometry and negative stain electron microscopy to show that purified Δ(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1-209) vRNPs requires the leucine-rich helix of the central disordered region and that this helix promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by phosphorylation.
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Affiliation(s)
- Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | | | - Abdullah M Syed
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Alison Ciling
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA; Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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17
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Castro V, Pérez-Berna AJ, Calvo G, Pereiro E, Gastaminza P. Three-Dimensional Remodeling of SARS-CoV2-Infected Cells Revealed by Cryogenic Soft X-ray Tomography. ACS NANO 2023; 17:22708-22721. [PMID: 37939169 PMCID: PMC10690842 DOI: 10.1021/acsnano.3c07265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Plus-strand RNA viruses are proficient at remodeling host cell membranes for optimal viral genome replication and the production of infectious progeny. These ultrastructural alterations result in the formation of viral membranous organelles and may be observed by different imaging techniques, providing nanometric resolution. Guided by confocal and electron microscopy, this study describes the generation of wide-field volumes using cryogenic soft-X-ray tomography (cryo-SXT) on SARS-CoV-2-infected human lung adenocarcinoma cells. Confocal microscopy showed accumulation of double-stranded RNA (dsRNA) and nucleocapsid (N) protein in compact perinuclear structures, preferentially found around centrosomes at late stages of the infection. Transmission electron microscopy (TEM) showed accumulation of membranous structures in the vicinity of the infected cell nucleus, forming a viral replication organelle containing characteristic double-membrane vesicles and virus-like particles within larger vesicular structures. Cryo-SXT revealed viral replication organelles very similar to those observed by TEM but indicated that the vesicular organelle observed in TEM sections is indeed a vesiculo-tubular network that is enlarged and elongated at late stages of the infection. Overall, our data provide additional insight into the molecular architecture of the SARS-CoV-2 replication organelle.
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Affiliation(s)
- Victoria Castro
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
| | | | - Gema Calvo
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
| | - Eva Pereiro
- ALBA
Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Valles, Spain
| | - Pablo Gastaminza
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
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18
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Desmarets L, Danneels A, Burlaud-Gaillard J, Blanchard E, Dubuisson J, Belouzard S. The KxGxYR and DxE motifs in the C-tail of the Middle East respiratory syndrome coronavirus membrane protein are crucial for infectious virus assembly. Cell Mol Life Sci 2023; 80:353. [PMID: 37940699 PMCID: PMC10632273 DOI: 10.1007/s00018-023-05008-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/21/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
The coronavirus' (CoV) membrane (M) protein is the driving force during assembly, but this process remains poorly characterized. Previously, we described two motifs in the C-tail of the Middle East respiratory syndrome CoV (MERS-CoV) M protein involved in its endoplasmic reticulum (ER) exit (211DxE213) and trans-Golgi network (TGN) retention (199KxGxYR204). Here, their function in virus assembly was investigated by two different virus-like particle (VLP) assays and by mutating both motifs in an infectious MERS-CoV cDNA clone. It was shown that the 199KxGxYR204 motif was essential for VLP and infectious virus assembly. Moreover, the mislocalization of the M protein induced by mutation of this motif prevented M-E interaction. Hampering the ER export of M by mutating its 211DxE213 motif still allowed the formation of nucleocapsid-empty VLPs, but prevented the formation of fully assembled VLPs and infectious particles. Taken together, these data show that the MERS-CoV assembly process highly depends on the correct intracellular trafficking of its M protein, and hence that not only specific protein-protein interacting motifs but also correct subcellular localization of the M protein in infected cells is essential for virus formation and should be taken into consideration when studying the assembly process.
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Affiliation(s)
- Lowiese Desmarets
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Adeline Danneels
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Julien Burlaud-Gaillard
- INSERM U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France
- Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Emmanuelle Blanchard
- INSERM U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France
- Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Jean Dubuisson
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Sandrine Belouzard
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France.
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19
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Hoffmann H, Ebensperger M, Schönsiegel A, Hamza H, Koch-Heier J, Schreiber A, Ludwig S, Schindler M, Planz O. Influenza A virus replication has a stronger dependency on Raf/MEK/ERK signaling pathway activity than SARS-CoV-2. Front Cell Infect Microbiol 2023; 13:1264983. [PMID: 37965261 PMCID: PMC10641236 DOI: 10.3389/fcimb.2023.1264983] [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: 07/21/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
The recent COVID-19 pandemic again highlighted the urgent need for broad-spectrum antivirals, both for therapeutic use in acute viral infection and for pandemic preparedness in general. The targeting of host cell factors hijacked by viruses during their replication cycle presents one possible strategy for development of broad-spectrum antivirals. By inhibiting the Raf/MEK/ERK signaling pathway, a central kinase cascade of eukaryotic cells, which is being exploited by numerous viruses of different virus phyla, the small-molecule MEK inhibitor zapnometinib has the potential to address this need. We here performed a side-by-side comparison of the antiviral efficacy of zapnometinib against IAV and SARS-CoV-2 to determine the concentration leading to 50% of its effect on the virus (EC50) and the concentration leading to 50% reduction of ERK phosphorylation (IC50) in a comparable manner, using the same experimental conditions. Our results show that the EC50 value and IC50 value of zapnometinib are indeed lower for IAV compared to SARS-CoV-2 using one representative strain for each. The results suggest that IAV's replication has a stronger dependency on an active Raf/MEK/ERK pathway and, thus, that IAV is more susceptible to treatment with zapnometinib than SARS-CoV-2. With zapnometinib's favorable outcome in a recent phase II clinical trial in hospitalized COVID-19 patients, the present results are even more promising for an upcoming phase II clinical trial in severe influenza virus infection.
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Affiliation(s)
- Helen Hoffmann
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls Universitaet Tuebingen, Tuebingen, Germany
- Atriva Therapeutics GmbH, Tuebingen, Germany
| | | | - Annika Schönsiegel
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls Universitaet Tuebingen, Tuebingen, Germany
- Atriva Therapeutics GmbH, Tuebingen, Germany
| | - Hazem Hamza
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls Universitaet Tuebingen, Tuebingen, Germany
- Virology Laboratory, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Julia Koch-Heier
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls Universitaet Tuebingen, Tuebingen, Germany
- Atriva Therapeutics GmbH, Tuebingen, Germany
| | - André Schreiber
- Institute of Virology (IVM), Westfaelische Wilhelms Universitaet, Muenster, Muenster, Germany
| | - Stephan Ludwig
- Institute of Virology (IVM), Westfaelische Wilhelms Universitaet, Muenster, Muenster, Germany
| | - Michael Schindler
- Department of Molecular Virology, Institute for Medical Virology and Epidemiology of Viral Disease, University Hospital Tuebingen, Tuebingen, Germany
| | - Oliver Planz
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls Universitaet Tuebingen, Tuebingen, Germany
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20
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Häring C, Jungwirth J, Schroeder J, Löffler B, Engert B, Ehrhardt C. The Local Anaesthetic Procaine Prodrugs ProcCluster ® and Procaine Hydrochloride Impair SARS-CoV-2 Replication and Egress In Vitro. Int J Mol Sci 2023; 24:14584. [PMID: 37834031 PMCID: PMC10572566 DOI: 10.3390/ijms241914584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
As vaccination efforts against SARS-CoV-2 progress in many countries, there is still an urgent need for efficient antiviral treatment strategies for those with severer disease courses, and lately, considerable efforts have been undertaken to repurpose existing drugs as antivirals. The local anaesthetic procaine has been investigated for antiviral properties against several viruses over the past decades. Here, we present data on the inhibitory effect of the procaine prodrugs ProcCluster® and procaine hydrochloride on SARS-CoV-2 infection in vitro. Both procaine prodrugs limit SARS-CoV-2 progeny virus titres as well as reduce interferon and cytokine responses in a proportional manner to the virus load. The addition of procaine during the early stages of the SARS-CoV-2 replication cycle in a cell culture first limits the production of subgenomic RNA transcripts, and later affects the replication of the viral genomic RNA. Interestingly, procaine additionally exerts a prominent effect on SARS-CoV-2 progeny virus release when added late during the replication cycle, when viral RNA production and protein production are already largely completed.
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Affiliation(s)
- Clio Häring
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Johannes Jungwirth
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Josefine Schroeder
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany;
| | | | - Christina Ehrhardt
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
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21
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Swain J, Merida P, Rubio K, Bracquemond D, Neyret A, Aguilar-Ordoñez I, Günther S, Barreto G, Muriaux D. F-actin nanostructures rearrangements and regulation are essential for SARS-CoV-2 particle production in host pulmonary cells. iScience 2023; 26:107384. [PMID: 37564698 PMCID: PMC10410521 DOI: 10.1016/j.isci.2023.107384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/24/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Our study focused on deciphering the role of F-actin and related regulatory factors during SARS-CoV-2 particle production and transmission in human pulmonary cells. Quantitative high-resolution microscopies revealed that the late phases of SARS-CoV-2 infection induce a strong rearrangement of F-actin nanostructures dependent on the viral M, E, and N structural proteins. Intracellular vesicles containing viral components are labeled with Rab7 and Lamp1 and are surrounded by F-actin ring-shaped structures, suggesting their role in viral trafficking toward the cell membrane for virus release. Furthermore, filopodia-like nanostructures were loaded with viruses, potentially facilitating their egress and transmission between lung cells. Gene expression analysis revealed the involvement of alpha-actinins under the regulation of the protein kinase N (PKN). The use of a PKN inhibitor efficiently reduces virus particle production, restoring endoplasmic reticulum and F-actin cellular shape. Our results highlight an important role of F-actin rearrangements during the productive phases of SARS-CoV-2 particles.
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Affiliation(s)
- Jitendriya Swain
- Institute of Research in Infectiology of Montpellier (IRIM), CNRS, University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Peggy Merida
- Institute of Research in Infectiology of Montpellier (IRIM), CNRS, University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Karla Rubio
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, 54000 Nancy, France
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
| | - David Bracquemond
- Institute of Research in Infectiology of Montpellier (IRIM), CNRS, University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Aymeric Neyret
- CEMIPAI, CNRS, University of Montpellier, UAR3725 CNRS, Montpellier, France
| | | | - Stefan Günther
- ECCPS Bioinformatics and Deep Sequencing, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Guillermo Barreto
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, 54000 Nancy, France
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
| | - Delphine Muriaux
- Institute of Research in Infectiology of Montpellier (IRIM), CNRS, University of Montpellier, UMR9004 CNRS, Montpellier, France
- CEMIPAI, CNRS, University of Montpellier, UAR3725 CNRS, Montpellier, France
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22
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Aloise C, Schipper JG, van Vliet A, Oymans J, Donselaar T, Hurdiss DL, de Groot RJ, van Kuppeveld FJM. SARS-CoV-2 nucleocapsid protein inhibits the PKR-mediated integrated stress response through RNA-binding domain N2b. PLoS Pathog 2023; 19:e1011582. [PMID: 37607209 PMCID: PMC10473545 DOI: 10.1371/journal.ppat.1011582] [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: 03/07/2023] [Revised: 09/01/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
The nucleocapsid protein N of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enwraps and condenses the viral genome for packaging but is also an antagonist of the innate antiviral defense. It suppresses the integrated stress response (ISR), purportedly by interacting with stress granule (SG) assembly factors G3BP1 and 2, and inhibits type I interferon responses. To elucidate its mode of action, we systematically deleted and over-expressed distinct regions and domains. We show that N via domain N2b blocks PKR-mediated ISR activation, as measured by suppression of ISR-induced translational arrest and SG formation. N2b mutations that prevent dsRNA binding abrogate these activities also when introduced in the intact N protein. Substitutions reported to block post-translation modifications of N or its interaction with G3BP1/2 did not have a detectable additive effect. In an encephalomyocarditis virus-based infection model, N2b - but not a derivative defective in RNA binding-prevented PKR activation, inhibited β-interferon expression and promoted virus replication. Apparently, SARS-CoV-2 N inhibits innate immunity by sequestering dsRNA to prevent activation of PKR and RIG-I-like receptors. Similar observations were made for the N protein of human coronavirus 229E, suggesting that this may be a general trait conserved among members of other orthocoronavirus (sub)genera.
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Affiliation(s)
- Chiara Aloise
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jelle G. Schipper
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Arno van Vliet
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Judith Oymans
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Tim Donselaar
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Daniel L. Hurdiss
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Raoul J. de Groot
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank J. M. van Kuppeveld
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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23
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Chen P, Wu M, He Y, Jiang B, He ML. Metabolic alterations upon SARS-CoV-2 infection and potential therapeutic targets against coronavirus infection. Signal Transduct Target Ther 2023; 8:237. [PMID: 37286535 DOI: 10.1038/s41392-023-01510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/18/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis, bringing enormous burden to our society. Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms. Although only a small proportion of patients progressed to severe COVID-19 with symptoms including acute respiratory distress syndrome (ARDS), disseminated coagulopathy, and cardiovascular disorders, severe COVID-19 is accompanied by high mortality rates with near 7 million deaths. Nowadays, effective therapeutic patterns for severe COVID-19 are still lacking. It has been extensively reported that host metabolism plays essential roles in various physiological processes during virus infection. Many viruses manipulate host metabolism to avoid immunity, facilitate their own replication, or to initiate pathological response. Targeting the interaction between SARS-CoV-2 and host metabolism holds promise for developing therapeutic strategies. In this review, we summarize and discuss recent studies dedicated to uncovering the role of host metabolism during the life cycle of SARS-CoV-2 in aspects of entry, replication, assembly, and pathogenesis with an emphasis on glucose metabolism and lipid metabolism. Microbiota and long COVID-19 are also discussed. Ultimately, we recapitulate metabolism-modulating drugs repurposed for COVID-19 including statins, ASM inhibitors, NSAIDs, Montelukast, omega-3 fatty acids, 2-DG, and metformin.
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Affiliation(s)
- Peiran Chen
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Binghua Jiang
- Cell Signaling and Proteomic Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China.
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24
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Wang Y, Ling X, Zhang C, Zou J, Luo B, Luo Y, Jia X, Jia G, Zhang M, Hu J, Liu T, Wang Y, Lu K, Li D, Ma J, Liu C, Su Z. Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly. MOLECULAR BIOMEDICINE 2023; 4:16. [PMID: 37211575 DOI: 10.1186/s43556-023-00129-z] [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: 01/13/2023] [Accepted: 04/09/2023] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the NIDR, the serine/arginine rich motif (SRIDR), and the CIDR. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (NFL) assembles into ring-like architecture whereas the truncated SRIDR-CTD-CIDR (N182-419) promotes filamentous assembly. Moreover, LLPS droplets of NFL and N182-419 are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N182-419 droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.
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Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Minghua Zhang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Junchao Hu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Ting Liu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yuanfeiyi Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Kefeng Lu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cong Liu
- Interdisciplinary Research Center On Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China.
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25
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Pillai S, Du L, Deiter F, Bouzidi M, Billaud JN, Graham S, Prerna D, Selvarajah S, Lingappa A, Michon M, Yu S, Paulvannan K, Lingappa V, Boushey H, Greenland J. A Novel Viral Assembly Inhibitor Blocks SARS-CoV-2 Replication in Airway Epithelial Cells. RESEARCH SQUARE 2023:rs.3.rs-2887435. [PMID: 37292622 PMCID: PMC10246244 DOI: 10.21203/rs.3.rs-2887435/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ongoing evolution of SARS-CoV-2 to evade vaccines and therapeutics underlines the need for novel therapies with high genetic barriers to resistance. The small molecule PAV-104, identified through a cell-free protein synthesis and assembly screen, was recently shown to target host protein assembly machinery in a manner specific to viral assembly. Here, we investigated the capacity of PAV-104 to inhibit SARS-CoV-2 replication in human airway epithelial cells (AECs). Our data demonstrate that PAV-104 inhibited > 99% of infection with diverse SARS-CoV-2 variants in primary and immortalized human AECs. PAV-104 suppressed SARS-CoV-2 production without affecting viral entry or protein synthesis. PAV-104 interacted with SARS-CoV-2 nucleocapsid (N) and interfered with its oligomerization, blocking particle assembly. Transcriptomic analysis revealed that PAV-104 reversed SARS-CoV-2 induction of the Type-I interferon response and the 'maturation of nucleoprotein' signaling pathway known to support coronavirus replication. Our findings suggest that PAV-104 is a promising therapeutic candidate for COVID-19.
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Affiliation(s)
| | - Li Du
- Vitalant Research Institute/UCSF
| | - Fred Deiter
- Veterans Administration Health Care System/UCSF
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26
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Lotti V, Lagni A, Diani E, Sorio C, Gibellini D. Crosslink between SARS-CoV-2 replication and cystic fibrosis hallmarks. Front Microbiol 2023; 14:1162470. [PMID: 37250046 PMCID: PMC10213757 DOI: 10.3389/fmicb.2023.1162470] [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: 02/09/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
SARS-CoV-2, the etiological cause of the COVID-19 pandemic, can cause severe illness in certain at-risk populations, including people with cystic fibrosis (pwCF). Nevertheless, several studies indicated that pwCF do not have higher risks of SARS-CoV-2 infection nor do they demonstrate worse clinical outcomes than those of the general population. Recent in vitro studies indicate cellular and molecular processes to be significant drivers in pwCF lower infection rates and milder symptoms than expected in cases of SARS-CoV-2 infection. These range from cytokine releases to biochemical alterations leading to morphological rearrangements inside the cells associated with CFTR impairment. Based on available data, the reported low incidence of SARS-CoV-2 infection among pwCF is likely a result of several variables linked to CFTR dysfunction, such as thick mucus, IL-6 reduction, altered ACE2 and TMPRSS2 processing and/or functioning, defective anions exchange, and autophagosome formation. An extensive analysis of the relation between SARS-CoV-2 infection and pwCF is essential to elucidate the mechanisms involved in this lower-than-expected infection impact and to possibly suggest potential new antiviral strategies.
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Affiliation(s)
- Virginia Lotti
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Anna Lagni
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Erica Diani
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Claudio Sorio
- General Pathology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Davide Gibellini
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
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27
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Salahandish R, Hyun JE, Haghayegh F, Tabrizi HO, Moossavi S, Khetani S, Ayala-Charca G, Berenger BM, Niu YD, Ghafar-Zadeh E, Nezhad AS. CoVSense: Ultrasensitive Nucleocapsid Antigen Immunosensor for Rapid Clinical Detection of Wildtype and Variant SARS-CoV-2. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206615. [PMID: 36995043 DOI: 10.1002/advs.202206615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/31/2023] [Indexed: 05/27/2023]
Abstract
The widespread accessibility of commercial/clinically-viable electrochemical diagnostic systems for rapid quantification of viral proteins demands translational/preclinical investigations. Here, Covid-Sense (CoVSense) antigen testing platform; an all-in-one electrochemical nano-immunosensor for sample-to-result, self-validated, and accurate quantification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N)-proteins in clinical examinations is developed. The platform's sensing strips benefit from a highly-sensitive, nanostructured surface, created through the incorporation of carboxyl-functionalized graphene nanosheets, and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) conductive polymers, enhancing the overall conductivity of the system. The nanoengineered surface chemistry allows for compatible direct assembly of bioreceptor molecules. CoVSense offers an inexpensive (<$2 kit) and fast/digital response (<10 min), measured using a customized hand-held reader (<$25), enabling data-driven outbreak management. The sensor shows 95% clinical sensitivity and 100% specificity (Ct<25), and overall sensitivity of 91% for combined symptomatic/asymptomatic cohort with wildtype SARS-CoV-2 or B.1.1.7 variant (N = 105, nasal/throat samples). The sensor correlates the N-protein levels to viral load, detecting high Ct values of ≈35, with no sample preparation steps, while outperforming the commercial rapid antigen tests. The current translational technology fills the gap in the workflow of rapid, point-of-care, and accurate diagnosis of COVID-19.
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Affiliation(s)
- Razieh Salahandish
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Laboratory of Advanced Biotechnologies for Health Assessments (LAB-HA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Jae Eun Hyun
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Fatemeh Haghayegh
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Hamed Osouli Tabrizi
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Shirin Moossavi
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, T2N 1N4, Canada
- International Microbiome Centre, Cumming School of Medicine, Health Sciences Centre, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Sultan Khetani
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Giancarlo Ayala-Charca
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Byron M Berenger
- Alberta Public Health Laboratory, Alberta Precision Laboratories, 3330 Hospital Drive, Calgary, AB, T2N 4W4, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Yan Dong Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators (BioSA), Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
| | - Amir Sanati Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Biomedical Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Cooper A, Girish V, Subramaniam AB. Osmotic Pressure Enables High-Yield Assembly of Giant Vesicles in Solutions of Physiological Ionic Strengths. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5579-5590. [PMID: 37021722 PMCID: PMC10116648 DOI: 10.1021/acs.langmuir.3c00457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Giant unilamellar vesicles (GUVs) are micrometer-scale minimal cellular mimics that are useful for bottom-up synthetic biology and drug delivery. Unlike assembly in low-salt solutions, assembly of GUVs in solutions with ionic concentrations of 100-150 mM Na/KCl (salty solutions) is challenging. Chemical compounds deposited on the substrate or incorporated into the lipid mixture could assist in the assembly of GUVs. Here, we investigate quantitatively the effects of temperature and chemical identity of six polymeric compounds and one small molecule compound on the molar yields of GUVs composed of three different lipid mixtures using high-resolution confocal microscopy and large data set image analysis. All the polymers moderately increased the yields of GUVs either at 22 or 37 °C, whereas the small molecule compound was ineffective. Low-gelling temperature agarose is the singular compound that consistently produces yields of GUVs of greater than 10%. We propose a free energy model of budding to explain the effects of polymers in assisting the assembly of GUVs. The osmotic pressure exerted on the membranes by the dissolved polymer balances the increased adhesion between the membranes, thus reducing the free energy for bud formation. Data obtained by modulating the ionic strength and ion valency of the solution shows that the evolution of the yield of GUVs supports our model's prediction. In addition, polymer-specific interactions with the substrate and the lipid mixture affects yields. The uncovered mechanistic insights provide a quantitative experimental and theoretical framework to guide future studies. Additionally, this work shows a facile means for obtaining GUVs in solutions of physiological ionic strengths.
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Affiliation(s)
- Alexis Cooper
- Department
of Chemistry and Biochemistry, University
of California, Merced, Merced, California 95343, United States
| | - Vaishnavi Girish
- Department
of Bioengineering, University of California,
Merced, Merced, California 95343, United States
| | - Anand Bala Subramaniam
- Department
of Bioengineering, University of California,
Merced, Merced, California 95343, United States
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29
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Mironov AA, Savin MA, Beznoussenko GV. COVID-19 Biogenesis and Intracellular Transport. Int J Mol Sci 2023; 24:ijms24054523. [PMID: 36901955 PMCID: PMC10002980 DOI: 10.3390/ijms24054523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
SARS-CoV-2 is responsible for the COVID-19 pandemic. The structure of SARS-CoV-2 and most of its proteins of have been deciphered. SARS-CoV-2 enters cells through the endocytic pathway and perforates the endosomes' membranes, and its (+) RNA appears in the cytosol. Then, SARS-CoV-2 starts to use the protein machines of host cells and their membranes for its biogenesis. SARS-CoV-2 generates a replication organelle in the reticulo-vesicular network of the zippered endoplasmic reticulum and double membrane vesicles. Then, viral proteins start to oligomerize and are subjected to budding within the ER exit sites, and its virions are passed through the Golgi complex, where the proteins are subjected to glycosylation and appear in post-Golgi carriers. After their fusion with the plasma membrane, glycosylated virions are secreted into the lumen of airways or (seemingly rarely) into the space between epithelial cells. This review focuses on the biology of SARS-CoV-2's interactions with cells and its transport within cells. Our analysis revealed a significant number of unclear points related to intracellular transport in SARS-CoV-2-infected cells.
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Affiliation(s)
- Alexander A. Mironov
- Department of Cell Biology, IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
- Correspondence:
| | - Maksim A. Savin
- The Department for Welding Production and Technology of Constructional Materials, Perm National Research Polytechnic University, Komsomolsky Prospekt, 29, 614990 Perm, Russia
| | - Galina V. Beznoussenko
- Department of Cell Biology, IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
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30
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Maghsood F, Ghorbani A, Yadegari H, Golsaz-Shirazi F, Amiri MM, Shokri F. SARS-CoV-2 nucleocapsid: Biological functions and implication for disease diagnosis and vaccine design. Rev Med Virol 2023; 33:e2431. [PMID: 36790816 DOI: 10.1002/rmv.2431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/16/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is transmitted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has affected millions of people all around the world, leading to more than 6.5 million deaths. The nucleocapsid (N) phosphoprotein plays important roles in modulating viral replication and transcription, virus-infected cell cycle progression, apoptosis, and regulation of host innate immunity. As an immunodominant protein, N protein induces strong humoral and cellular immune responses in COVID-19 patients, making it a key marker for studying N-specific B cell and T cell responses and the development of diagnostic serological assays and efficient vaccines. In this review, we focus on the structural and functional features and the kinetic and epitope mapping of B cell and T cell responses against SARS-CoV-2 N protein to extend our understanding on the development of sensitive and specific diagnostic immunological tests and effective vaccines.
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Affiliation(s)
- Faezeh Maghsood
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Ghorbani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Yadegari
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Forough Golsaz-Shirazi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Amiri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fazel Shokri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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31
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Peng X, Dela Cruz CS, Sharma L. Coronaviruses, Lysosomes, and Secondary Bacterial Infections: Coronaviruses Outsmart the Host. DNA Cell Biol 2023; 42:189-193. [PMID: 36763591 DOI: 10.1089/dna.2023.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Lysosomes are key organelles that contribute to homeostatic functions such as autophagy-mediated recycling of cellular components and innate immune response through phagocytosis-mediated pathogen killing during infections. Viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has developed unique adaptation to not only avoid lysosome-mediated destruction but also actively utilize lysosomal machinery to both enter and exit cells. To survive the highly hostile lysosomal environment, coronaviruses deacidify the lysosomes, potentially by manipulating H+ ion exchange across the lysosomal lumen, ensuring coronavirus survival. At the same time, this deacidification not only impairs cellular homeostatic functions such as autophagy but also renders the host susceptible to secondary bacterial infections. Furthermore, lysosomal enzymes promote extensive cell death and tissue damage during secondary bacterial infections. Thus, targeting lysosomal pathways provide a great opportunity to limit both viral replication and subsequent negative impact on host immunity against secondary bacterial infections.
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Affiliation(s)
- Xiaohua Peng
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Internal Medicine, Veterans Affairs Medical Center, West Haven, Connecticut, USA
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
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32
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Zheng Y, Gao C. Phase Separation: The Robust Modulator of Innate Antiviral Signaling and SARS-CoV-2 Infection. Pathogens 2023; 12:pathogens12020243. [PMID: 36839515 PMCID: PMC9962166 DOI: 10.3390/pathogens12020243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 has been a pandemic threat to human health and the worldwide economy, but efficient treatments are still lacking. Type I and III interferons are essential for controlling viral infection, indicating that antiviral innate immune signaling is critical for defense against viral infection. Phase separation, one of the basic molecular processes, governs multiple cellular activities, such as cancer progression, microbial infection, and signaling transduction. Notably, recent studies suggest that phase separation regulates antiviral signaling such as the RLR and cGAS-STING pathways. Moreover, proper phase separation of viral proteins is essential for viral replication and pathogenesis. These observations indicate that phase separation is a critical checkpoint for virus and host interaction. In this study, we summarize the recent advances concerning the regulation of antiviral innate immune signaling and SARS-CoV-2 infection by phase separation. Our review highlights the emerging notion that phase separation is the robust modulator of innate antiviral signaling and viral infection.
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33
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Chau BA, Chen V, Cochrane AW, Parent LJ, Mouland AJ. Liquid-liquid phase separation of nucleocapsid proteins during SARS-CoV-2 and HIV-1 replication. Cell Rep 2023; 42:111968. [PMID: 36640305 PMCID: PMC9790868 DOI: 10.1016/j.celrep.2022.111968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The leap of retroviruses and coronaviruses from animal hosts to humans has led to two ongoing pandemics and tens of millions of deaths worldwide. Retrovirus and coronavirus nucleocapsid proteins have been studied extensively as potential drug targets due to their central roles in virus replication, among which is their capacity to bind their respective genomic RNAs for packaging into nascent virions. This review focuses on fundamental studies of these nucleocapsid proteins and how their intrinsic abilities to condense through liquid-liquid phase separation (LLPS) contribute to viral replication. Therapeutic targeting of these condensates and methodological advances are also described to address future questions on how phase separation contributes to viral replication.
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Affiliation(s)
- Bao-An Chau
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Venessa Chen
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alan W Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leslie J Parent
- Division of Infectious Diseases and Epidemiology, Departments of Medicine and Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Lab, Lady Davis Institute at the Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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34
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Guan X, Yang Y, Du L. Advances in SARS-CoV-2 receptor-binding domain-based COVID-19 vaccines. Expert Rev Vaccines 2023; 22:422-439. [PMID: 37161869 PMCID: PMC10355161 DOI: 10.1080/14760584.2023.2211153] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023]
Abstract
INTRODUCTION The Coronavirus Disease 2019 (COVID-19) pandemic has caused devastating human and economic costs. Vaccination is an important step in controlling the pandemic. Severe acute respiratory coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, infects cells by binding a cellular receptor through the receptor-binding domain (RBD) within the S1 subunit of the spike (S) protein. Viral entry and membrane fusion are mediated by the S2 subunit. AREAS COVERED SARS-CoV-2 S protein, particularly RBD, serves as an important target for vaccines. Here we review the structure and function of SARS-CoV-2 S protein and its RBD, summarize current COVID-19 vaccines targeting the RBD, and outline potential strategies for improving RBD-based vaccines. Overall, this review provides important information that will facilitate rational design and development of safer and more effective COVID-19 vaccines. EXPERT OPINION The S protein of SARS-CoV-2 harbors numerous mutations, mostly in the RBD, resulting in multiple variant strains. Although many COVID-19 vaccines targeting the RBD of original virus strain (and previous variants) can prevent infection of these strains, their ability against recent dominant variants, particularly Omicron and its offspring, is significantly reduced. Collective efforts are needed to develop effective broad-spectrum vaccines to control current and future variants that have pandemic potential.
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Affiliation(s)
- Xiaoqing Guan
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Lanying Du
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
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35
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Li X, Yuan H, Li X, Wang H. Spike protein mediated membrane fusion during SARS-CoV-2 infection. J Med Virol 2023; 95:e28212. [PMID: 36224449 PMCID: PMC9874878 DOI: 10.1002/jmv.28212] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/15/2022] [Accepted: 10/10/2022] [Indexed: 01/27/2023]
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to public health and has quickly become a global concern. The infection of SARS-CoV-2 begins with the binding of its spike protein to the receptor-angiotensin-converting enzyme 2 (ACE2), which, after a series of conformation changes, results in the fusion of viral-cell membranes and the release of the viral RNA genome into the cytoplasm. In addition, infected host cells can express spike protein on their cell surface, which will interact with ACE2 on neighboring cells, leading to cell membrane fusion and the formation of multinucleated cells or syncytia. Both viral entry and syncytia formation are mediated by spike-ACE2 interaction and share some common mechanisms of membrane fusion. Here in this review, we will summarize our current understanding of spike-mediated membrane fusion, which may shed light on future broad-spectrum antiviral development.
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Affiliation(s)
- Xinyu Li
- Department of Pathogen Biology and ImmunologyXi'an Jiaotong University Health Science CenterXi'anChina
| | - Huijun Yuan
- Department of Pathogen Biology and ImmunologyXi'an Jiaotong University Health Science CenterXi'anChina
| | - Xiaozhen Li
- Department of Pathogen Biology and ImmunologyXi'an Jiaotong University Health Science CenterXi'anChina
| | - Hongliang Wang
- Department of Pathogen Biology and ImmunologyXi'an Jiaotong University Health Science CenterXi'anChina
- Key Laboratory of Environment and Genes Related to DiseasesXi'an Jiaotong UniversityXi'anChina
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36
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Bergner T, Zech F, Hirschenberger M, Stenger S, Sparrer KMJ, Kirchhoff F, Read C. Near-Native Visualization of SARS-CoV-2 Induced Membrane Remodeling and Virion Morphogenesis. Viruses 2022; 14:v14122786. [PMID: 36560790 PMCID: PMC9784144 DOI: 10.3390/v14122786] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Infection with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, leads to profound remodeling of cellular membranes, promoting viral replication and virion assembly. A full understanding of this drastic remodeling and the process of virion morphogenesis remains lacking. In this study, we applied room temperature transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) tomography to visualize the SARS-CoV-2 replication factory in Vero cells, and present our results in comparison with published cryo-EM studies. We obtained cryo-EM-like clarity of the ultrastructure by employing high-pressure freezing, freeze substitution (HPF-FS) and embedding, allowing room temperature visualization of double-membrane vesicles (DMVs) in a near-native state. In addition, our data illustrate the consecutive stages of virion morphogenesis and reveal that SARS-CoV-2 ribonucleoprotein assembly and membrane curvature occur simultaneously. Finally, we show the tethering of virions to the plasma membrane in 3D, and that accumulations of virus particles lacking spike protein in large vesicles are most likely not a result of defective virion assembly at their membrane. In conclusion, this study puts forward a room-temperature EM technique providing near-native ultrastructural information about SARS-CoV-2 replication, adding to our understanding of the interaction of this pandemic virus with its host cell.
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Affiliation(s)
- Tim Bergner
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Steffen Stenger
- Institute for Microbiology and Hygiene, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Clarissa Read
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany
- Correspondence:
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37
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Biondo C, Midiri A, Gerace E, Zummo S, Mancuso G. SARS-CoV-2 Infection in Patients with Cystic Fibrosis: What We Know So Far. Life (Basel) 2022; 12:2087. [PMID: 36556452 PMCID: PMC9786139 DOI: 10.3390/life12122087] [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: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Respiratory infections are the most common and most frequent diseases, especially in children and the elderly, characterized by a clear seasonality and with an incidence that usually tends to decrease with increasing age. These infections often resolve spontaneously, usually without the need for antibiotic treatment and/or with the possible use of symptomatic treatments aimed at reducing overproduction of mucus and decreasing coughing. However, when these infections occur in patients with weakened immune systems and/or underlying health conditions, their impact can become dramatic and in some cases life threatening. The rapid worldwide spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection has caused concern for everyone, becoming especially important for individuals with underlying lung diseases, such as CF patients, who have always paid close attention to implementing protective strategies to avoid infection. However, adult and pediatric CF patients contract coronavirus infection like everyone else. In addition, although numerous studies were published during the first wave of the pandemic on the risk for patients with cystic fibrosis (CF) to develop severe manifestations when infected with SARS-CoV-2, to date, a high risk has been found only for patients with poorer lung function and post-transplant status. In terms of preventive measures, vaccination remains key. The best protection for these patients is to strengthen preventive measures, such as social distancing and the use of masks. In this review, we aim to summarize and discuss recent advances in understanding the susceptibility of CF individuals to SARS-CoV-2 infection.
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Affiliation(s)
- Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
| | | | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy
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38
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SARS-CoV-2 Spike Protein Mutation at Cysteine-488 Impairs Its Golgi Localization and Intracellular S1/S2 Processing. Int J Mol Sci 2022; 23:ijms232415834. [PMID: 36555473 PMCID: PMC9779352 DOI: 10.3390/ijms232415834] [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: 10/08/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds to the cellular receptor-angiotensin-converting enzyme-2 (ACE2) as the first step in viral cell entry. SARS-CoV-2 spike protein expression in the ACE2-expressing cell surface induces cell-cell membrane fusion, thus forming syncytia. To exert its fusogenic activity, the spike protein is typically processed at a specific site (the S1/S2 site) by cellular proteases such as furin. The C488 residue, located at the spike-ACE2 interacting surface, is critical for the fusogenic and infectious roles of the SARS-CoV-2 spike protein. We have demonstrated that the C488 residue of the spike protein is involved in subcellular targeting and S1/S2 processing. C488 mutant spike localization to the Golgi apparatus and cell surface were impaired. Consequently, the S1/S2 processing of the spike protein, probed by anti-Ser-686-cleaved spike antibody, markedly decreased in C488 mutant spike proteins. Moreover, brefeldin-A-mediated endoplasmic-reticulum-to-Golgi traffic suppression also suppressed spike protein S1/S2 processing. As brefeldin A treatment and C488 mutation inhibited S1/S2 processing and syncytia formation, the C488 residue of spike protein is required for functional spike protein processing.
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39
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Carlson CR, Adly AN, Bi M, Howard CJ, Frost A, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. J Biol Chem 2022; 298:102560. [PMID: 36202211 PMCID: PMC9529352 DOI: 10.1016/j.jbc.2022.102560] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35 to 40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.
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Affiliation(s)
| | - Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Conor J Howard
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Adam Frost
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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40
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Jalloh S, Olejnik J, Berrigan J, Nisa A, Suder EL, Akiyama H, Lei M, Ramaswamy S, Tyagi S, Bushkin Y, Mühlberger E, Gummuluru S. CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses. PLoS Pathog 2022; 18:e1010479. [PMID: 36279285 PMCID: PMC9632919 DOI: 10.1371/journal.ppat.1010479] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 11/03/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
Exacerbated and persistent innate immune response marked by pro-inflammatory cytokine expression is thought to be a major driver of chronic COVID-19 pathology. Although macrophages are not the primary target cells of SARS-CoV-2 infection in humans, viral RNA and antigens in activated monocytes and macrophages have been detected in post-mortem samples, and dysfunctional monocytes and macrophages have been hypothesized to contribute to a protracted hyper-inflammatory state in COVID-19 patients. In this study, we demonstrate that CD169, a myeloid cell specific I-type lectin, facilitated ACE2-independent SARS-CoV-2 fusion and entry in macrophages. CD169-mediated SARS-CoV-2 entry in macrophages resulted in expression of viral genomic and subgenomic RNAs with minimal viral protein expression and no infectious viral particle release, suggesting a post-entry restriction of the SARS-CoV-2 replication cycle. Intriguingly this post-entry replication block was alleviated by exogenous ACE2 expression in macrophages. Restricted expression of viral genomic and subgenomic RNA in CD169+ macrophages elicited a pro-inflammatory cytokine expression (TNFα, IL-6 and IL-1β) in a RIG-I, MDA-5 and MAVS-dependent manner, which was suppressed by remdesivir treatment. These findings suggest that de novo expression of SARS-CoV-2 RNA in macrophages contributes to the pro-inflammatory cytokine signature and that blocking CD169-mediated ACE2 independent infection and subsequent activation of macrophages by viral RNA might alleviate COVID-19-associated hyperinflammatory response.
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Affiliation(s)
- Sallieu Jalloh
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Judith Olejnik
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Jacob Berrigan
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Annuurun Nisa
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Hisashi Akiyama
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Maohua Lei
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Sita Ramaswamy
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Suryaram Gummuluru
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
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41
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Chen D, Zhang H. Autophagy in SARS-CoV-2 infection. CURRENT OPINION IN PHYSIOLOGY 2022; 29:100596. [PMID: 36187896 PMCID: PMC9514017 DOI: 10.1016/j.cophys.2022.100596] [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] [Indexed: 11/17/2022]
Abstract
Severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) orchestrates host factors to remodel
endomembrane compartments for various steps of the infection cycle.
SARS-CoV-2 also intimately intersects with the catabolic autophagy
pathway during infection. In response to virus infection, autophagy acts
as an innate defensive system by delivering viral components/particles to
lysosomes for degradation. Autophagy also elicits antiviral immune
responses. SARS-CoV-2, like other positive-stranded RNA viruses, has
evolved various mechanisms to escape autophagic destruction and to hijack
the autophagic machinery for its own benefit. In this review, we will
focus on how the interplay between SARS-CoV-2 viral proteins and
autophagy promotes viral replication and transmission. We will also
discuss the pathogenic effects of SARS-CoV-2-elicited autophagy
dysregulation and pharmacological interventions targeting autophagy for
COVID-19 treatment.
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Affiliation(s)
- Di Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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42
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Li S, Zandi R. Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding. Viruses 2022; 14:2089. [PMID: 36298645 PMCID: PMC9611094 DOI: 10.3390/v14102089] [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: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022] Open
Abstract
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins: Envelope (E), Membrane (M), Nucleocapsid (N), and Spike (S), which self-assemble along with its RNA into the infectious virus by budding from intracellular lipid membranes. In this paper, we develop a model to explore the mechanisms of RNA condensation by structural proteins, protein oligomerization and cellular membrane-protein interactions that control the budding process and the ultimate virus structure. Using molecular dynamics simulations, we have deciphered how the positively charged N proteins interact and condense the very long genomic RNA resulting in its packaging by a lipid envelope decorated with structural proteins inside a host cell. Furthermore, considering the length of RNA and the size of the virus, we find that the intrinsic curvature of M proteins is essential for virus budding. While most current research has focused on the S protein, which is responsible for viral entry, and it has been motivated by the need to develop efficacious vaccines, the development of resistance through mutations in this crucial protein makes it essential to elucidate the details of the viral life cycle to identify other drug targets for future therapy. Our simulations will provide insight into the viral life cycle through the assembly of viral particles de novo and potentially identify therapeutic targets for future drug development.
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Affiliation(s)
- Siyu Li
- Songshan Lake Materials Laboratory, Dongguan 523808, China
| | - Roya Zandi
- Department of Physics and Astronomy, University of California Riverside, Riverside, CA 92521, USA
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43
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How many SARS-CoV-2 "viroporins" are really ion channels? Commun Biol 2022; 5:859. [PMID: 36008538 PMCID: PMC9411608 DOI: 10.1038/s42003-022-03669-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/01/2022] [Indexed: 11/23/2022] Open
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44
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Lai M, De Carli A, Filipponi C, Iacono E, La Rocca V, Lottini G, Piazza CR, Quaranta P, Sidoti M, Pistello M, Freer G. Lipid balance remodelling by human positive-strand RNA viruses and the contribution of lysosomes. Antiviral Res 2022; 206:105398. [PMID: 35985406 DOI: 10.1016/j.antiviral.2022.105398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/03/2022] [Accepted: 08/10/2022] [Indexed: 11/27/2022]
Abstract
A marked reorganization of internal membranes occurs in the cytoplasm of cells infected by single stranded positive-sense RNA viruses. Most cell compartments change their asset to provide lipids for membrane rearrangement into replication organelles, where to concentrate viral proteins and enzymes while hiding from pathogen pattern recognition molecules. Because the endoplasmic reticulum is a central hub for lipid metabolism, when viruses hijack the organelle to form their replication organelles, a cascade of events change the intracellular environment. This results in a marked increase in lipid consumption, both by lipolysis and lipophagy of lipid droplets. In addition, lipids are used to produce energy for viral replication. At the same time, inflammation is started by signalling lipids, where lysosomal processing plays a relevant role. This review is aimed at providing an overview on what takes place after human class IV viruses have released their genome into the host cell and the consequences on lipid metabolism, including lysosomes.
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Affiliation(s)
- Michele Lai
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Alessandro De Carli
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy; Department of Medical Biotechnologies, University of Siena, Italy.
| | - Carolina Filipponi
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Elena Iacono
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Veronica La Rocca
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy; Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy.
| | - Giulia Lottini
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy; Department of Medical Biotechnologies, University of Siena, Italy.
| | - Carmen Rita Piazza
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy; Department of Medical Biotechnologies, University of Siena, Italy.
| | - Paola Quaranta
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Maria Sidoti
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Mauro Pistello
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
| | - Giulia Freer
- Centro Retrovirus, Dipartimento di Ricerca Traslazionale, Strada Statale del Brennero 2, University of Pisa, Pisa, 56127, Italy.
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45
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Roden C, Dai Y, Giannetti C, Seim I, Lee M, Sealfon R, McLaughlin G, Boerneke M, Iserman C, Wey S, Ekena J, Troyanskaya O, Weeks K, You L, Chilkoti A, Gladfelter A. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res 2022; 50:8168-8192. [PMID: 35871289 PMCID: PMC9371935 DOI: 10.1093/nar/gkac596] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 12/11/2022] Open
Abstract
Nucleocapsid protein (N-protein) is required for multiple steps in betacoronaviruses replication. SARS-CoV-2-N-protein condenses with specific viral RNAs at particular temperatures making it a powerful model for deciphering RNA sequence specificity in condensates. We identify two separate and distinct double-stranded, RNA motifs (dsRNA stickers) that promote N-protein condensation. These dsRNA stickers are separately recognized by N-protein's two RNA binding domains (RBDs). RBD1 prefers structured RNA with sequences like the transcription-regulatory sequence (TRS). RBD2 prefers long stretches of dsRNA, independent of sequence. Thus, the two N-protein RBDs interact with distinct dsRNA stickers, and these interactions impart specific droplet physical properties that could support varied viral functions. Specifically, we find that addition of dsRNA lowers the condensation temperature dependent on RBD2 interactions and tunes translational repression. In contrast RBD1 sites are sequences critical for sub-genomic (sg) RNA generation and promote gRNA compression. The density of RBD1 binding motifs in proximity to TRS-L/B sequences is associated with levels of sub-genomic RNA generation. The switch to packaging is likely mediated by RBD1 interactions which generate particles that recapitulate the packaging unit of the virion. Thus, SARS-CoV-2 can achieve biochemical complexity, performing multiple functions in the same cytoplasm, with minimal protein components based on utilizing multiple distinct RNA motifs that control N-protein interactions.
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Affiliation(s)
- Christine A Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Catherine A Giannetti
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Ian Seim
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Rachel Sealfon
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Grace A McLaughlin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark A Boerneke
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Christiane Iserman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel A Wey
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Joanne L Ekena
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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46
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Pepe A, Pietropaoli S, Vos M, Barba-Spaeth G, Zurzolo C. Tunneling nanotubes provide a route for SARS-CoV-2 spreading. SCIENCE ADVANCES 2022; 8:eabo0171. [PMID: 35857849 PMCID: PMC9299553 DOI: 10.1126/sciadv.abo0171] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Neurological manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection represent a major issue in long coronavirus disease. How SARS-CoV-2 gains access to the brain and how infection leads to neurological symptoms are not clear because the principal means of viral entry by endocytosis, the angiotensin-converting enzyme 2 receptor, are barely detectable in the brain. We report that human neuronal cells, nonpermissive to infection through the endocytic pathway, can be infected when cocultured with permissive infected epithelial cells. SARS-CoV-2 induces the formation of tunneling nanotubes (TNTs) and exploits this route to spread to uninfected cells. In cellulo correlative fluorescence and cryo-electron tomography reveal that SARS-CoV-2 is associated with TNTs between permissive cells. Furthermore, multiple vesicular structures such as double-membrane vesicles, sites of viral replication, are observed inside TNTs between permissive and nonpermissive cells. Our data highlight a previously unknown mechanism of SARS-CoV-2 spreading, likely used as a route to invade nonpermissive cells and potentiate infection in permissive cells.
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Affiliation(s)
- Anna Pepe
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et Infection, Institut Pasteur, CNRS UMR3691, Université Paris Cité, 75015 Paris, France
| | - Stefano Pietropaoli
- Unité de Virologie Structurale, CNRS UMR 3569 Département de Virologie, Institut Pasteur 28 rue du Docteur Roux, Université Paris Cité, 75015 Paris, France
- Catalent Pharma Solutions, Strada Provinciale 12 Casilina, 41, 03012 Anagni, Frosinone, Italy
| | - Matthijn Vos
- Plateforme Technologique Nanoimagerie Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Giovanna Barba-Spaeth
- Unité de Virologie Structurale, CNRS UMR 3569 Département de Virologie, Institut Pasteur 28 rue du Docteur Roux, Université Paris Cité, 75015 Paris, France
| | - Chiara Zurzolo
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et Infection, Institut Pasteur, CNRS UMR3691, Université Paris Cité, 75015 Paris, France
- Corresponding author.
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47
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Deroubaix A, Kramvis A. Imaging Techniques: Essential Tools for the Study of SARS-CoV-2 Infection. Front Cell Infect Microbiol 2022; 12:794264. [PMID: 35937687 PMCID: PMC9355083 DOI: 10.3389/fcimb.2022.794264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/21/2022] [Indexed: 01/08/2023] Open
Abstract
The world has seen the emergence of a new virus in 2019, SARS-CoV-2, causing the COVID-19 pandemic and millions of deaths worldwide. Microscopy can be much more informative than conventional detection methods such as RT-PCR. This review aims to present the up-to-date microscopy observations in patients, the in vitro studies of the virus and viral proteins and their interaction with their host, discuss the microscopy techniques for detection and study of SARS-CoV-2, and summarize the reagents used for SARS-CoV-2 detection. From basic fluorescence microscopy to high resolution techniques and combined technologies, this article shows the power and the potential of microscopy techniques, especially in the field of virology.
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Affiliation(s)
- Aurélie Deroubaix
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Life Sciences Imaging Facility, University of the Witwatersrand, Johannesburg, South Africa
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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48
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Chen D, Zhao YG, Zhang H. Endomembrane remodeling in SARS-CoV-2 infection. CELL INSIGHT 2022; 1:100031. [PMID: 37193051 PMCID: PMC9112566 DOI: 10.1016/j.cellin.2022.100031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/18/2022]
Abstract
During severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the viral proteins intimately interact with host factors to remodel the endomembrane system at various steps of the viral lifecycle. The entry of SARS-CoV-2 can be mediated by endocytosis-mediated internalization. Virus-containing endosomes then fuse with lysosomes, in which the viral S protein is cleaved to trigger membrane fusion. Double-membrane vesicles generated from the ER serve as platforms for viral replication and transcription. Virions are assembled at the ER-Golgi intermediate compartment and released through the secretory pathway and/or lysosome-mediated exocytosis. In this review, we will focus on how SARS-CoV-2 viral proteins collaborate with host factors to remodel the endomembrane system for viral entry, replication, assembly and egress. We will also describe how viral proteins hijack the host cell surveillance system-the autophagic degradation pathway-to evade destruction and benefit virus production. Finally, potential antiviral therapies targeting the host cell endomembrane system will be discussed.
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Affiliation(s)
- Di Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan G. Zhao
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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49
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Carlson CR, Adly AN, Bi M, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.23.493138. [PMID: 35664996 PMCID: PMC9164447 DOI: 10.1101/2022.05.23.493138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The nucleocapsid (N) protein of coronaviruses is responsible for compaction of the ∼30-kb RNA genome in the ∼100-nm virion. Cryo-electron tomography suggests that each virion contains 35-40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined with viral RNA fragments in vitro, forms cylindrical 15-nm particles similar to the vRNP structures observed within coronavirus virions. These vRNPs form in the presence of stem-loop-containing RNA and depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine (SR) region weakens these interactions and disrupts vRNP assembly. We propose that unmodified N binds stem-loop-rich regions in genomic RNA to form compact vRNP complexes within the nucleocapsid, while phosphorylated N maintains uncompacted viral RNA to promote the protein's transcriptional function.
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Affiliation(s)
| | - Armin N. Adly
- Department of Physiology, University of California, San Francisco CA 94143
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - David O. Morgan
- Department of Physiology, University of California, San Francisco CA 94143
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50
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Evidence for the role of Rab11-positive recycling endosomes as intermediates in coronavirus egress from epithelial cells. Histochem Cell Biol 2022; 158:241-251. [PMID: 35604431 PMCID: PMC9124743 DOI: 10.1007/s00418-022-02115-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2022] [Indexed: 12/19/2022]
Abstract
AbstractAfter their assembly by budding into the lumen of the intermediate compartment (IC) at the endoplasmic reticulum (ER)–Golgi interface, coronaviruses (CoVs) are released from their host cells following a pathway that remains poorly understood. The traditional view that CoV exit occurs via the constitutive secretory route has recently been questioned by studies suggesting that this process involves unconventional secretion. Here, using the avian infectious bronchitis virus (IBV) as a well-established model virus, we have applied confocal microscopy to investigate the pathway of CoV egress from epithelial Vero cells. We report a novel effect of IBV infection on cellular endomembranes, namely, the compaction of the pericentrosomal endocytic recycling compartment (ERC) defined by the GTPase Rab11, which coincides with the previously described Golgi fragmentation, as well as virus release. Despite Golgi disassembly, the IC elements containing the major IBV membrane protein (M)—which mostly associates with newly formed virus particles—maintain their close spatial connection with the Rab11-positive endocytic recycling system. Moreover, partial colocalization of the M protein with Rab11 was observed, whereas M displayed negligible overlap with LAMP-1, indicating that IBV egress does not occur via late endosomes or lysosomes. Synchronization of virus release using temperature-shift protocols was accompanied by increased colocalization of M and Rab11 in vesicular and vacuolar structures in the pericentrosomal region and at the cell periphery, most likely representing IBV-containing transport carriers. In conclusion, these results add CoVs to the growing list of viruses exploiting the endocytic recycling apparatus defined by Rab11 for their assembly and/or release.
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