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Bostancıklıoğlu M, İğci M, Ulaşlı M. Nigella sativa, Anthemis hyaline and Citrus sinensis extracts reduce SARS-CoV-2 replication by fluctuating Rho GTPase, PI3K-AKT, and MAPK/ERK pathways in HeLa-CEACAM1a cells. Gene 2024; 911:148366. [PMID: 38485035 DOI: 10.1016/j.gene.2024.148366] [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: 01/07/2024] [Revised: 02/18/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Traditional remedies have long utilized Anthemis hyaline, Nigella sativa, and Citrus sinensis peel extracts as treatments for microbial infections. This study aimed to investigate the influence of Anthemis hyaline, Nigella sativa, and Citrus sinensis extracts on coronavirus replication and apoptosis-related pathways. HeLa-CEACAM1a cells were exposed to mouse hepatitis virus-A59. After viral inoculation, the mRNA levels of 36 genes were quantified using a Fluidigm Dynamic Array nanofluidic chip. IL-8 level and intracellular Ca2+ concentration was measured, and viral titer was assessed by the TCID50/ml assay to detect the extent of infection. Treatment with Nigella sativa extract surged the inflammatory cytokine IL-8 level at both 24 and 48-hour. Changes in gene expression were notable for RHOA, VAV3, ROCK2, CFL1, RASA1, and MPRIP genes following treatment with any of the extracts. The addition of Anthemis hyaline, Nigella sativa, or Citrus sinensis extracts to coronavirus-infected cells reduced viral presence, with Anthemis hyaline extract leading to a virtually undetectable viral load at 6- and 8-hours after infection. While all treatments influenced IL-8 production and viral levels, Anthemis hyaline extract displayed the most pronounced reduction in viral load. Consequently, Anthemis hyaline extract emerges as the most promising agent, harboring potential therapeutic compounds.
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Affiliation(s)
- Mehmet Bostancıklıoğlu
- Department of Physiology, Faculty of Medicine, Gaziantep University, 27310 Gaziantep, Turkey; Institute of Experimental and Clinical Research, Pole of Endocrinology, Diabetes and Nutrition, Université Catholique de Louvain, Brussels, Belgium
| | - Mehri İğci
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, 27310 Gaziantep, Turkey
| | - Mustafa Ulaşlı
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, 27310 Gaziantep, Turkey.
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Li M, Hou Y, Zhou Y, Yang Z, Zhao H, Jian T, Yu Q, Zeng F, Liu X, Zhang Z, Zhao YG. LLPS of FXR proteins drives replication organelle clustering for β-coronaviral proliferation. J Cell Biol 2024; 223:e202309140. [PMID: 38587486 PMCID: PMC11001562 DOI: 10.1083/jcb.202309140] [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: 09/27/2023] [Revised: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 04/09/2024] Open
Abstract
β-Coronaviruses remodel host endomembranes to form double-membrane vesicles (DMVs) as replication organelles (ROs) that provide a shielded microenvironment for viral RNA synthesis in infected cells. DMVs are clustered, but the molecular underpinnings and pathophysiological functions remain unknown. Here, we reveal that host fragile X-related (FXR) family proteins (FXR1/FXR2/FMR1) are required for DMV clustering induced by expression of viral non-structural proteins (Nsps) Nsp3 and Nsp4. Depleting FXRs results in DMV dispersion in the cytoplasm. FXR1/2 and FMR1 are recruited to DMV sites via specific interaction with Nsp3. FXRs form condensates driven by liquid-liquid phase separation, which is required for DMV clustering. FXR1 liquid droplets concentrate Nsp3 and Nsp3-decorated liposomes in vitro. FXR droplets facilitate recruitment of translation machinery for efficient translation surrounding DMVs. In cells depleted of FXRs, SARS-CoV-2 replication is significantly attenuated. Thus, SARS-CoV-2 exploits host FXR proteins to cluster viral DMVs via phase separation for efficient viral replication.
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Affiliation(s)
- Meng Li
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Yali Hou
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Yuzheng Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Zhenni Yang
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Hongyu Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Tao Jian
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Kowloon, P.R. China
| | - Qianxi Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Fuxing Zeng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Xiaotian Liu
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, P.R. China
| | - Yan G. Zhao
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P.R. China
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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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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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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [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: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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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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Lapierre LA, Roland JT, Manning EH, Caldwell C, Glenn HL, Vidalain PO, Tangy F, Hogue BG, de Haan CAM, Goldenring JR. Coronavirus M Protein Trafficking in Epithelial Cells Utilizes a Myosin Vb Splice Variant and Rab10. Cells 2024; 13:126. [PMID: 38247817 PMCID: PMC10814003 DOI: 10.3390/cells13020126] [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: 12/02/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The membrane (M) glycoprotein of coronaviruses (CoVs) serves as the nidus for virion assembly. Using a yeast two-hybrid screen, we identified the interaction of the cytosolic tail of Murine Hepatitis Virus (MHV-CoV) M protein with Myosin Vb (MYO5B), specifically with the alternative splice variant of cellular MYO5B including exon D (MYO5B+D), which mediates interaction with Rab10. When co-expressed in human lung epithelial A549 and canine kidney epithelial MDCK cells, MYO5B+D co-localized with the MHV-CoV M protein, as well as with the M proteins from Porcine Epidemic Diarrhea Virus (PEDV-CoV), Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome 2 (SARS-CoV-2). Co-expressed M proteins and MYO5B+D co-localized with endogenous Rab10 and Rab11a. We identified point mutations in MHV-CoV M that blocked the interaction with MYO5B+D in yeast 2-hybrid assays. One of these point mutations (E121K) was previously shown to block MHV-CoV virion assembly and its interaction with MYO5B+D. The E to K mutation at homologous positions in PEDV-CoV, MERS-CoV and SARS-CoV-2 M proteins also blocked colocalization with MYO5B+D. The knockdown of Rab10 blocked the co-localization of M proteins with MYO5B+D and was rescued by re-expression of CFP-Rab10. Our results suggest that CoV M proteins traffic through Rab10-containing systems, in association with MYO5B+D.
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Affiliation(s)
- Lynne A. Lapierre
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Nashville VA Medical Center, Nashville, TN 37212, USA
| | - Joseph T. Roland
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Elizabeth H. Manning
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Nashville VA Medical Center, Nashville, TN 37212, USA
| | - Catherine Caldwell
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Nashville VA Medical Center, Nashville, TN 37212, USA
| | - Honor L. Glenn
- Biodesign Institute Center for Immunotherapy, Vaccines & Virotherapy, Tempe, AZ 85287, USA; (H.L.G.); (B.G.H.)
| | - Pierre-Olivier Vidalain
- Equipe Infections Virales, Métabolisme et Immunité, Centre International de Recherche en Infectiologie (CIRI), Univ. Lyon, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France;
- Unité Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR3569, 75015 Paris, France
| | - Frederic Tangy
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR3569, 75015 Paris, France;
| | - Brenda G. Hogue
- Biodesign Institute Center for Immunotherapy, Vaccines & Virotherapy, Tempe, AZ 85287, USA; (H.L.G.); (B.G.H.)
- Center for Applied Structural Discovery, Biodesign Institute, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - C. A. M. de Haan
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Section Virology, University of Utrecht, 3584 CS Utrecht, The Netherlands;
| | - James R. Goldenring
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (L.A.L.); (J.T.R.); (E.H.M.); (C.C.)
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Nashville VA Medical Center, Nashville, TN 37212, USA
- Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Aguilera MO, Delgui LR, Reggiori F, Romano PS, Colombo MI. Autophagy as an innate immunity response against pathogens: a Tango dance. FEBS Lett 2024; 598:140-166. [PMID: 38101809 DOI: 10.1002/1873-3468.14788] [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: 08/23/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023]
Abstract
Intracellular infections as well as changes in the cell nutritional environment are main events that trigger cellular stress responses. One crucial cell response to stress conditions is autophagy. During the last 30 years, several scenarios involving autophagy induction or inhibition over the course of an intracellular invasion by pathogens have been uncovered. In this review, we will present how this knowledge was gained by studying different microorganisms. We intend to discuss how the cell, via autophagy, tries to repel these attacks with the objective of destroying the intruder, but also how some pathogens have developed strategies to subvert this. These two fates can be compared with a Tango, a dance originated in Buenos Aires, Argentina, in which the partner dancers are in close connection. One of them is the leader, embracing and involving the partner, but the follower may respond escaping from the leader. This joint dance is indeed highly synchronized and controlled, perfectly reflecting the interaction between autophagy and microorganism.
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Affiliation(s)
- Milton O Aguilera
- Laboratorio de Mecanismos Moleculares Implicados en el Tráfico Vesicular y la Autofagia-Instituto de Histología y Embriología (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
- Facultad de Odontología, Microbiología, Parasitología e Inmunología, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Laura R Delgui
- Instituto de Histología y Embriología de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro Universitario M5502JMA, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Denmark
| | - Patricia S Romano
- Laboratorio de Biología de Trypanosoma cruzi y la célula hospedadora - Instituto de Histología y Embriología de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro Universitario M5502JMA, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
- Facultad de Ciencias Médicas, Centro Universitario M5502JMA, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - María I Colombo
- Laboratorio de Mecanismos Moleculares Implicados en el Tráfico Vesicular y la Autofagia-Instituto de Histología y Embriología (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
- Facultad de Ciencias Médicas, Centro Universitario M5502JMA, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
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9
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Zimmermann L, Zhao X, Makroczyova J, Wachsmuth-Melm M, Prasad V, Hensel Z, Bartenschlager R, Chlanda P. SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle. Nat Commun 2023; 14:7894. [PMID: 38036567 PMCID: PMC10689437 DOI: 10.1038/s41467-023-43666-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus replication is associated with the remodeling of cellular membranes, resulting in the formation of double-membrane vesicles (DMVs). A DMV-spanning pore was identified as a putative portal for viral RNA. However, the exact components and the structure of the SARS-CoV-2 DMV pore remain to be determined. Here, we investigate the structure of the DMV pore by in situ cryo-electron tomography combined with subtomogram averaging. We identify non-structural protein (nsp) 3 and 4 as minimal components required for the formation of a DMV-spanning pore, which is dependent on nsp3-4 proteolytic cleavage. In addition, we show that Mac2-Mac3-DPUP-Ubl2 domains are critical for nsp3 oligomerization and crown integrity which influences membrane curvature required for biogenesis of DMVs. Altogether, SARS-CoV-2 nsp3-4 have a dual role by driving the biogenesis of replication organelles and assembly of DMV-spanning pores which we propose here to term replicopores.
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Affiliation(s)
- Liv Zimmermann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Xiaohan Zhao
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Vibhu Prasad
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, 2780-157, Oeiras, Portugal
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, 69120, Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany.
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10
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Bai L, Zhang R, Zheng H, Zhang Z, Zhang Z, Li Y. Seneca Valley Virus Degrades STING via PERK and ATF6-Mediated Reticulophagy. Viruses 2023; 15:2209. [PMID: 38005886 PMCID: PMC10674438 DOI: 10.3390/v15112209] [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: 09/28/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Seneca Valley Virus (SVV), a member of the Picornaviridae family, is an emerging porcine virus that can cause vesicular disease in pigs. However, the immune evasion mechanism of SVV remains unclear, as does its interaction with other pathways. STING (Stimulator of interferon genes) is typically recognized as a critical factor in innate immune responses to DNA virus infection, but its role during SVV infection remains poorly understood. In the present study, we observed that STING was degraded in SVV-infected PK-15 cells, and SVV replication in the cells was affected when STING was knockdown or overexpressed. The STING degradation observed was blocked when the SVV-induced autophagy was inhibited by using autophagy inhibitors (Chloroquine, Bafilomycin A1) or knockdown of autophagy related gene 5 (ATG5), suggesting that SVV-induced autophagy is responsible for STING degradation. Furthermore, the STING degradation was inhibited when reticulophagy regulator 1 (FAM134B), a reticulophagy related receptor, was knocked down, indicating that SVV infection induces STING degradation via reticulophagy. Further study showed that in eukaryotic translation initiation factor 2 alpha kinase 3 (PERK)/activating transcription factor 6 (ATF6) deficient cells, SVV infection failed to induce reticulophagy-medaited STING degradation, indicating that SVV infection caused STING degradation via PERK/ATF6-mediated reticulophagy. Notably, blocking reticulophagy effectively hindered SVV replication. Overall, our study suggested that SVV infection resulted in STING degradation via PERK and ATF6-mediated reticulophagy, which may be an immune escape strategy of SVV. This finding improves the understanding of the intricate interplay between viruses and their hosts and provides a novel strategy for the development of novel antiviral drugs.
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Affiliation(s)
- Ling Bai
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; (L.B.); (H.Z.); (Z.Z.)
| | - Rui Zhang
- College of Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China;
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; (L.B.); (H.Z.); (Z.Z.)
| | - Zhixiong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; (L.B.); (H.Z.); (Z.Z.)
| | - Zhidong Zhang
- College of Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China;
| | - Yanmin Li
- College of Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu 610041, China;
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11
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Li J, Gui Q, Liang FX, Sall J, Zhang Q, Duan Y, Dhabaria A, Askenazi M, Ueberheide B, Stapleford KA, Pagano M. The REEP5/TRAM1 complex binds SARS-CoV-2 NSP3 and promotes virus replication. J Virol 2023; 97:e0050723. [PMID: 37768083 PMCID: PMC10617467 DOI: 10.1128/jvi.00507-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Generation of virus-host protein-protein interactions (PPIs) maps may provide clues to uncover SARS-CoV-2-hijacked cellular processes. However, these PPIs maps were created by expressing each viral protein singularly, which does not reflect the life situation in which certain viral proteins synergistically interact with host proteins. Our results reveal the host-viral protein-protein interactome of SARS-CoV-2 NSP3, NSP4, and NSP6 expressed individually or in combination. Furthermore, REEP5/TRAM1 complex interacts with NSP3 at ROs and promotes viral replication. The significance of our research is identifying virus-host interactions that may be targeted for therapeutic intervention.
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Affiliation(s)
- Jie Li
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Qi Gui
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Feng-Xia Liang
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Joseph Sall
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Yatong Duan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- William A. Shine Great Neck South High School, Lake Success, New York, USA
| | - Avantika Dhabaria
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Biomedical Hosting LLC, Arlington, Massachusetts, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, New York, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, New York, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, New York, USA
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12
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Luo W, Qi H, Huang Z, Guo M, Peng D, Yang Z, Fan Z, Wang Q, Qin Q, Yang M, Lee X. Autophagy induced by Cyprinid herpesvirus 3 (CyHV-3) facilitated intracellular viral replication and extracellular viral yields in common carp brain cells. FISH & SHELLFISH IMMUNOLOGY 2023; 141:109049. [PMID: 37678483 DOI: 10.1016/j.fsi.2023.109049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023]
Abstract
Autophagy is a conservative and important process that exists in all eukaryotic cells in nature. Cyprinid herpesvirus 3 (CyHV-3), also known as KHV (Koi Herpesvirus), is a pathogen that mainly infecting common carp and koi. In the present study, we identified the CcLC3B gene, with a length of 379 bp and displaying a close evolutionary relationship with other sixteen different species, the tissue distribution and expression pattern of CcLC3 were also identified. We found that CyHV-3 infection could promote autophagy in CCB cells at the early stage but inhibit autophagy at the late stage by using confocal fluorescence microscopy, transmission electron microscopy and western blotting. And we measured the protein levels associated with the Akt/mTOR signalling pathway, intracellular replication of CyHV-3 at the mRNA and protein levels as well as viral titters. Collectively, the results taken together suggested that CyHV-3 infection could promote autophagy in CCB cells at the early stage but inhibit autophagy at the late stage via mTOR and that promoting autophagy could facilitate CyHV-3 intracellular replication and extracellular viral yields in CCB cells. These findings revealed the relationship between CyHV-3 and autophagy and provided a novel treatment strategy targeting the autophagy signalling pathway against CyHV-3 infection.
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Affiliation(s)
- Wei Luo
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Hemei Qi
- Guangzhou Jinan Biomedicine Research and Development Centre, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, PR China
| | - Zhihong Huang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Min Guo
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Dikuang Peng
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Zimin Yang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Zihan Fan
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Qing Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510380, Guangdong, China
| | - Qiwei Qin
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China
| | - Min Yang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China.
| | - Xuezhu Lee
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bio Resource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China.
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13
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Zhang J, Zhu Y, Wang X, Wang J. 25-hydroxycholesterol: an integrator of antiviral ability and signaling. Front Immunol 2023; 14:1268104. [PMID: 37781400 PMCID: PMC10533924 DOI: 10.3389/fimmu.2023.1268104] [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: 07/27/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Cholesterol, as an important component in mammalian cells, is efficient for viral entry, replication, and assembly. Oxysterols especially hydroxylated cholesterols are recognized as novel regulators of the innate immune response. The antiviral ability of 25HC (25-Hydroxycholesterol) is uncovered due to its role as a metabolic product of the interferon-stimulated gene CH25H (cholesterol-25-hydroxylase). With the advancement of research, the biological functions of 25HC and its structural functions have been interpreted gradually. Furthermore, the underlying mechanisms of antiviral effect of 25HC are not only limited to interferon regulation. Taken up by the special biosynthetic ways and structure, 25HC contributes to modulate not only the cholesterol metabolism but also autophagy and inflammation by regulating signaling pathways. The outcome of modulation by 25HC seems to be largely dependent on the cell types, viruses and context of cell microenvironments. In this paper, we review the recent proceedings on the regulatory effect of 25HC on interferon-independent signaling pathways related to its antiviral capacity and its putative underlying mechanisms.
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Affiliation(s)
- Jialu Zhang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- College of Veterinary Medicine, Sanya Institute of China Agricultural University, Sanya, China
| | - Yaohong Zhu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- College of Veterinary Medicine, Sanya Institute of China Agricultural University, Sanya, China
| | - Xiaojia Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- College of Veterinary Medicine, Sanya Institute of China Agricultural University, Sanya, China
| | - Jiufeng Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- College of Veterinary Medicine, Sanya Institute of China Agricultural University, Sanya, China
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14
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Yang Y, Chen H, Zhang C, Shin HJ, Qian Y, Jung YS. HDAC-Specific Inhibitors Induce the Release of Porcine Epidemic Diarrhea Virus via the COPII-Coated Vesicles. Viruses 2023; 15:1874. [PMID: 37766280 PMCID: PMC10534748 DOI: 10.3390/v15091874] [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: 07/01/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is an alpha-coronavirus causing acute diarrhea and high mortality in neonatal suckling piglets, resulting in huge economic losses for the global swine industry. The replication, assembly and cell egression of PEDV, an enveloped RNA virus, are mediated via altered intracellular trafficking. The underlying mechanisms of PEDV secretion are poorly understood. In this study, we found that the histone deacetylase (HDAC)-specific inhibitors, trichostatin A (TSA) and sodium butyrate (NaB), facilitate the secretion of infectious PEDV particles without interfering with its assembly. We found that PEDV N protein and its replicative intermediate dsRNA colocalize with coat protein complex II (COPII)-coated vesicles. We also showed that the colocalization of PEDV and COPII is enhanced by the HDAC-specific inhibitors. In addition, ultrastructural analysis revealed that the HDAC-specific inhibitors promote COPII-coated vesicles carrying PEDV virions and the secretion of COPII-coated vesicles. Consistently, HDAC-specific inhibitors-induced PEDV particle secretion was abolished by Sec24B knockdown, implying that the HDAC-specific inhibitors-mediated COPII-coated vesicles are required for PEDV secretion. Taken together, our findings provide initial evidence suggesting that PEDV virions can assemble in the endoplasmic reticulum (ER) and bud off from the ER in the COPII-coated vesicles. HDAC-specific inhibitors promote PEDV release by hijacking the COPII-coated vesicles.
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Affiliation(s)
- Ying Yang
- One Health Laboratory, Jiangsu Foreign Expert Workstation, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Chen
- One Health Laboratory, Jiangsu Foreign Expert Workstation, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Caisheng Zhang
- One Health Laboratory, Jiangsu Foreign Expert Workstation, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Hyun-Jin Shin
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Yingjuan Qian
- One Health Laboratory, Jiangsu Foreign Expert Workstation, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Veterinary Bio-Pharmaceutical, Taizhou 225300, China
| | - Yong-Sam Jung
- One Health Laboratory, Jiangsu Foreign Expert Workstation, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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15
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Williams JM, Chen YJ, Cho WJ, Tai AW, Tsai B. Reticulons promote formation of ER-derived double-membrane vesicles that facilitate SARS-CoV-2 replication. J Cell Biol 2023; 222:e202203060. [PMID: 37093123 PMCID: PMC10130743 DOI: 10.1083/jcb.202203060] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/24/2022] [Accepted: 04/06/2023] [Indexed: 04/25/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiologic agent for the global COVID-19 pandemic, triggers the formation of endoplasmic reticulum (ER)-derived replication organelles, including double-membrane vesicles (DMVs), in the host cell to support viral replication. Here, we clarify how SARS-CoV-2 hijacks host factors to construct the DMVs. We show that the ER morphogenic proteins reticulon-3 (RTN3) and RTN4 help drive DMV formation, enabling viral replication, which leads to productive infection. Different SARS-CoV-2 variants, including the delta variant, use the RTN-dependent pathway to promote infection. Mechanistically, our results reveal that the membrane-embedded reticulon homology domain (RHD) of the RTNs is sufficient to functionally support viral replication and physically engage NSP3 and NSP4, two viral non-structural membrane proteins known to induce DMV formation. Our findings thus identify the ER morphogenic RTN3 and RTN4 membrane proteins as host factors that help promote the biogenesis of SARS-CoV-2-induced DMVs, which can act as viral replication platforms.
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Affiliation(s)
- Jeffrey M. Williams
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yu-Jie Chen
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Woo Jung Cho
- Biomedical Research Core Facilities, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andrew W. Tai
- Department of Internal Medicine and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
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16
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Zimmermann L, Chlanda P. Cryo-electron tomography of viral infection - from applications to biosafety. Curr Opin Virol 2023; 61:101338. [PMID: 37348443 DOI: 10.1016/j.coviro.2023.101338] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/25/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
Cellular cryo-electron tomography (cryo-ET) offers 3D snapshots at molecular resolution capturing pivotal steps during viral infection. However, tomogram quality depends on the vitrification level of the sample and its thickness. In addition, mandatory inactivation protocols to assure biosafety when handling highly pathogenic viruses during cryo-ET can compromise sample preservation. Here, we focus on different strategies applied in cryo-ET and discuss their advantages and limitations with reference to severe acute respiratory syndrome coronavirus 2 studies. We highlight the importance of virus-like particle (VLP) and replicon systems to study virus assembly and replication in a cellular context without inactivation protocols. We discuss the application of chemical fixation and different irradiation methods in cryo-ET sample preparation and acquisition workflows.
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Affiliation(s)
- Liv Zimmermann
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
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17
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Shi D, Zhou L, Shi H, Zhang J, Zhang J, Zhang L, Liu D, Feng T, Zeng M, Chen J, Zhang X, Xue M, Jing Z, Liu J, Ji Z, He H, Guo L, Wu Y, Ma J, Feng L. Autophagy is induced by swine acute diarrhea syndrome coronavirus through the cellular IRE1-JNK-Beclin 1 signaling pathway after an interaction of viral membrane-associated papain-like protease and GRP78. PLoS Pathog 2023; 19:e1011201. [PMID: 36888569 PMCID: PMC9994726 DOI: 10.1371/journal.ppat.1011201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
Autophagy plays an important role in the infectious processes of diverse pathogens. For instance, cellular autophagy could be harnessed by viruses to facilitate replication. However, it is still uncertain about the interplay of autophagy and swine acute diarrhea syndrome coronavirus (SADS-CoV) in cells. In this study, we reported that SADS-CoV infection could induce a complete autophagy process both in vitro and in vivo, and an inhibition of autophagy significantly decreased SADS-CoV production, thus suggesting that autophagy facilitated the replication of SADS-CoV. We found that ER stress and its downstream IRE1 pathway were indispensable in the processes of SADS-CoV-induced autophagy. We also demonstrated that IRE1-JNK-Beclin 1 signaling pathway, neither PERK-EIF2S1 nor ATF6 pathways, was essential during SADS-CoV-induced autophagy. Importantly, our work provided the first evidence that expression of SADS-CoV PLP2-TM protein induced autophagy through the IRE1-JNK-Beclin 1 signaling pathway. Furthermore, the interaction of viral PLP2-TMF451-L490 domain and substrate-binding domain of GRP78 was identified to activate the IRE1-JNK-Beclin 1 signaling pathway, and thus resulting in autophagy, and in turn, enhancing SADS-CoV replication. Collectively, these results not only showed that autophagy promoted SADS-CoV replication in cultured cells, but also revealed that the molecular mechanism underlying SADS-CoV-induced autophagy in cells.
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Affiliation(s)
- Da Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Ling Zhou
- College of Animal Science, South China Agricultural University, Tianhe District, China
| | - Hongyan Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Jiyu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Jialin Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Liaoyuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Dakai Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Tingshuai Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Miaomiao Zeng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Jianfei Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Xin Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Mei Xue
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Zhaoyang Jing
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Jianbo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Zhaoyang Ji
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Haojie He
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Longjun Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Yang Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
| | - Jingyun Ma
- College of Animal Science, South China Agricultural University, Tianhe District, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, China
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18
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Ni X, Han Y, Zhou R, Zhou Y, Lei J. Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2. Commun Biol 2023; 6:193. [PMID: 36806252 PMCID: PMC9938351 DOI: 10.1038/s42003-023-04570-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 02/09/2023] [Indexed: 02/20/2023] Open
Abstract
The coronavirus nucleocapsid (N) protein interacts with non-structural protein 3 (Nsp3) to facilitate viral RNA synthesis and stabilization. However, structural information on the N-Nsp3 complex is limited. Here, we report a 2.6 Å crystal structure of the N-terminal domain (NTD) of the N protein in complex with the ubiquitin-like domain 1 (Ubl1) of Nsp3 in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One NTD and two Ubl1s formed a stable heterotrimer. We performed mutational analysis to reveal the key residues for this interaction. We confirmed the colocalization of SARS-CoV-2 N and Nsp3 in Huh-7 cells. N-Ubl1 interaction also exists in SARS-CoV and Middle East respiratory syndrome coronavirus. We found that SARS-CoV-2 Ubl1 competes with RNA to bind N protein in a dose-dependent manner. Based on our results, we propose a model for viral ribonucleoprotein dissociation through N protein binding to Ubl1 of Nsp3.
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Affiliation(s)
- Xincheng Ni
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yinze Han
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Renjie Zhou
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yanmei Zhou
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Jian Lei
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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19
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Waisner H, Grieshaber B, Saud R, Henke W, Stephens EB, Kalamvoki M. SARS-CoV-2 Harnesses Host Translational Shutoff and Autophagy To Optimize Virus Yields: the Role of the Envelope (E) Protein. Microbiol Spectr 2023; 11:e0370722. [PMID: 36622177 PMCID: PMC9927098 DOI: 10.1128/spectrum.03707-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/07/2022] [Indexed: 01/10/2023] Open
Abstract
The SARS-CoV-2 virion is composed of four structural proteins: spike (S), nucleocapsid (N), membrane (M), and envelope (E). E spans the membrane a single time and is the smallest, yet most enigmatic of the structural proteins. E is conserved among coronaviruses and has an essential role in virus-mediated pathogenesis. We found that ectopic expression of E had deleterious effects on the host cell as it activated stress responses, leading to LC3 lipidation and phosphorylation of the translation initiation factor eIF2α that resulted in host translational shutoff. During infection E is highly expressed, although only a small fraction is incorporated into virions, suggesting that E activity is regulated and harnessed by the virus to its benefit. Consistently, we found that proteins from heterologous viruses, such as the γ1 34.5 protein of herpes simplex virus 1, prevented deleterious effects of E on the host cell and allowed for E protein accumulation. This observation prompted us to investigate whether other SARS-CoV-2 structural proteins regulate E. We found that the N and M proteins enabled E protein accumulation, whereas S did not. While γ1 34.5 protein prevented deleterious effects of E on the host cells, it had a negative effect on SARS-CoV-2 replication. The negative effect of γ1 34.5 was most likely associated with failure of SARS-CoV-2 to divert the translational machinery and with deregulation of autophagy. Overall, our data suggest that SARS-CoV-2 causes stress responses and subjugates these pathways, including host protein synthesis (phosphorylated eIF2α) and autophagy, to support optimal virus replication. IMPORTANCE In late 2019, a new β-coronavirus, SARS-CoV-2, entered the human population causing a pandemic that has resulted in over 6 million deaths worldwide. Although closely related to SARS-CoV, the mechanisms of SARS-CoV-2 pathogenesis are not fully understood. We found that ectopic expression of the SARS-CoV-2 E protein had detrimental effects on the host cell, causing metabolic alterations, including shutoff of protein synthesis and mobilization of cellular resources through autophagy activation. Coexpression of E with viral proteins known to subvert host antiviral responses such as autophagy and translational inhibition, either from SARS-CoV-2 or from heterologous viruses, increased cell survival and E protein accumulation. However, such factors were found to negatively impact SARS-CoV-2 infection, as autophagy contributes to formation of viral membrane factories and translational control offers an advantage for viral gene expression. Overall, SARS-CoV-2 has evolved mechanisms to harness host functions that are essential for virus replication.
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Affiliation(s)
- Hope Waisner
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Brandon Grieshaber
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Rabina Saud
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Wyatt Henke
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Edward B. Stephens
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Maria Kalamvoki
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
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20
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Chen T, Tu S, Ding L, Jin M, Chen H, Zhou H. The role of autophagy in viral infections. J Biomed Sci 2023; 30:5. [PMID: 36653801 PMCID: PMC9846652 DOI: 10.1186/s12929-023-00899-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Autophagy is an evolutionarily conserved catabolic cellular process that exerts antiviral functions during a viral invasion. However, co-evolution and co-adaptation between viruses and autophagy have armed viruses with multiple strategies to subvert the autophagic machinery and counteract cellular antiviral responses. Specifically, the host cell quickly initiates the autophagy to degrade virus particles or virus components upon a viral infection, while cooperating with anti-viral interferon response to inhibit the virus replication. Degraded virus-derived antigens can be presented to T lymphocytes to orchestrate the adaptive immune response. Nevertheless, some viruses have evolved the ability to inhibit autophagy in order to evade degradation and immune responses. Others induce autophagy, but then hijack autophagosomes as a replication site, or hijack the secretion autophagy pathway to promote maturation and egress of virus particles, thereby increasing replication and transmission efficiency. Interestingly, different viruses have unique strategies to counteract different types of selective autophagy, such as exploiting autophagy to regulate organelle degradation, metabolic processes, and immune responses. In short, this review focuses on the interaction between autophagy and viruses, explaining how autophagy serves multiple roles in viral infection, with either proviral or antiviral functions.
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Affiliation(s)
- Tong Chen
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Shaoyu Tu
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Ling Ding
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Meilin Jin
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Huanchun Chen
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Hongbo Zhou
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
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21
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Jassey A, Wagner MA, Galitska G, Paudel B, Miller K, Jackson WT. Starvation after infection restricts enterovirus D68 replication. Autophagy 2023; 19:112-125. [PMID: 35446171 PMCID: PMC9809931 DOI: 10.1080/15548627.2022.2062888] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Enterovirus D68 (EV-D68) is a respiratory pathogen associated with acute flaccid myelitis, a childhood paralysis disease. No approved vaccine or antiviral treatment exists against EV-D68. Infection with this virus induces the formation of autophagosomes to enhance its replication but blocks the downstream autophagosome- lysosome fusion steps. Here, we examined the impact of autophagy induction through starvation, either before (starvation before infection, SBI) or after (starvation after infection, SAI) EV-D68 infection. We showed that SAI, but not SBI, attenuated EV-D68 replication in multiple cell lines and abrogated the viral-mediated cleavage of host autophagic flux-related proteins. Furthermore, SAI induced autophagic flux during EV-D68 replication and prevented production of virus-induced membranes, which are required for picornavirus replication. Pharmacological inhibition of autophagic flux during SAI did not rescue EV-D68 titers. SAI had the same effect in multiple cell types, and restricted the replication of several medically relevant picornaviruses. Our results highlight the significance of autophagosomes for picornavirus replication and identify SAI as an attractive broad-spectrum anti-picornavirus strategy.Abbreviations: BAF: bafilomycin A1; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CQ: chloroquine; CVB3: coxsackievirus B3; EV-D68: enterovirus D68; hpi: hour post-infection; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; NSP2B: nonstructural protein 2B; PV: poliovirus; RES: resveratrol; RV14: rhinovirus 14; SAI: starvation after infection; SBI: starvation before infection; SNAP29: synaptosome associated protein 29; SQSTM1/p62: sequestosome 1; TFEB: transcription factor EB.
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Affiliation(s)
- Alagie Jassey
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael A. Wagner
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ganna Galitska
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bimal Paudel
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Katelyn Miller
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William T. Jackson
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA,CONTACT William T. Jackson Department of Microbiology and Immunology and Center for Pathogen Research University of Maryland School of Medicine, Baltimore, USA
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22
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Niu TM, Yu LJ, Zhao JH, Zhang RR, Ata EB, Wang N, Zhang D, Yang YL, Qian JH, Chen QD, Yang GL, Huang HB, Shi CW, Jiang YL, Wang JZ, Cao X, Zeng Y, Wang N, Yang WT, Wang CF. Characterization and pathogenicity of the porcine epidemic diarrhea virus isolated in China. Microb Pathog 2023; 174:105924. [PMID: 36473667 DOI: 10.1016/j.micpath.2022.105924] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Piglet diarrhea caused by the porcine epidemic diarrhea virus (PEDV) is a common problem on pig farms in China associated with high morbidity and mortality rates. In this study, three PEDV isolates were successfully detected after the fourth blind passage in Vero cells. The samples were obtained from infected piglet farms in Jilin (Changchun), and Shandong (Qingdao) Provinces of China and were designated as CH/CC-1/2018, CH/CC-2/2018, and CH/QD/2018. According to the analysis of the complete S protein gene sequence, the CH/CC-1/2018 and CH/CC-2/2018 were allocated to the G2b branch, while CH/QD/2018 was located in the G1a interval and was closer to the vaccine strain CV777. Successful detection and identification of the isolated strains were carried out using electron microscopy and indirect immunofluorescence. Meanwhile, animal challenge experiments and viral RNA copies determination were used to compare the pathogenicity. The results showed that CH/CC-1/2018 in Changchun was more pathogenic than CH/QD/2018 in Qingdao. In conclusion, the discovery of these new strains is conducive to the development of vaccines to prevent the pandemic of PEDV, especially that the CH/CC-1/2018, and CH/CC-2/2018 were not related to the classical vaccine strain CV777.
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Affiliation(s)
- Tian-Ming Niu
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Ling-Jiao Yu
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jin-Hui Zhao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Rong-Rong Zhang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Emad Beshir Ata
- Parasitology and Animal Diseases Dep, Vet. Res. Institute, National Research Centre, 12622, Dokki, Cairo, Egypt
| | - Nan Wang
- Jilin Province Animal Disease Prevention and Control Center, Changchun, China
| | - Di Zhang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yong-Lei Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jia-Hao Qian
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Qiao-Dan Chen
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Gui-Lian Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Hai-Bin Huang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chun-Wei Shi
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan-Long Jiang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jian-Zhong Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xin Cao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan Zeng
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Nan Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Wen-Tao Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China.
| | - Chun-Feng Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China.
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23
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Brownsword MJ, Locker N. A little less aggregation a little more replication: Viral manipulation of stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1741. [PMID: 35709333 PMCID: PMC10078398 DOI: 10.1002/wrna.1741] [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: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
Recent exciting studies have uncovered how membrane-less organelles, also known as biocondensates, are providing cells with rapid response pathways, allowing them to re-organize their cellular contents and adapt to stressful conditions. Their assembly is driven by the phase separation of their RNAs and intrinsically disordered protein components into condensed foci. Among these, stress granules (SGs) are dynamic cytoplasmic biocondensates that form in response to many stresses, including activation of the integrated stress response or viral infections. SGs sit at the crossroads between antiviral signaling and translation because they concentrate signaling proteins and components of the innate immune response, in addition to translation machinery and stalled mRNAs. Consequently, they have been proposed to contribute to antiviral activities, and therefore are targeted by viral countermeasures. Equally, SGs components can be commandeered by viruses for their own efficient replication. Phase separation processes are an important component of the viral life cycle, for example, driving the assembly of replication factories or inclusion bodies. Therefore, in this review, we will outline the recent understanding of this complex interplay and tug of war between viruses, SGs, and their components. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Matthew J. Brownsword
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
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24
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Kondrashov OV, Akimov SA. A Mechanism of Double-Membrane Vesicle Formation from Liquid-Ordered/Liquid-Disordered Phase Separated Spherical Membrane. MEMBRANES 2022; 13:25. [PMID: 36676832 PMCID: PMC9862188 DOI: 10.3390/membranes13010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Genome replication of coronaviruses takes place in specific cellular compartments, in so-called double-membrane vesicles (DMVs), formed from the endoplasmic reticulum (ER). An intensive production of DMVs is induced by non-structural viral proteins. Here, we proposed a possible mechanism of the DMV formation from ER-derived spherical vesicles where liquid-ordered and liquid-disordered lipid phases coexist. These vesicles are supposed to divide into two homogeneous liquid-ordered and liquid-disordered vesicles. The formation of two spherical vesicles constituting DMV requires a mechanical work to be performed. We considered the excess energy of the boundary between the coexisting lipid phases as the main driving force behind the division of the initial vesicle. Explicitly accounting for the energy of elastic deformations and the interphase boundary energy, we analyzed a range of physical parameters where the DMV formation is possible. We concluded that this process can principally take place in a very narrow range of system parameters. The most probable diameter of DMVs formed according to the proposed mechanism appeared to be approximately 220 nm, in an agreement with the average diameter of DMVs observed in vivo. Our consideration predicts the DMV size to be strongly limited from above. The developed analysis can be utilized for the production of DMVs in model systems.
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25
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Montes de Oca-B P. Evidence of mitochondria origin of SARS-CoV-2 double-membrane vesicles: a review. F1000Res 2022; 10:1009. [PMID: 38827572 PMCID: PMC11140301 DOI: 10.12688/f1000research.73170.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 06/04/2024] Open
Abstract
Coronavirus Disease-19 (COVID-19) pandemic is caused by the coronavirus SARS-CoV-2 that has infected in a year more than 200 million people and has killed almost 4.5 million people worldwide. This infection affects mainly certain groups of people that have high susceptibility to present severe COVID-19 due to comorbidities. Moreover, the long-COVID-19 comprises a series of symptoms that may remain in some patients for months after infection that further compromises health of individuals. Therefore, this pandemic poses a serious emergency worldwide. Thus, since this pandemic is profoundly affecting economic and social life of societies, a deeper understanding of SARS-CoV-2 infection cycle could help to envisage novel therapeutic alternatives that limit or stop COVID-19. Several recent findings have unexpectedly found that mitochondria play a critical role in SARS-CoV-2 cell infection. Indeed, it has been suggested that this organelle could be the origin of its replication niches, the double membrane vesicles (DMV), as its been observed with another virus. In this regard, mitochondria derived vesicles (MDV), involved in mitochondria quality control, were discovered more than 10 years ago and interestingly there is a population characterized by a double membrane. MDV shedding is induced by mitochondrial stress and it has a fast assembly dynamic, reason that perhaps has precluded their identification in electron microscopy or tomography studies. These and other features of MDV together with recent SARS-CoV-2 protein interactome with the host and other findings linking SARS-CoV-2 to mitochondria, support that these vesicles are the precursors of SARS-CoV-2 induced DMV. In this work, the celular, molecular, phenotypical and biochemical evidence that supports this hypothesis is reviewed and integrated into the current model of SARS-CoV-2 cell infection. In this scheme, some relevant questions are raised as pending topics for research that would help in the near future to test this hypothesis. The intention (abstract truncated).
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Affiliation(s)
- Pavel Montes de Oca-B
- Neurociencia Cognitiva, Instituto de Fisiologia-UNAM, CDMX, CDMX, 04510, Mexico
- Unidad de Neurobiologia Dinamica, Instituto Nacional de Neurologia y Neurocirugia, CDMX, CDMX, 14269, Mexico
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26
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Intrinsic host susceptibility among multiple species to intranasal SARS-CoV-2 identifies diverse virological, biodistribution and pathological outcomes. Sci Rep 2022; 12:18694. [PMID: 36333445 PMCID: PMC9636276 DOI: 10.1038/s41598-022-23339-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022] Open
Abstract
SARS-CoV-2 exhibits a diverse host species range with variable outcomes, enabling differential host susceptibility studies to assess suitability for pre-clinical countermeasure and pathogenesis studies. Baseline virological, molecular and pathological outcomes were determined among multiple species-one Old World non-human primate (NHP) species (cynomolgus macaques), two New World NHP species (red-bellied tamarins; common marmosets) and Syrian hamsters-following single-dose, atraumatic intranasal administration of SARS-CoV-2/Victoria-01. After serial sacrifice 2, 10 and 28-days post-infection (dpi), hamsters and cynomolgus macaques displayed differential virus biodistribution across respiratory, gastrointestinal and cardiovascular systems. Uniquely, New World tamarins, unlike marmosets, exhibited high levels of acute upper airway infection, infectious virus recovery associated with mild lung pathology representing a host previously unrecognized as susceptible to SARS-CoV-2. Across all species, lung pathology was identified post-clearance of virus shedding (antigen/RNA), with an association of virus particles within replication organelles in lung sections analysed by electron microscopy. Disrupted cell ultrastructure and lung architecture, including abnormal morphology of mitochondria 10-28 dpi, represented on-going pathophysiological consequences of SARS-CoV-2 in predominantly asymptomatic hosts. Infection kinetics and host pathology comparators using standardized methodologies enables model selection to bridge differential outcomes within upper and lower respiratory tracts and elucidate longer-term consequences of asymptomatic SARS-CoV-2 infection.
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27
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Tulimilli SV, Dallavalasa S, Basavaraju CG, Kumar Rao V, Chikkahonnaiah P, Madhunapantula SV, Veeranna RP. Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Vaccine Effectiveness. Vaccines (Basel) 2022; 10:vaccines10101751. [PMID: 36298616 PMCID: PMC9607623 DOI: 10.3390/vaccines10101751] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The incidence and death toll due to SARS-CoV-2 infection varied time-to-time; and depended on several factors, including severity (viral load), immune status, age, gender, vaccination status, and presence of comorbidities. The RNA genome of SARS-CoV-2 has mutated and produced several variants, which were classified by the SARS-CoV-2 Interagency Group (SIG) into four major categories. The first category; “Variant Being Monitored (VBM)”, consists of Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Epsilon (B.1.427, B.1.429), Eta (B.1.525), Iota (B.1.526), Kappa (B.1.617.1), Mu (B.1.621), and Zeta (P.2); the second category; “Variants of Concern” consists of Omicron (B.1.1.529). The third and fourth categories include “Variants of Interest (VOI)”, and “Variants of High Consequence (VOHC)”, respectively, and contain no variants classified currently under these categories. The surge in VBM and VOC poses a significant threat to public health globally as they exhibit altered virulence, transmissibility, diagnostic or therapeutic escape, and the ability to evade the host immune response. Studies have shown that certain mutations increase the infectivity and pathogenicity of the virus as demonstrated in the case of SARS-CoV-2, the Omicron variant. It is reported that the Omicron variant has >60 mutations with at least 30 mutations in the Spike protein (“S” protein) and 15 mutations in the receptor-binding domain (RBD), resulting in rapid attachment to target cells and immune evasion. The spread of VBM and VOCs has affected the actual protective efficacy of the first-generation vaccines (ChAdOx1, Ad26.COV2.S, NVX-CoV2373, BNT162b2). Currently, the data on the effectiveness of existing vaccines against newer variants of SARS-CoV-2 are very scanty; hence additional studies are immediately warranted. To this end, recent studies have initiated investigations to elucidate the structural features of crucial proteins of SARS-CoV-2 variants and their involvement in pathogenesis. In addition, intense research is in progress to develop better preventive and therapeutic strategies to halt the spread of COVID-19 caused by variants. This review summarizes the structure and life cycle of SARS-CoV-2, provides background information on several variants of SARS-CoV-2 and mutations associated with these variants, and reviews recent studies on the safety and efficacy of major vaccines/vaccine candidates approved against SARS-CoV-2, and its variants.
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Affiliation(s)
- SubbaRao V. Tulimilli
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Siva Dallavalasa
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Chaithanya G. Basavaraju
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Vinay Kumar Rao
- Department of Medical Genetics, JSS Medical College & Hospital, JSS Academy of Higher Education & Research (JSS AHER), Mysore 570015, Karnataka, India
| | - Prashanth Chikkahonnaiah
- Department of Pulmonary Medicine, Mysore Medical College and Research Institute, Mysuru 570001, Karnataka, India
| | - SubbaRao V. Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR) Laboratory (DST-FIST Supported Center), Department of Biochemistry (DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
- Special Interest Group in Cancer Biology and Cancer Stem Cells (SIG-CBCSC), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru 570004, Karnataka, India
| | - Ravindra P. Veeranna
- Department of Biochemistry, Council of Scientific and Industrial Research (CSIR)-Central Food Technological Research Institute (CFTRI), Mysuru 570020, Karnataka, India
- Correspondence:
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Hepatitis Viruses Control Host Immune Responses by Modifying the Exosomal Biogenesis Pathway and Cargo. Int J Mol Sci 2022; 23:ijms231810862. [PMID: 36142773 PMCID: PMC9505460 DOI: 10.3390/ijms231810862] [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: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The development of smart immune evasion mechanisms is crucial for the establishment of acute and chronic viral hepatitis. Hepatitis is a major health problem worldwide arising from different causes, such as pathogens, metabolic disorders, and xenotoxins, with the five hepatitis viruses A, B, C, D, and E (HAV, HBV, HCV, HDV, and HEV) representing the majority of the cases. Most of the hepatitis viruses are considered enveloped. Recently, it was reported that the non-enveloped HAV and HEV are, in reality, quasi-enveloped viruses exploiting exosomal-like biogenesis mechanisms for budding. Regardless, all hepatitis viruses use exosomes to egress, regulate, and eventually escape from the host immune system, revealing another key function of exosomes apart from their recognised role in intercellular communication. This review will discuss how the hepatitis viruses exploit exosome biogenesis and transport capacity to establish successful infection and spread. Then, we will outline the contribution of exosomes in viral persistence and liver disease progression.
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Ultrastructural Characterization of Human Bronchial Epithelial Cells during SARS-CoV-2 Infection: Morphological Comparison of Wild-Type and CFTR-Modified Cells. Int J Mol Sci 2022; 23:ijms23179724. [PMID: 36077122 PMCID: PMC9455986 DOI: 10.3390/ijms23179724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2 replicates in host cell cytoplasm. People with cystic fibrosis, considered at risk of developing severe symptoms of COVID-19, instead, tend to show mild symptoms. We, thus, analyzed at the ultrastructural level the morphological effects of SARS-CoV-2 infection on wild-type (WT) and F508del (ΔF) CFTR-expressing CFBE41o- cells at early and late time points post infection. We also investigated ACE2 expression through immune-electron microscopy. At early times of infection, WT cells exhibited double-membrane vesicles, representing typical replicative structures, with granular and vesicular content, while at late time points, they contained vesicles with viral particles. ∆F cells exhibited double-membrane vesicles with an irregular shape and degenerative changes and at late time of infection, showed vesicles containing viruses lacking a regular structure and a well-organized distribution. ACE2 was expressed at the plasma membrane and present in the cytoplasm only at early times in WT, while it persisted even at late times of infection in ΔF cells. The autophagosome content also differed between the cells: in WT cells, it comprised vesicles associated with virus-containing structures, while in ΔF cells, it comprised ingested material for lysosomal digestion. Our data suggest that CFTR-modified cells infected with SARS-CoV-2 have impaired organization of normo-conformed replicative structures.
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Omasta B, Tomaskova J. Cellular Lipids—Hijacked Victims of Viruses. Viruses 2022; 14:v14091896. [PMID: 36146703 PMCID: PMC9501026 DOI: 10.3390/v14091896] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
Abstract
Over the millions of years-long co-evolution with their hosts, viruses have evolved plenty of mechanisms through which they are able to escape cellular anti-viral defenses and utilize cellular pathways and organelles for replication and production of infectious virions. In recent years, it has become clear that lipids play an important role during viral replication. Viruses use cellular lipids in a variety of ways throughout their life cycle. They not only physically interact with cellular membranes but also alter cellular lipid metabolic pathways and lipid composition to create an optimal replication environment. This review focuses on examples of how different viruses exploit cellular lipids in different cellular compartments during their life cycles.
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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: 48] [Impact Index Per Article: 24.0] [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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Lou Z, Rao Z. The Life of SARS-CoV-2 Inside Cells: Replication-Transcription Complex Assembly and Function. Annu Rev Biochem 2022; 91:381-401. [PMID: 35729072 DOI: 10.1146/annurev-biochem-052521-115653] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The persistence of the coronavirus disease 2019 (COVID-19) pandemic has resulted in increasingly disruptive impacts, and it has become the most devastating challenge to global health in a century. The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants challenges the currently available therapeutics for clinical application. Nonstructural proteins (also known as replicase proteins) with versatile biological functions play central roles in viral replication and transcription inside the host cells, and they are the most conserved target proteins among the SARS-CoV-2 variants. Specifically, they constitute the replication-transcription complexes (RTCs) dominating the synthesis of viral RNA. Knowledge of themolecular mechanisms of nonstructural proteins and their assembly into RTCs will benefit the development of antivirals targeting them against existing or potentially emerging variants. In this review, we summarize current knowledge of the structures and functions of coronavirus nonstructural proteins as well as the assembly and functions of RTCs in the life cycle of the virus.
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Affiliation(s)
- Zhiyong Lou
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; ,
| | - Zihe Rao
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; , .,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,School of Life Sciences, Tsinghua University, Beijing, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Guangzhou Laboratory, Guangzhou, China
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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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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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Prydz K, Saraste J. The life cycle and enigmatic egress of coronaviruses. Mol Microbiol 2022; 117:1308-1316. [PMID: 35434857 PMCID: PMC9321882 DOI: 10.1111/mmi.14907] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
There has been considerable recent interest in the life cycle of Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2), the causative agent of the Covid‐19 pandemic. Practically every step in CoV replication—from cell attachment and uptake via genome replication and expression to virion assembly has been considered as a specific event that potentially could be targeted by existing or novel drugs. Interference with cellular egress of progeny viruses could also be adopted as a possible therapeutic strategy; however, the situation is complicated by the fact that there is no broad consensus on how CoVs find their way out of their host cells. The viral nucleocapsid, consisting of the genomic RNA complexed with nucleocapsid proteins obtains a membrane envelope during virus budding into the lumen of the intermediate compartment (IC) at the endoplasmic reticulum (ER)–Golgi interface. From here, several alternative routes for CoV extracellular release have been proposed. Strikingly, recent studies have shown that CoV infection leads to the disassembly of the Golgi ribbon and the mobilization of host cell compartments and protein machineries that are known to promote Golgi‐independent trafficking to the cell surface. Here, we discuss the life cycle of CoVs with a special focus on different possible pathways for virus egress.
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Affiliation(s)
- Kristian Prydz
- Department of Biosciences, University of Oslo, Norway and Department of Biomedicine and Molecular Imaging Center University of Bergen Norway
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36
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Xue W, Ding C, Qian K, Liao Y. The Interplay Between Coronavirus and Type I IFN Response. Front Microbiol 2022; 12:805472. [PMID: 35317429 PMCID: PMC8934427 DOI: 10.3389/fmicb.2021.805472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/14/2022] Open
Abstract
In the past few decades, newly evolved coronaviruses have posed a global threat to public health and animal breeding. To control and prevent the coronavirus-related diseases, understanding the interaction of the coronavirus and the host immune system is the top priority. Coronaviruses have evolved multiple mechanisms to evade or antagonize the host immune response to ensure their replication. As the first line and main component of innate immune response, type I IFN response is able to restrict virus in the initial infection stage; it is thus not surprising that the primary aim of the virus is to evade or antagonize the IFN response. Gaining a profound understanding of the interaction between coronaviruses and type I IFN response will shed light on vaccine development and therapeutics. In this review, we provide an update on the current knowledge on strategies employed by coronaviruses to evade type I IFN response.
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Affiliation(s)
- Wenxiang Xue
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Kun Qian
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Ying Liao,
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Grootemaat AE, van der Niet S, Scholl ER, Roos E, Schurink B, Bugiani M, Miller SE, Larsen P, Pankras J, Reits EA, van der Wel NN. Lipid and Nucleocapsid N-Protein Accumulation in COVID-19 Patient Lung and Infected Cells. Microbiol Spectr 2022; 10:e0127121. [PMID: 35171025 PMCID: PMC8849100 DOI: 10.1128/spectrum.01271-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global outbreak and prompted an enormous research effort. Still, the subcellular localization of the coronavirus in lungs of COVID-19 patients is not well understood. Here, the localization of the SARS-CoV-2 proteins is studied in postmortem lung material of COVID-19 patients and in SARS-CoV-2-infected Vero cells, processed identically. Correlative light and electron microscopy on semithick cryo-sections demonstrated induction of electron-lucent, lipid-filled compartments after SARS-CoV-2 infection in both lung and cell cultures. In lung tissue, the nonstructural protein 4 and the stable nucleocapsid N-protein were detected on these novel lipid-filled compartments. The induction of such lipid-filled compartments and the localization of the viral proteins in lung of patients with fatal COVID-19 may explain the extensive inflammatory response and provide a new hallmark for SARS-CoV-2 infection at the final, fatal stage of infection. IMPORTANCE Visualization of the subcellular localization of SARS-CoV-2 proteins in lung patient material of COVID-19 patients is important for the understanding of this new virus. We detected viral proteins in the context of the ultrastructure of infected cells and tissues and discovered that some viral proteins accumulate in novel, lipid-filled compartments. These structures are induced in Vero cells but, more importantly, also in lung of patients with COVID-19. We have characterized these lipid-filled compartments and determined that this is a novel, virus-induced structure. Immunogold labeling demonstrated that cellular markers, such as CD63 and lipid droplet marker PLIN-2, are absent. Colocalization of lipid-filled compartments with the stable N-protein and nonstructural protein 4 in lung of the last stages of COVID-19 indicates that these compartments play a key role in the devastating immune response that SARS-CoV-2 infections provoke.
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Affiliation(s)
- Anita E. Grootemaat
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre (UMC), Amsterdam, the Netherlands
| | - Sanne van der Niet
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre (UMC), Amsterdam, the Netherlands
| | - Edwin R. Scholl
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre (UMC), Amsterdam, the Netherlands
| | - Eva Roos
- Department of Pathology, Amsterdam University Medical Centers (UMC), VU University Amsterdam, Amsterdam, the Netherlands
| | - Bernadette Schurink
- Department of Pathology, Amsterdam University Medical Centers (UMC), VU University Amsterdam, Amsterdam, the Netherlands
| | - Marianna Bugiani
- Department of Pathology, Amsterdam University Medical Centers (UMC), VU University Amsterdam, Amsterdam, the Netherlands
| | - Sara E. Miller
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Per Larsen
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre (UMC), Amsterdam, the Netherlands
- Department of Pathology, Amsterdam University Medical Centers (UMC), VU University Amsterdam, Amsterdam, the Netherlands
| | - Jeannette Pankras
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre (UMC), Amsterdam, the Netherlands
- Department of Pathology, Amsterdam University Medical Centers (UMC), VU University Amsterdam, Amsterdam, the Netherlands
| | - Eric A. Reits
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre (UMC), Amsterdam, the Netherlands
| | - Nicole N. van der Wel
- Electron Microscopy Centre Amsterdam, Medical Biology, Amsterdam University Medical Centre (UMC), Amsterdam, the Netherlands
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Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. Viruses 2022; 14:v14020366. [PMID: 35215963 PMCID: PMC8877023 DOI: 10.3390/v14020366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 01/31/2022] [Accepted: 02/08/2022] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has wreaked havoc across the globe for the last two years. More than 300 million cases and over 5 million deaths later, we continue battling the first real pandemic of the 21st century. SARS-CoV-2 spread quickly, reaching most countries within the first half of 2020, and New Zealand was not an exception. Here, we describe the first isolation and characterization of SARS-CoV-2 variants during the initial virus outbreak in New Zealand. Patient-derived nasopharyngeal samples were used to inoculate Vero cells and, three to four days later, a cytopathic effect was observed in seven viral cultures. Viral growth kinetics was characterized using Vero and VeroE6/TMPRSS2 cells. The identity of the viruses was verified by RT-qPCR, Western blot, indirect immunofluorescence assays, and electron microscopy. Whole-genome sequences were analyzed using two different yet complementary deep sequencing platforms (MiSeq/Illumina and Ion PGM™/Ion Torrent™), classifying the viruses as SARS-CoV-2 B.55, B.31, B.1, or B.1.369 based on the Pango Lineage nomenclature. All seven SARS-CoV-2 isolates were susceptible to remdesivir (EC50 values from 0.83 to 2.42 µM) and β-D-N4-hydroxycytidine (molnupiravir, EC50 values from 0.96 to 1.15 µM) but not to favipiravir (>10 µM). Interestingly, four SARS-CoV-2 isolates, carrying the D614G substitution originally associated with increased transmissibility, were more susceptible (2.4-fold) to a commercial monoclonal antibody targeting the spike glycoprotein than the wild-type viruses. Altogether, this seminal work allowed for early access to SARS-CoV-2 isolates in New Zealand, paving the way for numerous clinical and scientific research projects in the country, including the development and validation of diagnostic assays, antiviral strategies, and a national COVID-19 vaccine development program.
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da Silva Torres MK, Bichara CDA, de Almeida MDNDS, Vallinoto MC, Queiroz MAF, Vallinoto IMVC, dos Santos EJM, de Carvalho CAM, Vallinoto ACR. The Complexity of SARS-CoV-2 Infection and the COVID-19 Pandemic. Front Microbiol 2022; 13:789882. [PMID: 35222327 PMCID: PMC8870622 DOI: 10.3389/fmicb.2022.789882] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the death of millions of people worldwide and thousands more infected individuals developed sequelae due to the disease of the new coronavirus of 2019 (COVID-19). The development of several studies has contributed to the knowledge about the evolution of SARS-CoV2 infection and the disease to more severe forms. Despite this information being debated in the scientific literature, many mechanisms still need to be better understood in order to control the spread of the virus and treat clinical cases of COVID-19. In this article, we carried out an extensive literature review in order to bring together, in a single article, the biological, social, genetic, diagnostic, therapeutic, immunization, and even socioeconomic aspects that impact the SAR-CoV-2 pandemic. This information gathered in this article will enable a broad and consistent reading of the main aspects related to the current pandemic.
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Affiliation(s)
- Maria Karoliny da Silva Torres
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | - Carlos David Araújo Bichara
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | - Maria de Nazaré do Socorro de Almeida
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
- Laboratory of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Mariana Cayres Vallinoto
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- University Center of the State of Pará, Belém, Brazil
| | - Maria Alice Freitas Queiroz
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
| | | | - Eduardo José Melo dos Santos
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
- Laboratory of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Antonio Carlos R. Vallinoto
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Federal University of Pará, Belém, Brazil
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40
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Ullah MF, Ali Y, Khan MR, Khan IU, Yan B, Ijaz Khan M, Malik M. A review of COVID-19: Treatment strategies and CRISPR/Cas9 gene editing technology approaches to the coronavirus disease. Saudi J Biol Sci 2022; 29:860-871. [PMID: 34658640 PMCID: PMC8511869 DOI: 10.1016/j.sjbs.2021.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/12/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022] Open
Abstract
The new coronavirus SARS-CoV-2 pandemic has put the world on lockdown for the first time in decades. This has wreaked havoc on the global economy, put additional burden on local and global public health resources, and, most importantly, jeopardised human health. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, and the CRISPR associated (Cas) protein (CRISPR/Cas) was identified to have structures in E. coli. The most modern of these systems is CRISPR/Cas. Editing the genomes of plants and animals took several years and cost hundreds of thousands of dollars until the CRISPR approach was discovered in 2012. As a result, CRISPR/Cas has piqued the scientific community's attention, particularly for disease diagnosis and treatment, because it is faster, less expensive, and more precise than previous genome editing technologies. Data from gene mutations in specific patients gathered using CRISPR/Cas can aid in the identification of the best treatment strategy for each patient, as well as other research domains such as coronavirus replication in cell culture, such as SARS-CoV2. The implications of the most prevalent driver mutations, on the other hand, are often unknown, making treatment interpretation difficult. For detecting a wide range of target genes, the CRISPR/Cas categories provide highly sensitive and selective tools. Genome-wide association studies are a relatively new strategy to discovering genes involved in human disease when it comes to the next steps in genomic research. Furthermore, CRISPR/Cas provides a method for modifying non-coding portions of the genome, which will help advance whole genome libraries by speeding up the analysis of these poorly defined parts of the genome.
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Affiliation(s)
- Muhammad Farhat Ullah
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan
| | - Yasir Ali
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan
| | - Inam Ullah Khan
- University of Sheffield, Department of Chemical and Biological Engineering, Arts Tower Western Bank, Sheffield, S102TN, The University of Sheffield, Manchester, UK
| | - Bing Yan
- Department of Pharmacy, The First Affiliated Hospital of Huzhou University, Huzhou 313000, PR China
| | - M. Ijaz Khan
- Department of Mathematics and Statistics, Riphah International University, I-14, Islamabad 44000, Pakistan
| | - M.Y. Malik
- Department of Mathematics, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia
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41
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Batishchev OV. Physico-Chemical Mechanisms of the Functioning of Membrane-Active Proteins of Enveloped Viruses. BIOCHEMISTRY (MOSCOW) SUPPLEMENT. SERIES A, MEMBRANE AND CELL BIOLOGY 2022; 16:247-260. [PMCID: PMC9734521 DOI: 10.1134/s1990747822050038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/14/2022]
Abstract
Over the past few years, the attention of the whole world has been riveted to the emergence of new dangerous strains of viruses, among which a special place is occupied by coronaviruses that have overcome the interspecies barrier in the past 20 years: SARS viruses (SARS), Middle East respiratory syndrome (MERS), as well as a new coronavirus infection (SARS-CoV-2), which caused the largest pandemic since the Spanish flu in 1918. Coronaviruses are members of a class of enveloped viruses that have a lipoprotein envelope. This class also includes such serious pathogens as human immunodeficiency virus (HIV), hepatitis, Ebola virus, influenza, etc. Despite significant differences in the clinical picture of the course of disease caused by enveloped viruses, they themselves have a number of characteristic features, which determine their commonality. Regardless of the way of penetration into the cell—by endocytosis or direct fusion with the cell membrane—enveloped viruses are characterized by the following stages of interaction with the target cell: binding to receptors on the cell surface, interaction of the surface glycoproteins of the virus with the membrane structures of the infected cell, fusion of the lipid envelope of the virion with plasma or endosomal membrane, destruction of the protein capsid and its dissociation from the viral nucleoprotein. Subsequently, within the infected cell, the newly synthesized viral proteins must self-assemble on various membrane structures to form a progeny virion. Thus, both the initial stages of viral infection and the assembly and release of new viral particles are associated with the activity of viral proteins in relation to the cell membrane and its organelles. This review is devoted to the analysis of physicochemical mechanisms of functioning of the main structural proteins of a number of enveloped viruses in order to identify possible strategies for the membrane activity of such proteins at various stages of viral infection of the cell.
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Affiliation(s)
- O. V. Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia
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42
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Wade H, Duan Q, Su Q. Interaction between Sars-CoV-2 structural proteins and host cellular receptors: From basic mechanisms to clinical perspectives. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:243-277. [PMID: 36088078 PMCID: PMC9182089 DOI: 10.1016/bs.apcsb.2022.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2) has caused a global pandemic that has affected the lives of billions of individuals. Sars-CoV-2 primarily infects human cells by binding of the viral spike protein to angiotensin-converting enzyme 2 (ACE2). In addition, novel means of viral entry are currently being investigated, including Neuropillin 1, toll-like receptors (TLRs), cluster of differentiation 147 (CD147), and integrin α5β1. Enriched expression of these proteins across metabolic regulatory organs/tissues, including the circulatory system, liver, pancreas, and intestine contributes to major clinical complications among COVID-19 patients, particularly the development of hypertension, myocardial injury, arrhythmia, acute coronary syndrome and increased coagulation in the circulatory system during and post-infection. Pre-existing metabolic disease, such as cardiovascular disease, obesity, diabetes, and non-alcoholic fatty liver disease, is associated with increased risk of hospitalization, persistent post-infection complications and worse outcomes in patients with COVID-19. This review overviews the biological features of Sars-CoV-2, highlights recent findings that delineate the pathological mechanisms of COVID-19 and the consequent clinical diseases.
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43
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Ávila-Pérez G, Rejas MT, Chichón FJ, Guerra M, Fernández JJ, Rodríguez D. Architecture of torovirus replicative organelles. Mol Microbiol 2021; 117:837-850. [PMID: 34967475 DOI: 10.1111/mmi.14875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/29/2022]
Abstract
Plus-stranded RNA viruses replicate in the cytosol of infected cells, in membrane-bound replication complexes. We previously identified double membrane vesicles (DMVs) in the cytoplasm of cells infected with Berne virus (BEV), the prototype member of Torovirus genus (Nidovirales Order). Our previous analysis by transmission electron microscopy suggested that the DMVs form a reticulovesicular network (RVN) analogous those described for the related severe acute respiratory syndrome coronavirus (SARS-CoV-1). Here, we used serial sectioning and electron tomography to characterize the architecture of torovirus replication organelles, and to learn about their biogenesis and dynamics during the infection. The formation of a RVN in BEV infected cells was confirmed, where the outer membranes of the DMVs are interconnected with each other and with the ER. Paired or zippered ER membranes connected with the DMVs were also observed, and likely represent early structures that evolve to give rise to DMVs. Also, paired membranes forming small spherule-like invaginations were observed at late time post-infection. Although resembling in size, the tomographic analysis show that these structures are clearly different from the true spherules described previously for coronaviruses. Hence, BEV shows important similarities, but also some differences, in the architecture of the replication organelles with other nidoviruses.
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Affiliation(s)
- Ginés Ávila-Pérez
- Department of Molecular and Cellular Biology, Centro de Biología Molecular Severo Ochoa, CSIC, C/Nicolás Cabrera 1, 28049, Madrid, Spain
| | - María Teresa Rejas
- Servicio de Microscopía Electrónica, Centro de Biología Molecular Severo Ochoa, CSIC, C/Nicolás Cabrera 1, 28049, Madrid, Spain
| | - Francisco Javier Chichón
- Servicio de Criomicroscopía Electrónica (cryoEM-CSIC) and Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049, Madrid, Spain
| | - Milagros Guerra
- Servicio de Microscopía Electrónica, Centro de Biología Molecular Severo Ochoa, CSIC, C/Nicolás Cabrera 1, 28049, Madrid, Spain
| | - José Jesús Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), CINN-CSIC, Av Hospital Universitario s/n, 33011, Oviedo, Spain
| | - Dolores Rodríguez
- Department of Molecular and Cellular Biology, Centro de Biología Molecular Severo Ochoa, CSIC, C/Nicolás Cabrera 1, 28049, Madrid, Spain
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44
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Koetzner CA, Hurst-Hess KR, Kuo L, Masters PS. Analysis of a crucial interaction between the coronavirus nucleocapsid protein and the major membrane-bound subunit of the viral replicase-transcriptase complex. Virology 2021; 567:1-14. [PMID: 34933176 PMCID: PMC8669624 DOI: 10.1016/j.virol.2021.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022]
Abstract
The coronavirus nucleocapsid (N) protein comprises two RNA-binding domains connected by a central spacer, which contains a serine- and arginine-rich (SR) region. The SR region engages the largest subunit of the viral replicase-transcriptase, nonstructural protein 3 (nsp3), in an interaction that is essential for efficient initiation of infection by genomic RNA. We carried out an extensive genetic analysis of the SR region of the N protein of mouse hepatitis virus in order to more precisely define its role in RNA synthesis. We further examined the N-nsp3 interaction through construction of nsp3 mutants and by creation of an interspecies N protein chimera. Our results indicate a role for the central spacer as an interaction hub of the N molecule that is partially regulated by phosphorylation. These findings are discussed in relation to the recent discovery that nsp3 forms a molecular pore in the double-membrane vesicles that sequester the coronavirus replicase-transcriptase.
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Affiliation(s)
- Cheri A Koetzner
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Kelley R Hurst-Hess
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Lili Kuo
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA
| | - Paul S Masters
- Laboratory of Viral Replication and Vector Biology, Wadsworth Center, New York State Department of Health, Slingerlands, NY, 12159, USA; Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, NY, 12208, USA.
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45
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Grover A, Sinha R, Jyoti D, Faggio C. Imperative role of electron microscopy in toxicity assessment: A review. Microsc Res Tech 2021; 85:1976-1989. [PMID: 34904321 DOI: 10.1002/jemt.24029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
Electron microscope (EM) was developed in 1931 and since then microscopical examination of both the biological and non-biological samples has been revolutionized. Modifications in electron microscopy techniques, such as scanning EM and transmission EM, have widened their applicability in the various sectors such as understanding of drug toxicity, development of mechanism, criminal site investigation, and characterization of the nano-molecule. The present review summarizes its role in important aspects such as toxicity assessment and disease diagnosis in special reference to SARS-COV2. In the biological system, EM studies have elucidated the impact of toxicants at the ultra-structural level in various tissue in conformity to physiological alterations. Thus, EM can be concluded as an important tool in toxicity assessment and disease prognosis.
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Affiliation(s)
- Aseem Grover
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Reshma Sinha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Divya Jyoti
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
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46
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Sun L, Zhao C, Fu Z, Fu Y, Su Z, Li Y, Zhou Y, Tan Y, Li J, Xiang Y, Nie X, Zhang J, Liu F, Zhao S, Xie S, Peng G. Genome-scale CRISPR screen identifies TMEM41B as a multi-function host factor required for coronavirus replication. PLoS Pathog 2021; 17:e1010113. [PMID: 34871328 PMCID: PMC8675922 DOI: 10.1371/journal.ppat.1010113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 12/16/2021] [Accepted: 11/14/2021] [Indexed: 12/15/2022] Open
Abstract
Emerging coronaviruses (CoVs) pose a severe threat to human and animal health worldwide. To identify host factors required for CoV infection, we used α-CoV transmissible gastroenteritis virus (TGEV) as a model for genome-scale CRISPR knockout (KO) screening. Transmembrane protein 41B (TMEM41B) was found to be a bona fide host factor involved in infection by CoV and three additional virus families. We found that TMEM41B is critical for the internalization and early-stage replication of TGEV. Notably, our results also showed that cells lacking TMEM41B are unable to form the double-membrane vesicles necessary for TGEV replication, indicating that TMEM41B contributes to the formation of CoV replication organelles. Lastly, our data from a mouse infection model showed that the KO of this factor can strongly inhibit viral infection and delay the progression of a CoV disease. Our study revealed that targeting TMEM41B is a highly promising approach for the development of broad-spectrum anti-viral therapeutics.
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Affiliation(s)
- Limeng Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Changzhi Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China
| | - Zhen Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Yanan Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Zhelin Su
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Yangyang Li
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, P. R. China
| | - Yuan Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yubei Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yixin Xiang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
| | - Xiongwei Nie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China
| | - Jinfu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China
| | - Fei Liu
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, P. R. China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, P. R. China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China
- * E-mail: (SX); (GP)
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, P. R. China
- * E-mail: (SX); (GP)
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Srinivasan K, Pandey AK, Livingston A, Venkatesh S. Roles of host mitochondria in the development of COVID-19 pathology: Could mitochondria be a potential therapeutic target? MOLECULAR BIOMEDICINE 2021; 2:38. [PMID: 34841263 PMCID: PMC8608434 DOI: 10.1186/s43556-021-00060-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023] Open
Abstract
The recent emergence of severe acute respiratory syndrome-Corona Virus 2 (SARS-CoV-2) in late 2019 and its spread worldwide caused an acute pandemic of Coronavirus disease 19 (COVID-19). Since then, COVID-19 has been under intense scrutiny as its outbreak led to significant changes in healthcare, social activities, and economic settings worldwide. Although angiotensin-converting enzyme-2 (ACE-2) receptor is shown to be the primary port of SARS-CoV-2 entry in cells, the mechanisms behind the establishment and pathologies of COVID-19 are poorly understood. As recent studies have shown that host mitochondria play an essential role in virus-mediated innate immune response, pathologies, and infection, in this review, we will discuss in detail the entry and progression of SARS-CoV-2 and how mitochondria could play roles in COVID-19 disease. We will also review the potential interactions between SARS-CoV-2 and mitochondria and discuss possible treatments, including whether mitochondria as a potential therapeutic target in COVID-19. Understanding SARS-CoV-2 and mitochondrial interactions mediated virus establishment, inflammation, and other consequences may provide a unique mechanism and conceptual advancement in finding a novel treatment for COVID-19.
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Affiliation(s)
- Kavya Srinivasan
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers -New Jersey Medical School, The State University of New Jersey, Newark, NJ USA
- New York Institute of Technology, Old Westbury, NY USA
| | - Ashutosh Kumar Pandey
- Department of Pharmacology, Physiology and Neuroscience, Rutgers -New Jersey Medical School, The State University of New Jersey, Newark, NJ USA
| | | | - Sundararajan Venkatesh
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers -New Jersey Medical School, The State University of New Jersey, Newark, NJ USA
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48
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Alshammary AF, Al-Sulaiman AM. The journey of SARS-CoV-2 in human hosts: a review of immune responses, immunosuppression, and their consequences. Virulence 2021; 12:1771-1794. [PMID: 34251989 PMCID: PMC8276660 DOI: 10.1080/21505594.2021.1929800] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly infectious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Laboratory findings from a significant number of patients with COVID-19 indicate the occurrence of leukocytopenia, specifically lymphocytopenia. Moreover, infected patients can experience contrasting outcomes depending on lymphocytopenia status. Patients with resolved lymphocytopenia are more likely to recover, whereas critically ill patients with signs of unresolved lymphocytopenia develop severe complications, sometimes culminating in death. Why immunodepression manifests in patients with COVID-19 remains unclear. Therefore, the evaluation of clinical symptoms and laboratory findings from infected patients is critical for understanding the disease course and its consequences. In this review, we take a logical approach to unravel the reasons for immunodepression in patients with COVID-19. Following the footprints of the virus within host tissues, from entry to exit, we extrapolate the mechanisms underlying the phenomenon of immunodepression.
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Affiliation(s)
- Amal F. Alshammary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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49
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Chhajer H, Rizvi VA, Roy R. Life cycle process dependencies of positive-sense RNA viruses suggest strategies for inhibiting productive cellular infection. J R Soc Interface 2021; 18:20210401. [PMID: 34753308 PMCID: PMC8580453 DOI: 10.1098/rsif.2021.0401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/18/2021] [Indexed: 12/25/2022] Open
Abstract
Life cycle processes of positive-strand (+)RNA viruses are broadly conserved across families, yet they employ different strategies to grow in the cell. Using a generalized dynamical model for intracellular (+)RNA virus growth, we decipher these life cycle determinants and their dependencies for several viruses and parse the effects of viral mutations, drugs and host cell permissivity. We show that poliovirus employs rapid replication and virus assembly, whereas the Japanese encephalitis virus leverages its higher rate of translation and efficient cellular reorganization compared to the hepatitis C virus. Stochastic simulations demonstrate infection extinction if all seeding (inoculating) viral RNA degrade before establishing robust replication critical for infection. The probability of this productive cellular infection, 'cellular infectivity', is affected by virus-host processes and defined by early life cycle events and viral seeding. An increase in cytoplasmic RNA degradation and delay in vesicular compartment formation reduces infectivity, more so when combined. Synergy among these parameters in limiting (+)RNA virus infection as predicted by our model suggests new avenues for inhibiting infections by targeting the early life cycle bottlenecks.
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Affiliation(s)
- Harsh Chhajer
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Vaseef A. Rizvi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Rahul Roy
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
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50
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Rein T. Harnessing autophagy to fight SARS-CoV-2: An update in view of recent drug development efforts. J Cell Biochem 2021; 123:155-160. [PMID: 34668225 PMCID: PMC9088732 DOI: 10.1002/jcb.30166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 10/12/2021] [Indexed: 01/18/2023]
Abstract
Drug repurposing is an attractive option for identifying new treatment strategies, in particular in extraordinary situations of urgent need such as the current coronavirus disease 2019 (Covid-19) pandemic. Recently, the World Health Organization announced testing of three drugs as potential Covid-19 therapeutics that are known for their dampening effect on the immune system. Thus, the underlying concept of selecting these drugs is to temper the potentially life-threatening overshooting of the immune system reacting to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. This viewpoint discusses the possibility that the impact of these and other drugs on autophagy contributes to their therapeutic effect by hampering the SARS-CoV-2 life cycle.
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Affiliation(s)
- Theo Rein
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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