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Partiot E, Hirschler A, Colomb S, Lutz W, Claeys T, Delalande F, Deffieu MS, Bare Y, Roels JRE, Gorda B, Bons J, Callon D, Andreoletti L, Labrousse M, Jacobs FMJ, Rigau V, Charlot B, Martens L, Carapito C, Ganesh G, Gaudin R. Brain exposure to SARS-CoV-2 virions perturbs synaptic homeostasis. Nat Microbiol 2024; 9:1189-1206. [PMID: 38548923 DOI: 10.1038/s41564-024-01657-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 03/04/2024] [Indexed: 04/21/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with short- and long-term neurological complications. The variety of symptoms makes it difficult to unravel molecular mechanisms underlying neurological sequalae after coronavirus disease 2019 (COVID-19). Here we show that SARS-CoV-2 triggers the up-regulation of synaptic components and perturbs local electrical field potential. Using cerebral organoids, organotypic culture of human brain explants from individuals without COVID-19 and post-mortem brain samples from individuals with COVID-19, we find that neural cells are permissive to SARS-CoV-2 to a low extent. SARS-CoV-2 induces aberrant presynaptic morphology and increases expression of the synaptic components Bassoon, latrophilin-3 (LPHN3) and fibronectin leucine-rich transmembrane protein-3 (FLRT3). Furthermore, we find that LPHN3-agonist treatment with Stachel partially restored organoid electrical activity and reverted SARS-CoV-2-induced aberrant presynaptic morphology. Finally, we observe accumulation of relatively static virions at LPHN3-FLRT3 synapses, suggesting that local hindrance can contribute to synaptic perturbations. Together, our study provides molecular insights into SARS-CoV-2-brain interactions, which may contribute to COVID-19-related neurological disorders.
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Affiliation(s)
- Emma Partiot
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
- Univ Montpellier, Montpellier, France
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI─FR2048, Strasbourg, France
| | - Sophie Colomb
- EDPFM (Equipe de Droit Pénal et de Sciences Forensiques de Montpellier), Univ Montpellier, Montpellier, France
- Emergency Pole, Forensic Medicine Department, Montpellier University Hospital, Montpellier, France
| | - Willy Lutz
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
- Univ Montpellier, Montpellier, France
- UM-CNRS Laboratoire d'Informatique de Robotique et de Microelectronique de Montpellier (LIRMM), Montpellier, France
| | - Tine Claeys
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - François Delalande
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI─FR2048, Strasbourg, France
| | - Maika S Deffieu
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
- Univ Montpellier, Montpellier, France
| | - Yonis Bare
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
- Univ Montpellier, Montpellier, France
| | - Judith R E Roels
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Barbara Gorda
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
- Univ Montpellier, Montpellier, France
| | - Joanna Bons
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI─FR2048, Strasbourg, France
| | - Domitille Callon
- University of Reims Champagne-Ardenne, Medicine Faculty, Laboratory of Virology, CardioVir UMR-S 1320, Reims, France
- Forensic, Virology and ENT Departments, University Hospital Centre (CHU), Reims, France
| | - Laurent Andreoletti
- University of Reims Champagne-Ardenne, Medicine Faculty, Laboratory of Virology, CardioVir UMR-S 1320, Reims, France
- Forensic, Virology and ENT Departments, University Hospital Centre (CHU), Reims, France
| | - Marc Labrousse
- Forensic, Virology and ENT Departments, University Hospital Centre (CHU), Reims, France
- Anatomy laboratory, UFR Médecine, Université de Reims Champagne-Ardenne, Reims, France
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Valérie Rigau
- Univ Montpellier, Montpellier, France
- Pathological Department and Biological Resources Center BRC, Montpellier University Hospital, 'Cerebral plasticity, Stem cells and Glial tumors' team. IGF- Institut de génomique fonctionnelle INSERM U 1191 - CNRS UMR 5203, Univ Montpellier, Montpellier, France
| | - Benoit Charlot
- Univ Montpellier, Montpellier, France
- Institut d'Electronique et des Systèmes (IES), CNRS, Montpellier, France
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI─FR2048, Strasbourg, France
| | - Gowrishankar Ganesh
- Univ Montpellier, Montpellier, France
- UM-CNRS Laboratoire d'Informatique de Robotique et de Microelectronique de Montpellier (LIRMM), Montpellier, France
| | - Raphael Gaudin
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France.
- Univ Montpellier, Montpellier, France.
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Carrión F, Rammauro F, Olivero‐Deibe N, Fló M, Portela MM, Lima A, Durán R, Pritsch O, Bianchi S. Soluble SARS-CoV-2 RBD and human ACE2 peptidase domain produced in Drosophila S2 cells show functions evoking virus-cell interface. Protein Sci 2023; 32:e4721. [PMID: 37405395 PMCID: PMC10382795 DOI: 10.1002/pro.4721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/06/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023]
Abstract
The interaction between the receptor-binding domain (RBD) of the spike glycoprotein of SARS-CoV-2 and the peptidase domain of the human angiotensin-converting enzyme 2 (ACE2) allows the first specific contact at the virus-cell interface making it the main target of neutralizing antibodies. Here, we show a unique and cost-effective protocol using Drosophila S2 cells to produce both RBD and soluble human ACE2 peptidase domain (shACE2) as thermostable proteins, purified via Strep-tag with yields >40 mg L-1 in a laboratory scale. Furthermore, we demonstrate its binding with KD values in the lower nanomolar range (independently of Strep-tag removal) and its capability to be blocked by serum antibodies in a competition ELISA with Strep-Tactin-HRP as a proof-of-concept. In addition, we assess the capacity of RBD to bind native dimeric ACE2 overexpressed in human cells and its antigen properties with specific serum antibodies. Finally, for completeness, we analyzed RBD microheterogeneity associated with glycosylation and negative charges, with negligible effect on binding either with antibodies or shACE2. Our system represents an accessible and reliable tool for designing in-house surrogate virus neutralization tests (sVNTs), enabling the rapid characterization of neutralizing humoral responses elicited against vaccines or infection, especially in the absence of facilities to conduct virus neutralization tests. Moreover, our biophysical and biochemical characterization of RBD and shACE2 produced in S2 cells lays the groundwork for adapting to different variants of concern (VOCs) to study humoral responses elicited against different VOCs and vaccine formulations.
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Affiliation(s)
- Federico Carrión
- Laboratorio de InmunovirologíaInstitut Pasteur de MontevideoMontevideoUruguay
| | - Florencia Rammauro
- Laboratorio de InmunovirologíaInstitut Pasteur de MontevideoMontevideoUruguay
- Facultad de Medicina, Departamento de InmunobiologíaUniversidad de la RepúblicaMontevideoUruguay
| | | | - Martín Fló
- Laboratorio de InmunovirologíaInstitut Pasteur de MontevideoMontevideoUruguay
- Facultad de Medicina, Departamento de InmunobiologíaUniversidad de la RepúblicaMontevideoUruguay
| | - María Magdalena Portela
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo & Instituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
- Facultad de CienciasUniversidad de la RepúblicaMontevideoUruguay
| | - Analía Lima
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo & Instituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo & Instituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
| | - Otto Pritsch
- Laboratorio de InmunovirologíaInstitut Pasteur de MontevideoMontevideoUruguay
- Facultad de Medicina, Departamento de InmunobiologíaUniversidad de la RepúblicaMontevideoUruguay
| | - Sergio Bianchi
- Departamento de Fisiopatología, Laboratorio de Biomarcadores Moleculares, Hospital de ClínicasUniversidad de la RepúblicaMontevideoUruguay
- Laboratorio de Genómica FuncionalInstitut Pasteur de MontevideoMontevideoUruguay
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3
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Beaudoin CA, Petsolari E, Hamaia SW, Hala S, Alofi FS, Pandurangan AP, Blundell TL, Chaitanya Vedithi S, Huang CLH, Jackson AP. SARS-CoV-2 Omicron subvariant spike N405 unlikely to rapidly deamidate. Biochem Biophys Res Commun 2023; 666:61-67. [PMID: 37178506 PMCID: PMC10152834 DOI: 10.1016/j.bbrc.2023.04.088] [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: 04/04/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The RGD motif on the SARS-CoV-2 spike protein has been suggested to interact with RGD-binding integrins αVβ3 and α5β1 to enhance viral cell entry and alter downstream signaling cascades. The D405N mutation on the Omicron subvariant spike proteins, resulting in an RGN motif, has recently been shown to inhibit binding to integrin αVβ3. Deamidation of asparagines in protein ligand RGN motifs has been demonstrated to generate RGD and RGisoD motifs that permit binding to RGD-binding integrins. Two asparagines, N481 and N501, on the Wild-type spike receptor-binding domain have been previously shown to have deamidation half-lives of 16.5 and 123 days, respectively, which may occur during the viral life cycle. Deamidation of Omicron subvariant N405 may recover the ability to interact with RGD-binding integrins. Thus, herein, all-atom molecular dynamics simulations of the Wild-type and Omicron subvariant spike protein receptor-binding domains were conducted to investigate the potential for asparagines, the Omicron subvariant N405 in particular, to assume the optimized geometry for deamidation to occur. In summary, the Omicron subvariant N405 was primarily found to be stabilized in a state unfavourable for deamidation after hydrogen bonding with downstream E406. Nevertheless, a small number of RGD or RGisoD motifs on the Omicron subvariant spike proteins may restore the ability to interact with RGD-binding integrins. The simulations also provided structural clarification regarding the deamidation rates of Wild-type N481 and N501 and highlighted the utility of tertiary structure dynamics information in predicting asparagine deamidation. Further work is needed to characterize the effects of deamidation on spike-integrin interactions.
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Affiliation(s)
- Christopher A Beaudoin
- Department of Biochemistry, Hopkins Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom.
| | - Emmanouela Petsolari
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Samir W Hamaia
- Department of Biochemistry, Hopkins Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom
| | - Sharif Hala
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia; King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Fadwa S Alofi
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Arun P Pandurangan
- Heart and Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, United Kingdom
| | - Tom L Blundell
- Heart and Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, United Kingdom
| | - Sundeep Chaitanya Vedithi
- Heart and Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, CB2 0BB, United Kingdom
| | - Christopher L-H Huang
- Department of Biochemistry, Hopkins Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom; Physiological Laboratory, University of Cambridge, Downing Street, Cambridge, CB2 3EG, United Kingdom
| | - Antony P Jackson
- Department of Biochemistry, Hopkins Building, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom.
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Dyakin VV, Uversky VN. Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality. Int J Mol Sci 2022; 23:ijms23073687. [PMID: 35409047 PMCID: PMC8998916 DOI: 10.3390/ijms23073687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Orangeburg, NY 10962, USA
- Correspondence:
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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