1
|
Baggen J, Jacquemyn M, Persoons L, Vanstreels E, Pye VE, Wrobel AG, Calvaresi V, Martin SR, Roustan C, Cronin NB, Reading E, Thibaut HJ, Vercruysse T, Maes P, De Smet F, Yee A, Nivitchanyong T, Roell M, Franco-Hernandez N, Rhinn H, Mamchak AA, Ah Young-Chapon M, Brown E, Cherepanov P, Daelemans D. TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry. Cell 2023; 186:3427-3442.e22. [PMID: 37421949 PMCID: PMC10409496 DOI: 10.1016/j.cell.2023.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/24/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
SARS-CoV-2 is associated with broad tissue tropism, a characteristic often determined by the availability of entry receptors on host cells. Here, we show that TMEM106B, a lysosomal transmembrane protein, can serve as an alternative receptor for SARS-CoV-2 entry into angiotensin-converting enzyme 2 (ACE2)-negative cells. Spike substitution E484D increased TMEM106B binding, thereby enhancing TMEM106B-mediated entry. TMEM106B-specific monoclonal antibodies blocked SARS-CoV-2 infection, demonstrating a role of TMEM106B in viral entry. Using X-ray crystallography, cryogenic electron microscopy (cryo-EM), and hydrogen-deuterium exchange mass spectrometry (HDX-MS), we show that the luminal domain (LD) of TMEM106B engages the receptor-binding motif of SARS-CoV-2 spike. Finally, we show that TMEM106B promotes spike-mediated syncytium formation, suggesting a role of TMEM106B in viral fusion. Together, our findings identify an ACE2-independent SARS-CoV-2 infection mechanism that involves cooperative interactions with the receptors heparan sulfate and TMEM106B.
Collapse
Affiliation(s)
- Jim Baggen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium.
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Leentje Persoons
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Els Vanstreels
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Valeria Calvaresi
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London SE1 1DB, UK
| | - Stephen R Martin
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, Francis Crick Institute, London NW1 1AT, UK
| | - Nora B Cronin
- LonCEM Facility, Francis Crick Institute, London NW1 1AT, UK
| | - Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London SE1 1DB, UK
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven 3000, Belgium
| | - Frederik De Smet
- KU Leuven Department of Imaging and Pathology, Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Leuven 3000, Belgium
| | - Angie Yee
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | - Toey Nivitchanyong
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | - Marina Roell
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | | | - Herve Rhinn
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | - Alusha Andre Mamchak
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | | | - Eric Brown
- Alector LLC, 131 Oyster Point Blvd. Suite 600, South San Francisco, CA 94080, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK; Department of Infectious Disease, Section of Virology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK.
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven 3000, Belgium.
| |
Collapse
|
2
|
Wrobel AG. Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike. Curr Opin Struct Biol 2023; 81:102619. [PMID: 37285618 PMCID: PMC10183628 DOI: 10.1016/j.sbi.2023.102619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023]
Abstract
Spike glycoprotein of SARS-CoV-2 mediates viral entry into host cells by facilitating virus attachment and membrane fusion. ACE2 is the main receptor of SARS-CoV-2 and its interaction with spike has shaped the virus' emergence from an animal reservoir and subsequent evolution in the human host. Many structural studies on the spike:ACE2 interaction have provided insights into mechanisms driving viral evolution during the on-going pandemic. This review describes the molecular basis of spike binding to ACE2, outlines mechanisms that have optimised this interaction during viral evolution, and suggests directions for future research.
Collapse
Affiliation(s)
- Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, United Kingdom.
| |
Collapse
|
3
|
Olajide OM, Osman MK, Robert J, Kessler S, Toews LK, Thamamongood T, Neefjes J, Wrobel AG, Schwemmle M, Ciminski K, Reuther P. Evolutionarily conserved amino acids in MHC-II mediate bat influenza A virus entry into human cells. PLoS Biol 2023; 21:e3002182. [PMID: 37410798 DOI: 10.1371/journal.pbio.3002182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
The viral hemagglutinins of conventional influenza A viruses (IAVs) bind to sialylated glycans on host cell surfaces for attachment and subsequent infection. In contrast, hemagglutinins of bat-derived IAVs target major histocompatibility complex class II (MHC-II) for cell entry. MHC-II proteins from various vertebrate species can facilitate infection with the bat IAV H18N11. Yet, it has been difficult to biochemically determine the H18:MHC-II binding. Here, we followed a different approach and generated MHC-II chimeras from the human leukocyte antigen DR (HLA-DR), which supports H18-mediated entry, and the nonclassical MHC-II molecule HLA-DM, which does not. In this context, viral entry was supported only by a chimera containing the HLA-DR α1, α2, and β1 domains. Subsequent modeling of the H18:HLA-DR interaction identified the α2 domain as central for this interaction. Further mutational analyses revealed highly conserved amino acids within loop 4 (N149) and β-sheet 6 (V190) of the α2 domain as critical for virus entry. This suggests that conserved residues in the α1, α2, and β1 domains of MHC-II mediate H18-binding and virus propagation. The conservation of MHC-II amino acids, which are critical for H18N11 binding, may explain the broad species specificity of this virus.
Collapse
Affiliation(s)
- Okikiola M Olajide
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maria Kaukab Osman
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jonathan Robert
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Susanne Kessler
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lina Kathrin Toews
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thiprampai Thamamongood
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Nueng, Khlong Luang District, Pathum Thani, Thailand
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kevin Ciminski
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Reuther
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
4
|
Le TT, Benton DJ, Wrobel AG, Gamblin SJ. Development of high affinity broadly reactive aptamers for spike protein of multiple SARS-CoV-2 variants. RSC Adv 2023; 13:15322-15326. [PMID: 37213341 PMCID: PMC10197177 DOI: 10.1039/d3ra01382k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023] Open
Abstract
We have developed broadly reactive aptamers against multiple variants by alternating the target between spike proteins from different SARS-CoV-2 variants during the selection process. In this process we have developed aptamers which can recognise all variants, from the original wild-type 'Wuhan' strain to Omicron, with high affinity (Kd values in the pM range).
Collapse
Affiliation(s)
- Thao T Le
- Department of Chemistry, Imperial College London UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute UK
| | - Steven J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute UK
| |
Collapse
|
5
|
Jaki L, Weigang S, Kern L, Kramme S, Wrobel AG, Grawitz AB, Nawrath P, Martin SR, Dähne T, Beer J, Disch M, Kolb P, Gutbrod L, Reuter S, Warnatz K, Schwemmle M, Gamblin SJ, Neumann-Haefelin E, Schnepf D, Welte T, Kochs G, Huzly D, Panning M, Fuchs J. Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient. Nat Commun 2023; 14:1999. [PMID: 37037847 PMCID: PMC10085998 DOI: 10.1038/s41467-023-37591-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
Monoclonal antibodies (mAbs) directed against the spike of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are effective therapeutic options to combat infections in high-risk patients. Here, we report the adaptation of SARS-CoV-2 to the mAb cocktail REGN-COV in a kidney transplant patient with hypogammaglobulinemia. Following mAb treatment, the patient did not clear the infection. During viral persistence, SARS-CoV-2 acquired three novel spike mutations. Neutralization and mouse protection analyses demonstrate a complete viral escape from REGN-COV at the expense of ACE-2 binding. Final clearance of the virus occurred upon reduction of the immunosuppressive regimen and total IgG substitution. Serology suggests that the development of highly neutralizing IgM rather than IgG substitution aids clearance. Our findings emphasise that selection pressure by mAbs on SARS-CoV-2 can lead to development of escape variants in immunocompromised patients. Thus, modification of immunosuppressive therapy, if possible, might be preferable to control and clearance of the viral infection.
Collapse
Affiliation(s)
- Lena Jaki
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Weigang
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lisa Kern
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefanie Kramme
- Institute for Infection Prevention and Hospital Epidemiology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Antoni G Wrobel
- The Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Andrea B Grawitz
- Institute for Clinical Chemistry and Laboratory Medicine, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Nawrath
- The Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Stephen R Martin
- The Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Theo Dähne
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julius Beer
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Disch
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp Kolb
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lisa Gutbrod
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven J Gamblin
- The Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Elke Neumann-Haefelin
- Renal Division, Department of Medicine, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel Schnepf
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Welte
- Renal Division, Department of Medicine, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kochs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniela Huzly
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Jonas Fuchs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
6
|
Gonzalez-Rodriguez E, Zol-Hanlon M, Bineva-Todd G, Marchesi A, Skehel M, Mahoney KE, Roustan C, Borg A, Di Vagno L, Kjær S, Wrobel AG, Benton DJ, Nawrath P, Flitsch SL, Joshi D, González-Ramírez A, Wilkinson KA, Wilkinson RJ, Wall EC, Hurtado-Guerrero R, Malaker SA, Schumann B. O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Likely Contribute to the Mutational Trajectory in Variants of Concern. ACS Cent Sci 2023; 9:393-404. [PMID: 36968546 PMCID: PMC10037455 DOI: 10.1021/acscentsci.2c01349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 06/18/2023]
Abstract
The emergence of a polybasic cleavage motif for the protease furin in SARS-CoV-2 spike has been established as a major factor for human viral transmission. The region N-terminal to that motif is extensively mutated in variants of concern (VOCs). Besides furin, spikes from these variants appear to rely on other proteases for maturation, including TMPRSS2. Glycans near the cleavage site have raised questions about proteolytic processing and the consequences of variant-borne mutations. Here, we identify that sialic acid-containing O-linked glycans on Thr678 of SARS-CoV-2 spike influence furin and TMPRSS2 cleavage and posit O-linked glycosylation as a likely driving force for the emergence of VOC mutations. We provide direct evidence that the glycosyltransferase GalNAc-T1 primes glycosylation at Thr678 in the living cell, an event that is suppressed by mutations in the VOCs Alpha, Delta, and Omicron. We found that the sole incorporation of N-acetylgalactosamine did not impact furin activity in synthetic O-glycopeptides, but the presence of sialic acid reduced the furin rate by up to 65%. Similarly, O-glycosylation with a sialylated trisaccharide had a negative impact on TMPRSS2 cleavage. With a chemistry-centered approach, we substantiate O-glycosylation as a major determinant of spike maturation and propose disruption of O-glycosylation as a substantial driving force for VOC evolution.
Collapse
Affiliation(s)
- Edgar Gonzalez-Rodriguez
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mia Zol-Hanlon
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Signalling
and Structural Biology Lab, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Ganka Bineva-Todd
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
| | - Andrea Marchesi
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mark Skehel
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Keira E. Mahoney
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Chloë Roustan
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Annabel Borg
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lucia Di Vagno
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjær
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Antoni G. Wrobel
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Donald J. Benton
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Philipp Nawrath
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Sabine L. Flitsch
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Dhira Joshi
- Chemical
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Katalin A. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Robert J. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
- Department
of Infectious Diseases, Imperial College
London, W12 0NN London, United Kingdom
- Institute
of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Emma C. Wall
- The Francis
Crick Institute, NW1 1AT London, United Kingdom
- University
College London Hospitals (UCLH) Biomedical Research Centre, W1T 7DN London, United Kingdom
| | - Ramón Hurtado-Guerrero
- Institute
of Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018 Zaragoza, Spain
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Fundación
ARAID, 50018 Zaragoza, Spain
| | - Stacy A. Malaker
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Benjamin Schumann
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| |
Collapse
|
7
|
Calvaresi V, Wrobel AG, Toporowska J, Hammerschmid D, Doores KJ, Bradshaw RT, Parsons RB, Benton DJ, Roustan C, Reading E, Malim MH, Gamblin SJ, Politis A. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Nat Commun 2023; 14:1421. [PMID: 36918534 PMCID: PMC10013288 DOI: 10.1038/s41467-023-36745-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/15/2023] [Indexed: 03/15/2023] Open
Abstract
SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic surface. Spikes of variants of concern (VOCs) acquired amino acid changes linked to increased virulence and immune evasion. Here, using HDX-MS, we identified changes in spike dynamics that we associate with the transition from closed to open conformations, to ACE2 binding, and to specific mutations in VOCs. We show that the RBD-associated subdomain plays a role in spike opening, whereas the NTD acts as a hotspot of conformational divergence of VOC spikes driving immune evasion. Alpha, beta and delta spikes assume predominantly open conformations and ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly closed conformations, presumably enabling it to escape antibodies. At the same time, its core helices show characteristics of being pre-primed for fusion even in the absence of ACE2. These data inform on SARS-CoV-2 evolution and omicron variant emergence.
Collapse
Affiliation(s)
- Valeria Calvaresi
- Department of Chemistry, King's College London, SE1 1DB, London, UK.
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
| | | | | | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT, London, UK
| | | | | | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT, London, UK
| | - Eamonn Reading
- Department of Chemistry, King's College London, SE1 1DB, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT, London, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, SE1 1DB, London, UK.
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, M13 9PT, Manchester, UK.
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN, Manchester, UK.
| |
Collapse
|
8
|
Nawrath P, Wrobel AG. Hold your horses: The receptor-binding domains of SARS-CoV-2, SARS-CoV, and hCoV-NL63 bind equine ACE2. Structure 2022; 30:1367-1368. [PMID: 36206735 PMCID: PMC9535849 DOI: 10.1016/j.str.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this issue of Structure, Lan and colleagues seek to identify regions on the ACE2 receptor and coronavirus spikes that are essential for the viral attachment. They achieve it through a detailed comparative analysis of the binding of coronaviruses NL63, SARS-CoV, and several SARS-CoV-2 variants with human and horse ACE2.
Collapse
Affiliation(s)
- Philipp Nawrath
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Antoni G. Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK,Corresponding author
| |
Collapse
|
9
|
Zaccai NR, Kadlecova Z, Dickson VK, Korobchevskaya K, Kamenicky J, Kovtun O, Umasankar PK, Wrobel AG, Kaufman JGG, Gray SR, Qu K, Evans PR, Fritzsche M, Sroubek F, Höning S, Briggs JAG, Kelly BT, Owen DJ, Traub LM. FCHO controls AP2's initiating role in endocytosis through a PtdIns(4,5)P 2-dependent switch. Sci Adv 2022; 8:eabn2018. [PMID: 35486718 PMCID: PMC9054013 DOI: 10.1126/sciadv.abn2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo adaptor AP2 requires membrane-localized Fer/Cip4 homology domain-only proteins (FCHO). Here, live-cell enhanced total internal reflection fluorescence-structured illumination microscopy shows that FCHO marks sites of clathrin-coated pit (CCP) initiation, which mature into uniform-sized CCPs comprising a central patch of AP2 and clathrin corralled by an FCHO/Epidermal growth factor potential receptor substrate number 15 (Eps15) ring. We dissect the network of interactions between the FCHO interdomain linker and AP2, which concentrates, orients, tethers, and partially destabilizes closed AP2 at the plasma membrane. AP2's subsequent membrane deposition drives its opening, which triggers FCHO displacement through steric competition with phosphatidylinositol 4,5-bisphosphate, clathrin, cargo, and CME accessory factors. FCHO can now relocate toward a CCP's outer edge to engage and activate further AP2s to drive CCP growth/maturation.
Collapse
Affiliation(s)
- Nathan R. Zaccai
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Zuzana Kadlecova
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Kseniya Korobchevskaya
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK
| | - Jan Kamenicky
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - Oleksiy Kovtun
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Perunthottathu K. Umasankar
- Intracellular Trafficking Laboratory, Transdisciplinary Biology Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Antoni G. Wrobel
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | | | - Sally R. Gray
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Kun Qu
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | | | - Marco Fritzsche
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK
- Rosalind Franklin Institute, Harwell Campus, Didcot, UK
| | - Filip Sroubek
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - Stefan Höning
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Straße 52, 50931 Cologne, Germany
| | - John A. G. Briggs
- MRC LMB Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Bernard T. Kelly
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - David J. Owen
- CIMR, University of Cambridge, Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Linton M. Traub
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, Pittsburgh, PA, USA
| |
Collapse
|
10
|
Ng KW, Faulkner N, Wrobel AG, Gamblin SJ, Kassiotis G. Heterologous humoral immunity to human and zoonotic coronaviruses: Aiming for the achilles heel. Semin Immunol 2021; 55:101507. [PMID: 34716096 PMCID: PMC8542444 DOI: 10.1016/j.smim.2021.101507] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 02/04/2023]
Abstract
Coronaviruses are evolutionarily successful RNA viruses, common to multiple avian, amphibian and mammalian hosts. Despite their ubiquity and potential impact, knowledge of host immunity to coronaviruses remains incomplete, partly owing to the lack of overt pathogenicity of endemic human coronaviruses (HCoVs), which typically cause common colds. However, the need for deeper understanding became pressing with the zoonotic introduction of three novel coronaviruses in the past two decades, causing severe acute respiratory syndromes in humans, and the unfolding pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This renewed interest not only triggered the discovery of two of the four HCoVs, but also uncovered substantial cellular and humoral cross-reactivity with shared or related coronaviral antigens. Here, we review the evidence for cross-reactive B cell memory elicited by HCoVs and its potential impact on the puzzlingly variable outcome of SARS-CoV-2 infection. The available data indicate targeting of highly conserved regions primarily in the S2 subunits of the spike glycoproteins of HCoVs and SARS-CoV-2 by cross-reactive B cells and antibodies. Rare monoclonal antibodies reactive with conserved S2 epitopes and with potent virus neutralising activity have been cloned, underscoring the potential functional relevance of cross-reactivity. We discuss B cell and antibody cross-reactivity in the broader context of heterologous humoral immunity to coronaviruses, as well as the limits of protective immune memory against homologous re-infection. Given the bidirectional nature of cross-reactivity, the unprecedented current vaccination campaign against SARS-CoV-2 is expected to impact HCoVs, as well as future zoonotic coronaviruses attempting to cross the species barrier. However, emerging SARS-CoV-2 variants with resistance to neutralisation by vaccine-induced antibodies highlight a need for targeting more constrained, less mutable parts of the spike. The delineation of such cross-reactive areas, which humoral immunity can be trained to attack, may offer the key to permanently shifting the balance of our interaction with current and future coronaviruses in our favour.
Collapse
Affiliation(s)
- Kevin W. Ng
- Retroviral Immunology Laboratory, London, NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology Laboratory, London, NW1 1AT, UK,National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Antoni G. Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Steve J. Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, London, NW1 1AT, UK,Department of Infectious Disease, St Mary's Hospital, Imperial College London, London W2 1PG, UK,Corresponding author at: Retroviral Immunology Laboratory, London, NW1 1AT, UK
| |
Collapse
|
11
|
Rosa A, Pye VE, Graham C, Muir L, Seow J, Ng KW, Cook NJ, Rees-Spear C, Parker E, Dos Santos MS, Rosadas C, Susana A, Rhys H, Nans A, Masino L, Roustan C, Christodoulou E, Ulferts R, Wrobel AG, Short CE, Fertleman M, Sanders RW, Heaney J, Spyer M, Kjær S, Riddell A, Malim MH, Beale R, MacRae JI, Taylor GP, Nastouli E, van Gils MJ, Rosenthal PB, Pizzato M, McClure MO, Tedder RS, Kassiotis G, McCoy LE, Doores KJ, Cherepanov P. SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity. Sci Adv 2021; 7:eabg7607. [PMID: 33888467 PMCID: PMC8163077 DOI: 10.1126/sciadv.abg7607] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/02/2021] [Indexed: 05/11/2023]
Abstract
The coronaviral spike is the dominant viral antigen and the target of neutralizing antibodies. We show that SARS-CoV-2 spike binds biliverdin and bilirubin, the tetrapyrrole products of heme metabolism, with nanomolar affinity. Using cryo-electron microscopy and x-ray crystallography, we mapped the tetrapyrrole interaction pocket to a deep cleft on the spike N-terminal domain (NTD). At physiological concentrations, biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of neutralizing antibodies. Access to the tetrapyrrole-sensitive epitope is gated by a flexible loop on the distal face of the NTD. Accompanied by profound conformational changes in the NTD, antibody binding requires relocation of the gating loop, which folds into the cleft vacated by the metabolite. Our results indicate that SARS-CoV-2 spike NTD harbors a dominant epitope, access to which can be controlled by an allosteric mechanism that is regulated through recruitment of a metabolite.
Collapse
Affiliation(s)
- Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Kevin W Ng
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Eleanor Parker
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | | | - Carolina Rosadas
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Alberto Susana
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Hefin Rhys
- Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Laura Masino
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK
| | - Charlotte-Eve Short
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Michael Fertleman
- Cutrale Perioperative and Ageing Group, Imperial College London, London, UK
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
- Weill Medical College of Cornell University, New York, NY, USA
| | - Judith Heaney
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
| | - Moira Spyer
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Andy Riddell
- Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London, UK
| | - James I MacRae
- Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Graham P Taylor
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Eleni Nastouli
- Advanced Pathogen Diagnostic Unit, University College London Hospitals NHS Foundation Trust, London, UK
- Crick COVID-19 Consortium, The Francis Crick Institute, London, UK
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, UK
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Myra O McClure
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Richard S Tedder
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK.
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, St. Mary's Campus, Imperial College London, London, UK
| |
Collapse
|
12
|
Wrobel AG, Benton DJ, Xu P, Calder LJ, Borg A, Roustan C, Martin SR, Rosenthal PB, Skehel JJ, Gamblin SJ. Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2. Nat Commun 2021; 12:837. [PMID: 33547281 PMCID: PMC7864994 DOI: 10.1038/s41467-021-21006-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/04/2021] [Indexed: 01/07/2023] Open
Abstract
Coronaviruses of bats and pangolins have been implicated in the origin and evolution of the pandemic SARS-CoV-2. We show that spikes from Guangdong Pangolin-CoVs, closely related to SARS-CoV-2, bind strongly to human and pangolin ACE2 receptors. We also report the cryo-EM structure of a Pangolin-CoV spike protein and show it adopts a fully-closed conformation and that, aside from the Receptor-Binding Domain, it resembles the spike of a bat coronavirus RaTG13 more than that of SARS-CoV-2.
Collapse
Affiliation(s)
- Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT, London, UK.
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT, London, UK.
| | - Pengqi Xu
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT, London, UK
- Precision Medicine Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Lesley J Calder
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, NW1 1AT, London, UK
| | - Annabel Borg
- Structural Biology Science Technology Platform, Francis Crick Institute, NW1 1AT, London, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, Francis Crick Institute, NW1 1AT, London, UK
| | - Stephen R Martin
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT, London, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, NW1 1AT, London, UK
| | - John J Skehel
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT, London, UK
| | - Steven J Gamblin
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT, London, UK.
| |
Collapse
|
13
|
Ng KW, Faulkner N, Cornish GH, Rosa A, Harvey R, Hussain S, Ulferts R, Earl C, Wrobel AG, Benton DJ, Roustan C, Bolland W, Thompson R, Agua-Doce A, Hobson P, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Thomson K, Sanchez E, Shin GY, Spyer MJ, Joshi D, O'Reilly N, Walker PA, Kjaer S, Riddell A, Moore C, Jebson BR, Wilkinson M, Marshall LR, Rosser EC, Radziszewska A, Peckham H, Ciurtin C, Wedderburn LR, Beale R, Swanton C, Gandhi S, Stockinger B, McCauley J, Gamblin SJ, McCoy LE, Cherepanov P, Nastouli E, Kassiotis G. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 2020; 370:1339-1343. [PMID: 33159009 DOI: 10.1101/2020.05.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 05/20/2023]
Abstract
Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Judith Heaney
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Hannah Rickman
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | | | - Catherine F Houlihan
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Kirsty Thomson
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Emilie Sanchez
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Gee Yen Shin
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Moira J Spyer
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Dhira Joshi
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip A Walker
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Riddell
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Meredyth Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Eleni Nastouli
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK.
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| |
Collapse
|
14
|
Ng KW, Faulkner N, Cornish GH, Rosa A, Harvey R, Hussain S, Ulferts R, Earl C, Wrobel AG, Benton DJ, Roustan C, Bolland W, Thompson R, Agua-Doce A, Hobson P, Heaney J, Rickman H, Paraskevopoulou S, Houlihan CF, Thomson K, Sanchez E, Shin GY, Spyer MJ, Joshi D, O'Reilly N, Walker PA, Kjaer S, Riddell A, Moore C, Jebson BR, Wilkinson M, Marshall LR, Rosser EC, Radziszewska A, Peckham H, Ciurtin C, Wedderburn LR, Beale R, Swanton C, Gandhi S, Stockinger B, McCauley J, Gamblin SJ, McCoy LE, Cherepanov P, Nastouli E, Kassiotis G. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science 2020; 370:1339-1343. [PMID: 33159009 PMCID: PMC7857411 DOI: 10.1126/science.abe1107] [Citation(s) in RCA: 578] [Impact Index Per Article: 144.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
Zoonotic introduction of novel coronaviruses may encounter preexisting immunity in humans. Using diverse assays for antibodies recognizing SARS-CoV-2 proteins, we detected preexisting humoral immunity. SARS-CoV-2 spike glycoprotein (S)-reactive antibodies were detectable using a flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. They were predominantly of the immunoglobulin G (IgG) class and targeted the S2 subunit. By contrast, SARS-CoV-2 infection induced higher titers of SARS-CoV-2 S-reactive IgG antibodies targeting both the S1 and S2 subunits, and concomitant IgM and IgA antibodies, lasting throughout the observation period. SARS-CoV-2-uninfected donor sera exhibited specific neutralizing activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes. Distinguishing preexisting and de novo immunity will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikhil Faulkner
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Saira Hussain
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Christopher Earl
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Chloe Roustan
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Hobson
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Judith Heaney
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Hannah Rickman
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | | | - Catherine F Houlihan
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK
| | - Kirsty Thomson
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Emilie Sanchez
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Gee Yen Shin
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
| | - Moira J Spyer
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Dhira Joshi
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip A Walker
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjaer
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Riddell
- Flow Cytometry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Bethany R Jebson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Meredyth Wilkinson
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Lucy R Marshall
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, WC1E 6BT, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, Great Ormond Street Hospital (GOSH), London WC1N 3JH, UK
- UCL Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | - John McCauley
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London (UCL), London WC1E 6BT, UK.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Eleni Nastouli
- University College London Hospitals (UCLH) NHS Trust, London NW1 2BU, UK.
- Department of Population, Policy and Practice, Great Ormond Street Institute for Child Health (ICH), UCL, London WC1N 1EH, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| |
Collapse
|
15
|
Ng KW, Attig J, Bolland W, Young GR, Major J, Wrobel AG, Gamblin S, Wack A, Kassiotis G. Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option. Nat Genet 2020; 52:1294-1302. [PMID: 33077915 PMCID: PMC7610354 DOI: 10.1038/s41588-020-00732-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/29/2020] [Indexed: 01/07/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) is an entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and a regulator of several physiological processes. ACE2 has recently been proposed to be interferon (IFN) inducible, suggesting that SARS-CoV-2 may exploit this phenomenon to enhance viral spread and questioning the efficacy of IFN treatment in coronavirus disease 2019. Using a recent de novo transcript assembly that captured previously unannotated transcripts, we describe a new isoform of ACE2, generated by co-option of intronic retroelements as promoter and alternative exon. The new transcript, termed MIRb-ACE2, exhibits specific expression patterns across the aerodigestive and gastrointestinal tracts and is highly responsive to IFN stimulation. In contrast, canonical ACE2 expression is unresponsive to IFN stimulation. Moreover, the MIRb-ACE2 translation product is a truncated, unstable ACE2 form, lacking domains required for SARS-CoV-2 binding and is therefore unlikely to contribute to or enhance viral infection.
Collapse
Affiliation(s)
- Kevin W Ng
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - William Bolland
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - George R Young
- Retrovirus-Host Interactions, The Francis Crick Institute, London, UK
| | - Jack Major
- Immunoregulation, The Francis Crick Institute, London, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes, The Francis Crick Institute, London, UK
| | - Steve Gamblin
- Structural Biology of Disease Processes, The Francis Crick Institute, London, UK
| | - Andreas Wack
- Immunoregulation, The Francis Crick Institute, London, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London, UK.
| |
Collapse
|
16
|
Benton DJ, Wrobel AG, Xu P, Roustan C, Martin SR, Rosenthal PB, Skehel JJ, Gamblin SJ. Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion. Nature 2020; 588:327-330. [PMID: 32942285 PMCID: PMC7116727 DOI: 10.1038/s41586-020-2772-0] [Citation(s) in RCA: 525] [Impact Index Per Article: 131.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/11/2020] [Indexed: 11/09/2022]
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface receptors1-4, followed by fusion of the virus and cell membranes to release the virus genome into the cell. Both receptor binding and membrane fusion activities are mediated by the virus spike glycoprotein5-7. As with other class-I membrane-fusion proteins, the spike protein is post-translationally cleaved, in this case by furin, into the S1 and S2 components that remain associated after cleavage8-10. Fusion activation after receptor binding is proposed to involve the exposure of a second proteolytic site (S2'), cleavage of which is required for the release of the fusion peptide11,12. Here we analyse the binding of ACE2 to the furin-cleaved form of the SARS-CoV-2 spike protein using cryo-electron microscopy. We classify ten different molecular species, including the unbound, closed spike trimer, the fully open ACE2-bound trimer and dissociated monomeric S1 bound to ACE2. The ten structures describe ACE2-binding events that destabilize the spike trimer, progressively opening up, and out, the individual S1 components. The opening process reduces S1 contacts and unshields the trimeric S2 core, priming the protein for fusion activation and dissociation of ACE2-bound S1 monomers. The structures also reveal refolding of an S1 subdomain after ACE2 binding that disrupts interactions with S2, which involves Asp61413-15 and leads to the destabilization of the structure of S2 proximal to the secondary (S2') cleavage site.
Collapse
Affiliation(s)
- Donald J Benton
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| | - Antoni G Wrobel
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| | - Pengqi Xu
- Precision Medicine Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Francis Crick Institute, London, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Stephen R Martin
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, UK
| | - John J Skehel
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK
| | - Steven J Gamblin
- Strutural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| |
Collapse
|
17
|
Wrobel AG, Benton DJ, Xu P, Roustan C, Martin SR, Rosenthal PB, Skehel JJ, Gamblin SJ. Author Correction: SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat Struct Mol Biol 2020; 27:1001. [PMID: 32848232 PMCID: PMC7448700 DOI: 10.1038/s41594-020-0509-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| | - Pengqi Xu
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.,Precision Medicine Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Chloë Roustan
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, UK
| | - John J Skehel
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK
| | - Steven J Gamblin
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| |
Collapse
|
18
|
Wrobel AG, Benton DJ, Xu P, Roustan C, Martin SR, Rosenthal PB, Skehel JJ, Gamblin SJ. SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat Struct Mol Biol 2020; 27:763-767. [PMID: 32647346 PMCID: PMC7610980 DOI: 10.1038/s41594-020-0468-7] [Citation(s) in RCA: 364] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 06/24/2020] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary host. Here, we investigate the relationship of spike (S) glycoprotein from SARS-CoV-2 with the S protein of a closely related bat virus, RaTG13. We determined cryo-EM structures for RaTG13 S and for both furin-cleaved and uncleaved SARS-CoV-2 S; we compared these with recently reported structures for uncleaved SARS-CoV-2 S. We also biochemically characterized their relative stabilities and affinities for the SARS-CoV-2 receptor ACE2. Although the overall structures of human and bat virus S proteins are similar, there are key differences in their properties, including a more stable precleavage form of human S and about 1,000-fold tighter binding of SARS-CoV-2 to human receptor. These observations suggest that cleavage at the furin-cleavage site decreases the overall stability of SARS-CoV-2 S and facilitates the adoption of the open conformation that is required for S to bind to the ACE2 receptor.
Collapse
MESH Headings
- Angiotensin-Converting Enzyme 2
- Animals
- Betacoronavirus/genetics
- Betacoronavirus/metabolism
- Betacoronavirus/ultrastructure
- Binding Sites
- COVID-19
- Chiroptera/virology
- Coronavirus Infections/virology
- Cryoelectron Microscopy
- Evolution, Molecular
- Furin/chemistry
- Gene Expression
- HEK293 Cells
- Host-Pathogen Interactions/genetics
- Humans
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/virology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Stability
- Proteolysis
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Structural Homology, Protein
Collapse
Affiliation(s)
- Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| | - Pengqi Xu
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK
- Precision Medicine Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Chloë Roustan
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, UK
| | - John J Skehel
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK
| | - Steven J Gamblin
- Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK.
| |
Collapse
|
19
|
Wrobel AG, Kadlecova Z, Kamenicky J, Yang JC, Herrmann T, Kelly BT, McCoy AJ, Evans PR, Martin S, Müller S, Salomon S, Sroubek F, Neuhaus D, Höning S, Owen DJ. Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation. Dev Cell 2019; 50:494-508.e11. [PMID: 31430451 PMCID: PMC6706699 DOI: 10.1016/j.devcel.2019.07.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/18/2019] [Accepted: 07/15/2019] [Indexed: 11/23/2022]
Abstract
Clathrin-mediated endocytosis (CME) is key to maintaining the transmembrane protein composition of cells' limiting membranes. During mammalian CME, a reversible phosphorylation event occurs on Thr156 of the μ2 subunit of the main endocytic clathrin adaptor, AP2. We show that this phosphorylation event starts during clathrin-coated pit (CCP) initiation and increases throughout CCP lifetime. μ2Thr156 phosphorylation favors a new, cargo-bound conformation of AP2 and simultaneously creates a binding platform for the endocytic NECAP proteins but without significantly altering AP2's cargo affinity in vitro. We describe the structural bases of both. NECAP arrival at CCPs parallels that of clathrin and increases with μ2Thr156 phosphorylation. In turn, NECAP recruits drivers of late stages of CCP formation, including SNX9, via a site distinct from where NECAP binds AP2. Disruption of the different modules of this phosphorylation-based temporal regulatory system results in CCP maturation being delayed and/or stalled, hence impairing global rates of CME.
Collapse
Affiliation(s)
| | | | - Jan Kamenicky
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Torsten Herrmann
- University of Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | | | - Airlie J McCoy
- CIMR, WT/MRC Building, Hills Road, Cambridge CB2 0QQ, UK
| | - Philip R Evans
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen Martin
- The Francis Crick Institute, 1 Midland Road, London NW1 1ST, UK
| | - Stefan Müller
- Center for Molecular Medicine (CMMC), University of Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| | - Susanne Salomon
- Institute for Biochemistry I, Medical Faulty, University of Cologne, Joseph-Stelzmann-Straße 52, 50931 Cologne, Germany
| | - Filip Sroubek
- Czech Academy of Sciences, Institute of Information Theory and Automation, Pod Vodarenskou vezi 4, 182 08 Prague 8, Czech Republic
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stefan Höning
- Institute for Biochemistry I, Medical Faulty, University of Cologne, Joseph-Stelzmann-Straße 52, 50931 Cologne, Germany.
| | - David J Owen
- CIMR, WT/MRC Building, Hills Road, Cambridge CB2 0QQ, UK
| |
Collapse
|
20
|
Navarro Negredo P, Edgar JR, Wrobel AG, Zaccai NR, Antrobus R, Owen DJ, Robinson MS. Contribution of the clathrin adaptor AP-1 subunit µ1 to acidic cluster protein sorting. J Cell Biol 2017; 216:2927-2943. [PMID: 28743825 PMCID: PMC5584140 DOI: 10.1083/jcb.201602058] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2017] [Accepted: 07/07/2017] [Indexed: 11/22/2022] Open
Abstract
Acidic clusters act as sorting signals for packaging cargo into clathrin-coated vesicles (CCVs), and also facilitate down-regulation of MHC-I by HIV-1 Nef. To find acidic cluster sorting machinery, we performed a gene-trap screen and identified the medium subunit (µ1) of the clathrin adaptor AP-1 as a top hit. In µ1 knockout cells, intracellular CCVs still form, but acidic cluster proteins are depleted, although several other CCV components were either unaffected or increased, indicating that cells can compensate for long-term loss of AP-1. In vitro experiments showed that the basic patch on µ1 that interacts with the Nef acidic cluster also contributes to the binding of endogenous acidic cluster proteins. Surprisingly, µ1 mutant proteins lacking the basic patch and/or the tyrosine-based motif binding pocket could rescue the µ1 knockout phenotype completely. In contrast, these mutants failed to rescue Nef-induced down-regulation of MHC class I, suggesting a possible mechanism for attacking the virus while sparing the host cell.
Collapse
Affiliation(s)
- Paloma Navarro Negredo
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Antoni G Wrobel
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Nathan R Zaccai
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - David J Owen
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| |
Collapse
|
21
|
Ma L, Umasankar PK, Wrobel AG, Lymar A, McCoy AJ, Holkar SS, Jha A, Pradhan-Sundd T, Watkins SC, Owen DJ, Traub LM. Transient Fcho1/2⋅Eps15/R⋅AP-2 Nanoclusters Prime the AP-2 Clathrin Adaptor for Cargo Binding. Dev Cell 2016; 37:428-43. [PMID: 27237791 PMCID: PMC4921775 DOI: 10.1016/j.devcel.2016.05.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 04/08/2016] [Accepted: 05/02/2016] [Indexed: 11/26/2022]
Abstract
Clathrin-coated vesicles form by rapid assembly of discrete coat constituents into a cargo-sorting lattice. How the sequential phases of coat construction are choreographed is unclear, but transient protein-protein interactions mediated by short interaction motifs are pivotal. We show that arrayed Asp-Pro-Phe (DPF) motifs within the early-arriving endocytic pioneers Eps15/R are differentially decoded by other endocytic pioneers Fcho1/2 and AP-2. The structure of an Eps15/R⋅Fcho1 μ-homology domain complex reveals a spacing-dependent DPF triad, bound in a mechanistically distinct way from the mode of single DPF binding to AP-2. Using cells lacking FCHO1/2 and with Eps15 sequestered from the plasma membrane, we establish that without these two endocytic pioneers, AP-2 assemblies are fleeting and endocytosis stalls. Thus, distinct DPF-based codes within the unstructured Eps15/R C terminus direct the assembly of temporary Fcho1/2⋅Eps15/R⋅AP-2 ternary complexes to facilitate conformational activation of AP-2 by the Fcho1/2 interdomain linker to promote AP-2 cargo engagement. The endocytic pioneer protein Eps15 engages AP-2 and Fcho1/2 noncompetitively Structural analysis shows arrayed DPF motif triad in Eps15 for Fcho1/2 μHD binding DPF-based codes direct transient Fcho1/2⋅Eps15/R⋅AP-2 ternary complex formation In ternary complex, Fcho1 interdomain linker primes AP-2 for cargo capture
Collapse
Affiliation(s)
- Li Ma
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA
| | - Perunthottathu K Umasankar
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA
| | - Antoni G Wrobel
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Anastasia Lymar
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA
| | - Airlie J McCoy
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Sachin S Holkar
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA
| | - Anupma Jha
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA
| | - Tirthadipa Pradhan-Sundd
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA
| | - David J Owen
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Linton M Traub
- Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S312 BST, Pittsburgh, PA 15261, USA.
| |
Collapse
|