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Bou-Antoun S, Rokadiya S, Ashiru-Oredope D, Demirjian A, Sherwood E, Ellaby N, Gerver S, Grossi C, Harman K, Hartman H, Lochen A, Ragonnet-Cronin M, Squire H, Sutton JM, Thelwall S, Tree J, Bahar MW, Stuart DI, Brown CS, Chand M, Hopkins S. COVID-19 therapeutics: stewardship in England and considerations for antimicrobial resistance. J Antimicrob Chemother 2023; 78:ii37-ii42. [PMID: 37995354 PMCID: PMC10666993 DOI: 10.1093/jac/dkad314] [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] [Indexed: 11/25/2023] Open
Abstract
The COVID-19 pandemic saw unprecedented resources and funds driven into research for the development, and subsequent rapid distribution, of vaccines, diagnostics and directly acting antivirals (DAAs). DAAs have undeniably prevented progression and life-threatening conditions in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, there are concerns of antimicrobial resistance (AMR), antiviral resistance specifically, for DAAs. To preserve activity of DAAs for COVID-19 therapy, as well as detect possible mutations conferring resistance, antimicrobial stewardship and surveillance were rapidly implemented in England. This paper expands on the ubiquitous ongoing public health activities carried out in England, including epidemiologic, virologic and genomic surveillance, to support the stewardship of DAAs and assess the deployment, safety, effectiveness and resistance potential of these novel and repurposed therapeutics.
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Affiliation(s)
- Sabine Bou-Antoun
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - Sakib Rokadiya
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Diane Ashiru-Oredope
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - Alicia Demirjian
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
- Department of Paediatric Infectious Diseases & Immunology, Evelina London Children's Hospital, London, UK
- Faculty of Life Sciences & Medicine, King’s College London, London, UK
| | - Emma Sherwood
- Clinical and Emerging Infections (CEI), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Nicholas Ellaby
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Sarah Gerver
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - Carlota Grossi
- COVID-19 Rapid Evidence Service Public Health Advice, Guidance and Expertise (PHAGE), UK Health Security Agency, London NW9 5EQ, UK
| | - Katie Harman
- COVID-19 Vaccines and Applied Epidemiology Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Hassan Hartman
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Alessandra Lochen
- Tuberculosis (TB), Acute Respiratory, Zoonoses, Emerging and Travel infections Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Manon Ragonnet-Cronin
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Hanna Squire
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - J Mark Sutton
- Research and Evaluation, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
- Institute of Pharmaceutical Sciences, King’s College London, London, UK
| | - Simon Thelwall
- COVID-19 Vaccines and Applied Epidemiology Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Julia Tree
- Research and Evaluation, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Mohammad W Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Colin S Brown
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - Meera Chand
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Susan Hopkins
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
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Cooray S, Price-Kuehne F, Hong Y, Omoyinmi E, Burleigh A, Gilmour KC, Ahmad B, Choi S, Bahar MW, Torpiano P, Gagunashvili A, Jensen B, Bellos E, Sancho-Shimizu V, Herberg JA, Mankad K, Kumar A, Kaliakatsos M, Worth AJJ, Eleftheriou D, Whittaker E, Brogan PA. Neuroinflammation, autoinflammation, splenomegaly and anemia caused by bi-allelic mutations in IRAK4. Front Immunol 2023; 14:1231749. [PMID: 37744344 PMCID: PMC10516541 DOI: 10.3389/fimmu.2023.1231749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
We describe a novel, severe autoinflammatory syndrome characterized by neuroinflammation, systemic autoinflammation, splenomegaly, and anemia (NASA) caused by bi-allelic mutations in IRAK4. IRAK-4 is a serine/threonine kinase with a pivotal role in innate immune signaling from toll-like receptors and production of pro-inflammatory cytokines. In humans, bi-allelic mutations in IRAK4 result in IRAK-4 deficiency and increased susceptibility to pyogenic bacterial infections, but autoinflammation has never been described. We describe 5 affected patients from 2 unrelated families with compound heterozygous mutations in IRAK4 (c.C877T (p.Q293*)/c.G958T (p.D320Y); and c.A86C (p.Q29P)/c.161 + 1G>A) resulting in severe systemic autoinflammation, massive splenomegaly and severe transfusion dependent anemia and, in 3/5 cases, severe neuroinflammation and seizures. IRAK-4 protein expression was reduced in peripheral blood mononuclear cells (PBMC) in affected patients. Immunological analysis demonstrated elevated serum tumor necrosis factor (TNF), interleukin (IL) 1 beta (IL-1β), IL-6, IL-8, interferon α2a (IFN-α2a), and interferon β (IFN-β); and elevated cerebrospinal fluid (CSF) IL-6 without elevation of CSF IFN-α despite perturbed interferon gene signature. Mutations were located within the death domain (DD; p.Q29P and splice site mutation c.161 + 1G>A) and kinase domain (p.Q293*/p.D320Y) of IRAK-4. Structure-based modeling of the DD mutation p.Q29P showed alteration in the alignment of a loop within the DD with loss of contact distance and hydrogen bond interactions with IRAK-1/2 within the myddosome complex. The kinase domain mutation p.D320Y was predicted to stabilize interactions within the kinase active site. While precise mechanisms of autoinflammation in NASA remain uncertain, we speculate that loss of negative regulation of IRAK-4 and IRAK-1; dysregulation of myddosome assembly and disassembly; or kinase active site instability may drive dysregulated IL-6 and TNF production. Blockade of IL-6 resulted in immediate and complete amelioration of systemic autoinflammation and anemia in all 5 patients treated; however, neuroinflammation has, so far proven recalcitrant to IL-6 blockade and the janus kinase (JAK) inhibitor baricitinib, likely due to lack of central nervous system penetration of both drugs. We therefore highlight that bi-allelic mutation in IRAK4 may be associated with a severe and complex autoinflammatory and neuroinflammatory phenotype that we have called NASA (neuroinflammation, autoinflammation, splenomegaly and anemia), in addition to immunodeficiency in humans.
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Affiliation(s)
- Samantha Cooray
- Infection, Immunity and Inflammation Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Fiona Price-Kuehne
- Infection, Immunity and Inflammation Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ying Hong
- Infection, Immunity and Inflammation Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ebun Omoyinmi
- Infection, Immunity and Inflammation Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Alice Burleigh
- Infection, Immunity and Inflammation Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
- Centre for Adolescent Rheumatology Versus Arthritis, University College London, London, United Kingdom
| | - Kimberly C. Gilmour
- Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Bilal Ahmad
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Mohammad W. Bahar
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Paul Torpiano
- Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Andrey Gagunashvili
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Barbara Jensen
- Infection, Immunity and Inflammation Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Evangelos Bellos
- Section of Paediatric Infectious Diseases, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Vanessa Sancho-Shimizu
- Section of Paediatric Infectious Diseases, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jethro A. Herberg
- Section of Paediatric Infectious Diseases, Imperial College London, London, United Kingdom
- Department of Paediatric Infectious Diseases, St Mary’s Hospital, Imperial College NHS Healthcare Trust, London, United Kingdom
| | - Kshitij Mankad
- Department of Radiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Atul Kumar
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Marios Kaliakatsos
- Department of Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Austen J. J. Worth
- Department of Immunology and Gene Therapy, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Despina Eleftheriou
- Infection, Immunity and Inflammation Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Elizabeth Whittaker
- Section of Paediatric Infectious Diseases, Imperial College London, London, United Kingdom
- Department of Paediatric Infectious Diseases, St Mary’s Hospital, Imperial College NHS Healthcare Trust, London, United Kingdom
| | - Paul A. Brogan
- Infection, Immunity and Inflammation Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
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Ragonnet-Cronin M, Nutalai R, Huo J, Dijokaite-Guraliuc A, Das R, Tuekprakhon A, Supasa P, Liu C, Selvaraj M, Groves N, Hartman H, Ellaby N, Mark Sutton J, Bahar MW, Zhou D, Fry E, Ren J, Brown C, Klenerman P, Dunachie SJ, Mongkolsapaya J, Hopkins S, Chand M, Stuart DI, Screaton GR, Rokadiya S. Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy. Nat Commun 2023; 14:3334. [PMID: 37286554 PMCID: PMC10246534 DOI: 10.1038/s41467-023-37826-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 10/06/2022] [Accepted: 04/03/2023] [Indexed: 06/09/2023] Open
Abstract
COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the antibody epitopes and for casirivimab+imdevimab multiple mutations are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum.
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Affiliation(s)
- Manon Ragonnet-Cronin
- Genomics Public Health Analysis, UK Health Security Agency, London, UK.
- Centre for Global Infectious Disease Analysis, Imperial College London, London, England.
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie Groves
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Hassan Hartman
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Nicholas Ellaby
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - J Mark Sutton
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Mohammad W Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Elizabeth Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Colin Brown
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford, UK
| | - Susan Hopkins
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - Meera Chand
- Genomics Public Health Analysis, UK Health Security Agency, London, UK
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Sakib Rokadiya
- Genomics Public Health Analysis, UK Health Security Agency, London, UK.
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Bahar MW, Nasta V, Fox H, Sherry L, Grehan K, Porta C, Macadam AJ, Stonehouse NJ, Rowlands DJ, Fry EE, Stuart DI. Publisher Correction: A conserved glutathione binding site in poliovirus is a target for antivirals and vaccine stabilisation. Commun Biol 2022; 5:1413. [PMID: 36564504 PMCID: PMC9789091 DOI: 10.1038/s42003-022-04378-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Mohammad W Bahar
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
| | - Veronica Nasta
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | - Helen Fox
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Lee Sherry
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Keith Grehan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Claudine Porta
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
- The Pirbright Institute, Pirbright, Surrey, GU24 0NF, UK
| | - Andrew J Macadam
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Nicola J Stonehouse
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Rowlands
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
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Bahar MW, Nasta V, Fox H, Sherry L, Grehan K, Porta C, Macadam AJ, Stonehouse NJ, Rowlands DJ, Fry EE, Stuart DI. A conserved glutathione binding site in poliovirus is a target for antivirals and vaccine stabilisation. Commun Biol 2022; 5:1293. [PMID: 36434067 PMCID: PMC9700776 DOI: 10.1038/s42003-022-04252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
Strategies to prevent the recurrence of poliovirus (PV) after eradication may utilise non-infectious, recombinant virus-like particle (VLP) vaccines. Despite clear advantages over inactivated or attenuated virus vaccines, instability of VLPs can compromise their immunogenicity. Glutathione (GSH), an important cellular reducing agent, is a crucial co-factor for the morphogenesis of enteroviruses, including PV. We report cryo-EM structures of GSH bound to PV serotype 3 VLPs showing that it can enhance particle stability. GSH binds the positively charged pocket at the interprotomer interface shown recently to bind GSH in enterovirus F3 and putative antiviral benzene sulphonamide compounds in other enteroviruses. We show, using high-resolution cryo-EM, the binding of a benzene sulphonamide compound with a PV serotype 2 VLP, consistent with antiviral activity through over-stabilizing the interprotomer pocket, preventing the capsid rearrangements necessary for viral infection. Collectively, these results suggest GSH or an analogous tight-binding antiviral offers the potential for stabilizing VLP vaccines.
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Affiliation(s)
- Mohammad W Bahar
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
| | - Veronica Nasta
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy
| | - Helen Fox
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Lee Sherry
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Keith Grehan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Claudine Porta
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
- The Pirbright Institute, Pirbright, Surrey, GU24 0NF, UK
| | - Andrew J Macadam
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Nicola J Stonehouse
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Rowlands
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
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Sherry L, Grehan K, Swanson JJ, Bahar MW, Porta C, Fry EE, Stuart DI, Rowlands DJ, Stonehouse NJ. Production and Characterisation of Stabilised PV-3 Virus-like Particles Using Pichia pastoris. Viruses 2022; 14:2159. [PMID: 36298714 PMCID: PMC9611624 DOI: 10.3390/v14102159] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/16/2022] [Revised: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
Following the success of global vaccination programmes using the live-attenuated oral and inactivated poliovirus vaccines (OPV and IPV), wild poliovirus (PV) is now only endemic in Afghanistan and Pakistan. However, the continued use of these vaccines poses potential risks to the eradication of PV. The production of recombinant PV virus-like particles (VLPs), which lack the viral genome offer great potential as next-generation vaccines for the post-polio world. We have previously reported production of PV VLPs using Pichia pastoris, however, these VLPs were in the non-native conformation (C Ag), which would not produce effective protection against PV. Here, we build on this work and show that it is possible to produce wt PV-3 and thermally stabilised PV-3 (referred to as PV-3 SC8) VLPs in the native conformation (D Ag) using Pichia pastoris. We show that the PV-3 SC8 VLPs provide a much-improved D:C antigen ratio as compared to wt PV-3, whilst exhibiting greater thermostability than the current IPV vaccine. Finally, we determine the cryo-EM structure of the yeast-derived PV-3 SC8 VLPs and compare this to previously published PV-3 D Ag structures, highlighting the similarities between these recombinantly expressed VLPs and the infectious virus, further emphasising their potential as a next-generation vaccine candidate for PV.
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Affiliation(s)
- Lee Sherry
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Keith Grehan
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Jessica J. Swanson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Mohammad W. Bahar
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Claudine Porta
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Elizabeth E. Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - David I. Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - David J. Rowlands
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nicola J. Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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7
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Bahar MW, Porta C, Fox H, Macadam AJ, Fry EE, Stuart DI. Mammalian expression of virus-like particles as a proof of principle for next generation polio vaccines. NPJ Vaccines 2021; 6:5. [PMID: 33420068 PMCID: PMC7794334 DOI: 10.1038/s41541-020-00267-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Global vaccination programs using live-attenuated oral and inactivated polio vaccine (OPV and IPV) have almost eradicated poliovirus (PV) but these vaccines or their production pose significant risk in a polio-free world. Recombinant PV virus-like particles (VLPs), lacking the viral genome, represent safe next-generation vaccines, however their production requires optimisation. Here we present an efficient mammalian expression strategy producing good yields of wild-type PV VLPs for all three serotypes and a thermostabilised variant for PV3. Whilst the wild-type VLPs were predominantly in the non-native C-antigenic form, the thermostabilised PV3 VLPs adopted the native D-antigenic conformation eliciting neutralising antibody titres equivalent to the current IPV and were indistinguishable from natural empty particles by cryo-electron microscopy with a similar stabilising lipidic pocket-factor in the VP1 β-barrel. This factor may not be available in alternative expression systems, which may require synthetic pocket-binding factors. VLPs equivalent to these mammalian expressed thermostabilized particles, represent safer non-infectious vaccine candidates for the post-eradication era.
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Affiliation(s)
- Mohammad W Bahar
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
| | - Claudine Porta
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
- The Pirbright Institute, Pirbright, Surrey, GU24 0NF, UK
| | - Helen Fox
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Andrew J Macadam
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
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8
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Marsian J, Fox H, Bahar MW, Kotecha A, Fry EE, Stuart DI, Macadam AJ, Rowlands DJ, Lomonossoff GP. Plant-made polio type 3 stabilized VLPs-a candidate synthetic polio vaccine. Nat Commun 2017; 8:245. [PMID: 28811473 PMCID: PMC5557999 DOI: 10.1038/s41467-017-00090-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [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: 11/24/2016] [Accepted: 05/31/2017] [Indexed: 11/24/2022] Open
Abstract
Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust neutralizing response. Developing a synthetically produced stabilized virus-like particle (sVLP)-based vaccine with D antigenicity, without the drawbacks of current vaccines, will be a major step towards the final eradication of poliovirus. Such a sVLP would retain the native antigenic conformation and the repetitive structure of the original virus particle, but lack infectious genomic material. In this study, we report the production of synthetically stabilized PV VLPs in plants. Mice carrying the gene for the human PV receptor are protected from wild-type PV when immunized with the plant-made PV sVLPs. Structural analysis of the stabilized mutant at 3.6 Å resolution by cryo-electron microscopy and single-particle reconstruction reveals a structure almost indistinguishable from wild-type PV3.Despite the success of current vaccination against poliomyelitis, safe, cheap and effective vaccines remain sought for continuing eradication effort. Here the authors use plants to express stabilized virus-like particles of type 3 poliovirus that can induce a protective immune response in mice transgenic for the human poliovirus receptor.
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Affiliation(s)
- Johanna Marsian
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Helen Fox
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - Mohammad W Bahar
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - Abhay Kotecha
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Andrew J Macadam
- The National Institute for Biological Standards and Control, Potters Bar, EN6 3QG, UK
| | - David J Rowlands
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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Bahar MW, Sarin LP, Graham SC, Pang J, Bamford DH, Stuart DI, Grimes JM. Structure of a VP1-VP3 complex suggests how birnaviruses package the VP1 polymerase. J Virol 2013; 87:3229-36. [PMID: 23283942 PMCID: PMC3592137 DOI: 10.1128/jvi.02939-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [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: 10/18/2012] [Accepted: 12/27/2012] [Indexed: 11/20/2022] Open
Abstract
Infectious pancreatic necrosis virus (IPNV), a member of the family Birnaviridae, infects young salmon, with a severe impact on the commercial sea farming industry. Of the five mature proteins encoded by the IPNV genome, the multifunctional VP3 has an essential role in morphogenesis; interacting with the capsid protein VP2, the viral double-stranded RNA (dsRNA) genome and the RNA-dependent RNA polymerase VP1. Here we investigate one of these VP3 functions and present the crystal structure of the C-terminal 12 residues of VP3 bound to the VP1 polymerase. This interaction, visualized for the first time, reveals the precise molecular determinants used by VP3 to bind the polymerase. Competition binding studies confirm that this region of VP3 is necessary and sufficient for VP1 binding, while biochemical experiments show that VP3 attachment has no effect on polymerase activity. These results indicate how VP3 recruits the polymerase into birnavirus capsids during morphogenesis.
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Affiliation(s)
- Mohammad W. Bahar
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - L. Peter Sarin
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Stephen C. Graham
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Jances Pang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Science Division, Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Science Division, Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
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Bahar MW, Graham SC, Stuart DI, Grimes JM. Insights into the evolution of a complex virus from the crystal structure of vaccinia virus D13. Structure 2011; 19:1011-20. [PMID: 21742267 PMCID: PMC3136756 DOI: 10.1016/j.str.2011.03.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/29/2011] [Accepted: 03/31/2011] [Indexed: 11/27/2022]
Abstract
The morphogenesis of poxviruses such as vaccinia virus (VACV) sees the virion shape mature from spherical to brick-shaped. Trimeric capsomers of the VACV D13 protein form a transitory, stabilizing lattice on the surface of the initial spherical immature virus particle. The crystal structure of D13 reveals that this major scaffolding protein comprises a double β barrel "jelly-roll" subunit arranged as pseudo-hexagonal trimers. These structural features are characteristic of the major capsid proteins of a lineage of large icosahedral double-stranded DNA viruses including human adenovirus and the bacteriophages PRD1 and PM2. Structure-based phylogenetic analysis confirms that VACV belongs to this lineage, suggesting that (analogously to higher organism embryogenesis) early poxvirus morphogenesis reflects their evolution from a lineage of viruses sharing a common icosahedral ancestor.
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Affiliation(s)
- Mohammad W Bahar
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
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Graham SC, Sarin LP, Bahar MW, Myers RA, Stuart DI, Bamford DH, Grimes JM. The N-terminus of the RNA polymerase from infectious pancreatic necrosis virus is the determinant of genome attachment. PLoS Pathog 2011; 7:e1002085. [PMID: 21731487 PMCID: PMC3121795 DOI: 10.1371/journal.ppat.1002085] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [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: 10/29/2010] [Accepted: 04/11/2011] [Indexed: 12/30/2022] Open
Abstract
The RNA-dependent RNA polymerase VP1 of infectious pancreatic necrosis virus (IPNV) is a single polypeptide responsible for both viral RNA transcription and genome replication. Sequence analysis identifies IPNV VP1 as having an unusual active site topology. We have purified, crystallized and solved the structure of IPNV VP1 to 2.3 Å resolution in its apo form and at 2.2 Å resolution bound to the catalytically-activating metal magnesium. We find that recombinantly-expressed VP1 is highly active for RNA transcription and replication, yielding both free and polymerase-attached RNA products. IPNV VP1 also possesses terminal (deoxy)nucleotide transferase, RNA-dependent DNA polymerase (reverse transcriptase) and template-independent self-guanylylation activity. The N-terminus of VP1 interacts with the active-site cleft and we show that the N-terminal serine residue is required for formation of covalent RNA∶polymerase complexes, providing a mechanism for the genesis of viral genome∶polymerase complexes observed in vivo. Infectious pancreatic necrosis virus (IPNV) is highly contagious and causes severe disease in fish. As a result of intensive rearing conditions it has become a serious problem for the salmon and trout farming industries. IPNV, like many other viruses, replicates its genome using a protein (a ‘polymerase’) that is itself encoded by the viral genome. Unusually, in infectious IPNV particles the polymerase is found chemically linked to the viral genome. We have determined the atomic structure of IPNV polymerase using X-ray crystallography, revealing some significant differences in the fold of the protein chain compared to other well-characterized viral polymerases. By mutating an amino acid residue at the beginning of the protein we show how the chemical linkage to the viral genome can be disrupted. This provides an elegant mechanism for the attachment of the viral genome to the polymerase observed in vivo.
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Affiliation(s)
- Stephen C. Graham
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - L. Peter Sarin
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Biocenter 2, Helsinki, Finland
| | - Mohammad W. Bahar
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Reg A. Myers
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Biocenter 2, Helsinki, Finland
- * E-mail: (DHB); (JMG)
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (DHB); (JMG)
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Benfield CTO, Mansur DS, McCoy LE, Ferguson BJ, Bahar MW, Oldring AP, Grimes JM, Stuart DI, Graham SC, Smith GL. Mapping the IkappaB kinase beta (IKKbeta)-binding interface of the B14 protein, a vaccinia virus inhibitor of IKKbeta-mediated activation of nuclear factor kappaB. J Biol Chem 2011; 286:20727-35. [PMID: 21474453 PMCID: PMC3121528 DOI: 10.1074/jbc.m111.231381] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [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: 02/15/2011] [Revised: 04/06/2011] [Indexed: 12/24/2022] Open
Abstract
The IκB kinase (IKK) complex regulates activation of NF-κB, a critical transcription factor in mediating inflammatory and immune responses. Not surprisingly, therefore, many viruses seek to inhibit NF-κB activation. The vaccinia virus B14 protein contributes to virus virulence by binding to the IKKβ subunit of the IKK complex and preventing NF-κB activation in response to pro-inflammatory stimuli. Previous crystallographic studies showed that the B14 protein has a Bcl-2-like fold and forms homodimers in the crystal. However, multi-angle light scattering indicated that B14 is in monomer-dimer equilibrium in solution. This transient self-association suggested that the hydrophobic dimerization interface of B14 might also mediate its interaction with IKKβ, and this was investigated by introducing amino acid substitutions on the dimer interface. One mutant (Y35E) was entirely monomeric but still co-immunoprecipitated with IKKβ and blocked both NF-κB nuclear translocation and NF-κB-dependent gene expression. Therefore, B14 homodimerization is nonessential for binding and inhibition of IKKβ. In contrast, a second monomeric mutant (F130K) neither bound IKKβ nor inhibited NF-κB-dependent gene expression, demonstrating that this residue is required for the B14-IKKβ interaction. Thus, the dimerization and IKKβ-binding interfaces overlap and lie on a surface used for protein-protein interactions in many viral and cellular Bcl-2-like proteins.
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Affiliation(s)
- Camilla T. O. Benfield
- From the Section of Virology, Department of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG
| | - Daniel S. Mansur
- From the Section of Virology, Department of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG
| | - Laura E. McCoy
- From the Section of Virology, Department of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG
| | - Brian J. Ferguson
- From the Section of Virology, Department of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG
| | - Mohammad W. Bahar
- the Division of Structural Biology and Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN
| | - Asa P. Oldring
- the Division of Structural Biology and Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN
| | - Jonathan M. Grimes
- the Division of Structural Biology and Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN
- the Science Division, Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, and
| | - David I. Stuart
- the Division of Structural Biology and Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN
- the Science Division, Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, and
| | - Stephen C. Graham
- the Division of Structural Biology and Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN
- the Cambridge Institute for Medical Research and Department of Clinical Biochemistry, University of Cambridge and Addenbrooke's Hospital, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Geoffrey L. Smith
- From the Section of Virology, Department of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG
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Bahar MW, Graham SC, Chen RAJ, Cooray S, Smith GL, Stuart DI, Grimes JM. How vaccinia virus has evolved to subvert the host immune response. J Struct Biol 2011; 175:127-34. [PMID: 21419849 PMCID: PMC3477310 DOI: 10.1016/j.jsb.2011.03.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/10/2011] [Accepted: 03/14/2011] [Indexed: 01/06/2023]
Abstract
Viruses are obligate intracellular parasites and are some of the most rapidly evolving and diverse pathogens encountered by the host immune system. Large complicated viruses, such as poxviruses, have evolved a plethora of proteins to disrupt host immune signalling in their battle against immune surveillance. Recent X-ray crystallographic analysis of these viral immunomodulators has helped form an emerging picture of the molecular details of virus-host interactions. In this review we consider some of these immune evasion strategies as they apply to poxviruses, from a structural perspective, with specific examples from the European SPINE2-Complexes initiative. Structures of poxvirus immunomodulators reveal the capacity of viruses to mimic and compete against the host immune system, using a diverse range of structural folds that are unique or acquired from their hosts with both enhanced and unexpectedly divergent functions.
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Affiliation(s)
- Mohammad W Bahar
- Division of Structural Biology and Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX37BN, United Kingdom
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14
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Graham SC, Bahar MW, Cooray S, Chen RAJ, Whalen DM, Abrescia NGA, Alderton D, Owens RJ, Stuart DI, Smith GL, Grimes JM. Vaccinia virus proteins A52 and B14 Share a Bcl-2-like fold but have evolved to inhibit NF-kappaB rather than apoptosis. PLoS Pathog 2008; 4:e1000128. [PMID: 18704168 PMCID: PMC2494871 DOI: 10.1371/journal.ppat.1000128] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [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: 04/29/2008] [Accepted: 07/17/2008] [Indexed: 12/18/2022] Open
Abstract
Vaccinia virus (VACV), the prototype poxvirus, encodes numerous proteins that modulate the host response to infection. Two such proteins, B14 and A52, act inside infected cells to inhibit activation of NF-kappaB, thereby blocking the production of pro-inflammatory cytokines. We have solved the crystal structures of A52 and B14 at 1.9 A and 2.7 A resolution, respectively. Strikingly, both these proteins adopt a Bcl-2-like fold despite sharing no significant sequence similarity with other viral or cellular Bcl-2-like proteins. Unlike cellular and viral Bcl-2-like proteins described previously, A52 and B14 lack a surface groove for binding BH3 peptides from pro-apoptotic Bcl-2-like proteins and they do not modulate apoptosis. Structure-based phylogenetic analysis of 32 cellular and viral Bcl-2-like protein structures reveals that A52 and B14 are more closely related to each other and to VACV N1 and myxoma virus M11 than they are to other viral or cellular Bcl-2-like proteins. This suggests that a progenitor poxvirus acquired a gene encoding a Bcl-2-like protein and, over the course of evolution, gene duplication events have allowed the virus to exploit this Bcl-2 scaffold for interfering with distinct host signalling pathways.
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Affiliation(s)
- Stephen C. Graham
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mohammad W. Bahar
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Samantha Cooray
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Ron A.-J. Chen
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Daniel M. Whalen
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicola G. A. Abrescia
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David Alderton
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Raymond J. Owens
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David I. Stuart
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Geoffrey L. Smith
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Jonathan M. Grimes
- The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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15
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Bahar MW, Kenyon JC, Putz MM, Abrescia NGA, Pease JE, Wise EL, Stuart DI, Smith GL, Grimes JM. Structure and function of A41, a vaccinia virus chemokine binding protein. PLoS Pathog 2008; 4:e5. [PMID: 18208323 PMCID: PMC2211551 DOI: 10.1371/journal.ppat.0040005] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [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: 08/20/2007] [Accepted: 11/27/2007] [Indexed: 12/11/2022] Open
Abstract
The vaccinia virus (VACV) A41L gene encodes a secreted 30 kDa glycoprotein that is nonessential for virus replication but affects the host response to infection. The A41 protein shares sequence similarity with another VACV protein that binds CC chemokines (called vCKBP, or viral CC chemokine inhibitor, vCCI), and strains of VACV lacking the A41L gene induced stronger CD8+ T-cell responses than control viruses expressing A41. Using surface plasmon resonance, we screened 39 human and murine chemokines and identified CCL21, CCL25, CCL26 and CCL28 as A41 ligands, with Kds of between 8 nM and 118 nM. Nonetheless, A41 was ineffective at inhibiting chemotaxis induced by these chemokines, indicating it did not block the interaction of these chemokines with their receptors. However the interaction of A41 and chemokines was inhibited in a dose-dependent manner by heparin, suggesting that A41 and heparin bind to overlapping sites on these chemokines. To better understand the mechanism of action of A41 its crystal structure was solved to 1.9 Å resolution. The protein has a globular β sandwich structure similar to that of the poxvirus vCCI family of proteins, but there are notable structural differences, particularly in surface loops and electrostatic charge distribution. Structural modelling suggests that the binding paradigm as defined for the vCCI–chemokine interaction is likely to be conserved between A41 and its chemokine partners. Additionally, sequence analysis of chemokines binding to A41 identified a signature for A41 binding. The biological and structural data suggest that A41 functions by forming moderately strong (nM) interactions with certain chemokines, sufficient to interfere with chemokine-glycosaminoglycan interactions at the cell surface (μM–nM) and thereby to destroy the chemokine concentration gradient, but not strong enough to disrupt the (pM) chemokine–chemokine receptor interactions. As part of the innate immune response (for example to virus infection), the body produces proteins called chemokines, which act by directing white blood cells (leukocytes) to the areas of infection and inflammation. Viruses have evolved mechanisms to fight this immune response. Indeed, so important is this need to protect themselves from the immune system that some viruses, such as poxviruses, devote up to half their genetic information to this battle. We have studied a protein called A41, one component of the response of vaccinia virus (the vaccine used to eradicate smallpox) to the immune system and shown that it interferes with the function of a group of chemokines. These chemokines function by forming concentration gradients along which the white blood cells migrate, and A41 sequesters the chemokines, thereby preventing formation of the gradient. Interestingly, we show also that A41 is very similar in structure to another group of proteins, called vCCIs, that bind chemokines more tightly, blocking their attachment to white blood cells, suggesting that both mechanisms are important for virus virulence.
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Affiliation(s)
- Mohammad W Bahar
- The Division of Structural Biology and The Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Julia C Kenyon
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Mike M Putz
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
| | - Nicola G. A Abrescia
- The Division of Structural Biology and The Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James E Pease
- Leukocyte Biology Section, NHLI Division, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Emma L Wise
- Leukocyte Biology Section, NHLI Division, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London, United Kingdom
| | - David I Stuart
- The Division of Structural Biology and The Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Geoffrey L Smith
- Department of Virology, Faculty of Medicine, Imperial College London, St. Mary's Campus, London, United Kingdom
- * To whom correspondence should be addressed. E-mail: (GLS); (JMG)
| | - Jonathan M Grimes
- The Division of Structural Biology and The Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * To whom correspondence should be addressed. E-mail: (GLS); (JMG)
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16
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Graham SC, Bahar MW, Abrescia NGA, Smith GL, Stuart DI, Grimes JM. Structure of CrmE, a Virus-encoded Tumour Necrosis Factor Receptor. J Mol Biol 2007; 372:660-71. [PMID: 17681535 DOI: 10.1016/j.jmb.2007.06.082] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [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: 05/10/2007] [Revised: 06/18/2007] [Accepted: 06/28/2007] [Indexed: 11/17/2022]
Abstract
Vaccinia virus (VACV), the smallpox vaccine, encodes many proteins that subvert the host immune response. One of these, cytokine response modifier E (CrmE), is secreted by infected cells and protects these cells from apoptotic challenge by tumour necrosis factor alpha (TNFalpha). We have expressed recombinant CrmE from VACV strain Lister in Escherichia coli, shown that the purified protein is monomeric in solution and competent to bind TNFalpha, and solved the structure to 2.0 A resolution. This is the first structure of a virus-encoded tumour necrosis factor receptor (TNFR). CrmE shares significant sequence similarity with mammalian type 2 TNF receptors (TNFSFR1B, p75; TNFR type 2). The structure confirms that CrmE adopts the canonical TNFR fold but only one of the two "ligand-binding" loops of TNFRSF1A is conserved in CrmE, suggesting a mechanism for the higher affinity of poxvirus TNFRs for TNFalpha over lymphotoxin-alpha. The roles of dimerisation and pre-ligand-assembly domains (PLADs) in poxvirus and mammalian TNFR activity are discussed.
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MESH Headings
- Amino Acid Sequence
- Crystallography, X-Ray
- Humans
- Hydrophobic and Hydrophilic Interactions
- Ligands
- Models, Molecular
- Molecular Sequence Data
- Protein Binding
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- Receptors, Tumor Necrosis Factor/chemistry
- Receptors, Tumor Necrosis Factor/isolation & purification
- Receptors, Tumor Necrosis Factor/metabolism
- Receptors, Tumor Necrosis Factor, Type I/chemistry
- Receptors, Tumor Necrosis Factor, Type I/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Tumor Necrosis Factor-alpha/isolation & purification
- Tumor Necrosis Factor-alpha/metabolism
- Vaccinia virus/chemistry
- Viral Proteins/chemistry
- Viral Proteins/isolation & purification
- Viral Proteins/metabolism
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Affiliation(s)
- Stephen C Graham
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Oxford Protein Production Facility Roosevelt Drive, Headington, Oxford OX3 7BN, UK
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17
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Cooray S, Bahar MW, Abrescia NGA, McVey CE, Bartlett NW, Chen RAJ, Stuart DI, Grimes JM, Smith GL. Functional and structural studies of the vaccinia virus virulence factor N1 reveal a Bcl-2-like anti-apoptotic protein. J Gen Virol 2007; 88:1656-1666. [PMID: 17485524 PMCID: PMC2885619 DOI: 10.1099/vir.0.82772-0] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [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: 12/06/2006] [Accepted: 03/06/2007] [Indexed: 02/07/2023] Open
Abstract
Vaccinia virus (VACV) encodes many immunomodulatory proteins, including inhibitors of apoptosis and modulators of innate immune signalling. VACV protein N1 is an intracellular homodimer that contributes to virus virulence and was reported to inhibit nuclear factor (NF)-kappaB signalling. However, analysis of NF-kappaB signalling in cells infected with recombinant viruses with or without the N1L gene showed no difference in NF-kappaB-dependent gene expression. Given that N1 promotes virus virulence, other possible functions of N1 were investigated and this revealed that N1 is an inhibitor of apoptosis in cells transfected with the N1L gene and in the context of VACV infection. In support of this finding virally expressed N1 co-precipitated with endogenous pro-apoptotic Bcl-2 proteins Bid, Bad and Bax as well as with Bad and Bax expressed by transfection. In addition, the crystal structure of N1 was solved to 2.9 A resolution (0.29 nm). Remarkably, although N1 shows no sequence similarity to cellular proteins, its three-dimensional structure closely resembles Bcl-x(L) and other members of the Bcl-2 protein family. The structure also reveals that N1 has a constitutively open surface groove similar to the grooves of other anti-apoptotic Bcl-2 proteins, which bind the BH3 motifs of pro-apoptotic Bcl-2 family members. Molecular modelling of BH3 peptides into the N1 surface groove, together with analysis of their physico-chemical properties, suggests a mechanism for the specificity of peptide recognition. This study illustrates the importance of the evolutionary conservation of structure, rather than sequence, in protein function and reveals a novel anti-apoptotic protein from orthopoxviruses.
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Affiliation(s)
- Samantha Cooray
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Mohammad W. Bahar
- The Oxford Protein Production Facility and The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Nicola G. A. Abrescia
- The Oxford Protein Production Facility and The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Colin E. McVey
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Nathan W. Bartlett
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Ron A.-J. Chen
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - David I. Stuart
- The Oxford Protein Production Facility and The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jonathan M. Grimes
- The Oxford Protein Production Facility and The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Geoffrey L. Smith
- Department of Virology, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
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Mohd Jaafar F, Attoui H, Bahar MW, Siebold C, Sutton G, Mertens PPC, De Micco P, Stuart DI, Grimes JM, De Lamballerie X. The Structure and Function of the Outer Coat Protein VP9 of Banna Virus. Structure 2005; 13:17-28. [PMID: 15642258 DOI: 10.1016/j.str.2004.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Revised: 10/21/2004] [Accepted: 10/21/2004] [Indexed: 11/22/2022]
Abstract
Banna virus (BAV: genus Seadornavirus, family Reoviridae) has a double-shelled morphology similar to rotavirus and bluetongue virus. The structure of BAV outer-capsid protein VP9 was determined by X-ray crystallography at 2.6 A resolution, revealing a trimeric molecule, held together by an N-terminal helical bundle, reminiscent of coiled-coil structures found in fusion-active proteins such as HIV gp41. The major domain of VP9 contains stacked beta sheets with marked structural similarities to the receptor binding protein VP8 of rotavirus. Anti-VP9 antibodies neutralize viral infectivity, and, remarkably, pretreatment of cells with trimeric VP9 increased viral infectivity, indicating that VP9 is involved in virus attachment to cell surface and subsequent internalization. Sequence similarities were also detected between BAV VP10 and VP5 portion of rotavirus VP4, suggesting that the receptor binding and internalization apparatus, which is a single gene product activated by proteoloysis in rotavirus, is the product of two separate genome segments in BAV.
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Affiliation(s)
- Fauziah Mohd Jaafar
- Unité des Virus Emergents EA3292, EFS Alpes-Méditerranée and Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13005 Marseille, France
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