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Meldal BHM, Perfetto L, Combe C, Lubiana T, Ferreira Cavalcante JV, Bye-A-Jee H, Waagmeester A, del-Toro N, Shrivastava A, Barrera E, Wong E, Mlecnik B, Bindea G, Panneerselvam K, Willighagen E, Rappsilber J, Porras P, Hermjakob H, Orchard S. Complex Portal 2022: new curation frontiers. Nucleic Acids Res 2022; 50:D578-D586. [PMID: 34718729 PMCID: PMC8689886 DOI: 10.1093/nar/gkab991] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 09/15/2021] [Revised: 10/07/2021] [Accepted: 10/10/2021] [Indexed: 01/02/2023] Open
Abstract
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from a range of model organisms. It summarizes complex composition, topology and function along with links to a large range of domain-specific resources (i.e. wwPDB, EMDB and Reactome). Since the last update in 2019, we have produced a first draft complexome for Escherichia coli, maintained and updated that of Saccharomyces cerevisiae, added over 40 coronavirus complexes and increased the human complexome to over 1100 complexes that include approximately 200 complexes that act as targets for viral proteins or are part of the immune system. The display of protein features in ComplexViewer has been improved and the participant table is now colour-coordinated with the nodes in ComplexViewer. Community collaboration has expanded, for example by contributing to an analysis of putative transcription cofactors and providing data accessible to semantic web tools through Wikidata which is now populated with manually curated Complex Portal content through a new bot. Our data license is now CC0 to encourage data reuse. Users are encouraged to get in touch, provide us with feedback and send curation requests through the 'Support' link.
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Affiliation(s)
- Birgit H M Meldal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Livia Perfetto
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Fondazione Human Technopole, 20157 Milan, Italy
| | - Colin Combe
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Tiago Lubiana
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, Av. Professor Lineu Prestes 580, CEP 05508-000 São Paulo SP, Brasil
| | - João Vitor Ferreira Cavalcante
- Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, Federal University of Rio Grande do Norte, Av. Odilon Gomes de Lima 1722, Capim Macio, 59078-400 Natal/RN, Brasil
| | - Hema Bye-A-Jee
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Noemi del-Toro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anjali Shrivastava
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Elisabeth Barrera
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Edith Wong
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Bernhard Mlecnik
- Laboratory of Integrative Cancer Immunology, INSERM, 75006 Paris, France
- Equipe Labellisée Ligue Contre le Cancer, 75006 Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, 75006 Paris, France
- Inovarion, 75005 Paris, France
| | - Gabriela Bindea
- Laboratory of Integrative Cancer Immunology, INSERM, 75006 Paris, France
- Equipe Labellisée Ligue Contre le Cancer, 75006 Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Kalpana Panneerselvam
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Egon Willighagen
- Dept of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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2
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Robinson SA, Raybould MIJ, Schneider C, Wong WK, Marks C, Deane CM. Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies. PLoS Comput Biol 2021; 17:e1009675. [PMID: 34898603 PMCID: PMC8700021 DOI: 10.1371/journal.pcbi.1009675] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 06/06/2021] [Revised: 12/23/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. Sequence-based clonal clustering can identify antibodies with similar epitope complementarity, however, antibodies from markedly different lineages but with similar structures can engage the same epitope. We describe a novel computational method for epitope profiling based on structural modelling and clustering. Using the method, we demonstrate that sequence dissimilar but functionally similar antibodies can be found across the Coronavirus Antibody Database, with high accuracy (92% of antibodies in multiple-occupancy structural clusters bind to consistent domains). Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than is suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis. Antibodies are a key component of the immune system that combat pathogens by binding to a defined region of their molecular surface (known as an ‘epitope’). The ability to map which antibodies target the same epitopes is crucial when designing non-competing antibody therapeutics or predicting the influence of pathogen mutation on population immunity. While one can use laboratory experiments to deduce when pairs of antibodies engage the same epitope, such experiments are very expensive and time consuming if used to compare on the order of thousands of antibodies. In this work, we report a new computational algorithm (SPACE) that clusters antibodies that target the same epitope based on their predicted 3D structure, as binding site structure is a property often conserved between binders complementary to the same epitope. Unlike existing antibody epitope profiling tools which assume two antibodies must share a high sequence identity/similar genetic basis to engage the same region, our orthogonal method can detect broader patterns of convergent evolution across binders to different pathogen strains, and between antibodies with different genetic and even species origins.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/metabolism
- Antibody Specificity
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/genetics
- Antigen-Antibody Reactions/genetics
- Antigen-Antibody Reactions/immunology
- Antigens, Viral/chemistry
- COVID-19/immunology
- COVID-19/virology
- Computational Biology
- Coronavirus/chemistry
- Coronavirus/genetics
- Coronavirus/immunology
- Databases, Chemical
- Epitope Mapping
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Humans
- Mice
- Models, Molecular
- Pandemics
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Single-Domain Antibodies/immunology
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Affiliation(s)
- Sarah A Robinson
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Constantin Schneider
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Wing Ki Wong
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Claire Marks
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
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3
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Sugiyama MG, Cui H, Redka DS, Karimzadeh M, Rujas E, Maan H, Hayat S, Cheung K, Misra R, McPhee JB, Viirre RD, Haller A, Botelho RJ, Karshafian R, Sabatinos SA, Fairn GD, Madani Tonekaboni SA, Windemuth A, Julien JP, Shahani V, MacKinnon SS, Wang B, Antonescu CN. Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. Sci Rep 2021; 11:23315. [PMID: 34857794 PMCID: PMC8640055 DOI: 10.1038/s41598-021-02432-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic has highlighted the urgent need for the identification of new antiviral drug therapies for a variety of diseases. COVID-19 is caused by infection with the human coronavirus SARS-CoV-2, while other related human coronaviruses cause diseases ranging from severe respiratory infections to the common cold. We developed a computational approach to identify new antiviral drug targets and repurpose clinically-relevant drug compounds for the treatment of a range of human coronavirus diseases. Our approach is based on graph convolutional networks (GCN) and involves multiscale host-virus interactome analysis coupled to off-target drug predictions. Cell-based experimental assessment reveals several clinically-relevant drug repurposing candidates predicted by the in silico analyses to have antiviral activity against human coronavirus infection. In particular, we identify the MET inhibitor capmatinib as having potent and broad antiviral activity against several coronaviruses in a MET-independent manner, as well as novel roles for host cell proteins such as IRAK1/4 in supporting human coronavirus infection, which can inform further drug discovery studies.
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Affiliation(s)
- Michael G Sugiyama
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Haotian Cui
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | | | | | - Edurne Rujas
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Hassaan Maan
- Vector Institute, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Centre, Toronto, ON, Canada
| | - Sikander Hayat
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Kyle Cheung
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Rahul Misra
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Joseph B McPhee
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Russell D Viirre
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Andrew Haller
- Phoenox Pharma, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Roberto J Botelho
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Raffi Karshafian
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
- Institute for Biomedical Engineering, Science and Technology (iBEST), a partnership between Ryerson University and St. Michael's Hospital, Toronto, ON, Canada
- Department of Physics, Ryerson University, Toronto, ON, Canada
| | - Sarah A Sabatinos
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
| | | | | | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Immunology, Toronto, ON, Canada
| | | | | | - Bo Wang
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Vector Institute, Toronto, ON, Canada.
- Peter Munk Cardiac Centre, University Health Centre, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | - Costin N Antonescu
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada.
- Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada.
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada.
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4
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Kim JM, Jung S, Jeon EJ, Kim BK, No JY, Kim MJ, Kim H, Song CS, Kim SK. Highly Selective Multiplex Quantitative Polymerase Chain Reaction with a Nanomaterial Composite Hydrogel for Precise Diagnosis of Viral Infection. ACS Appl Mater Interfaces 2021; 13:30295-30305. [PMID: 34165969 DOI: 10.1021/acsami.1c03434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As viruses have been threatening global public health, fast diagnosis has been critical to effective disease management and control. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is now widely used as the gold standard for detecting viruses. Although a multiplex assay is essential for identifying virus types and subtypes, the poor multiplicity of RT-qPCR makes it laborious and time-consuming. In this paper, we describe the development of a multiplex RT-qPCR platform with hydrogel microparticles acting as independent reactors in a single reaction. To build target-specific particles, target-specific primers and probes are integrated into the particles in the form of noncovalent composites with boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs). The thermal release characteristics of DNA, primer, and probe from the composites of primer-BNNT and probe-CNT allow primer and probe to be stored in particles during particle production and to be delivered into the reaction. In addition, BNNT did not absorb but preserved the fluorescent signal, while CNT protected the fluorophore of the probe from the free radicals present during particle production. Bicompartmental primer-incorporated network (bcPIN) particles were designed to harness the distinctive properties of two nanomaterials. The bcPIN particles showed a high RT-qPCR efficiency of over 90% and effective suppression of non-specific reactions. 16-plex RT-qPCR has been achieved simply by recruiting differently coded bcPIN particles for each target. As a proof of concept, multiplex one-step RT-qPCR was successfully demonstrated with a simple reaction protocol.
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Affiliation(s)
- Jung Min Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Eui Ju Jeon
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bong Kyun Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Biomedical Engineering, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Jin Yong No
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Myung Jong Kim
- Functional Composite Materials Research Center, KIST, Jeonbuk 55324, Republic of Korea
| | - Heesuk Kim
- Photo-Electronic Hybrids Research Center, KIST, Seoul 02792, Republic of Korea
- Division of Energy and Environmental Technology, KIST School, UST, Daejeon 34113, Republic of Korea
| | - Chang Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
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5
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Tagliamonte MS, Abid N, Borocci S, Sangiovanni E, Ostrov DA, Kosakovsky Pond SL, Salemi M, Chillemi G, Mavian C. Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements. Int J Mol Sci 2020; 22:E80. [PMID: 33374797 PMCID: PMC7794730 DOI: 10.3390/ijms22010080] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 10/31/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/12/2023] Open
Abstract
Our evolutionary and structural analyses revealed that the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) spike gene is a complex mosaic resulting from several recombination events. Additionally, the fixation of variants has mainly been driven by purifying selection, suggesting the presence of conserved structural features. Our dynamic simulations identified two main long-range covariant dynamic movements of the novel glycoprotein, and showed that, as a result of the evolutionary duality, they are preserved. The first movement involves the receptor binding domain with the N-terminal domain and the C-terminal domain 2 and is maintained across human, bat and pangolin coronaviruses. The second is a complex network of long-range dynamics specific to SARS-CoV-2 involving the novel PRRA and the conserved KR*SF cleavage sites, as well as conserved segments in C-terminal domain 3. These movements, essential for host cell binding, are maintained by hinges conserved across human, bat, and pangolin coronaviruses glycoproteins. The hinges, located around Threonine 333 and Proline 527 within the N-terminal domain and C-terminal domain 2, represent candidate targets for the future development of novel pan-coronavirus inhibitors. In summary, we show that while recombination created a new configuration that increased the covariant dynamic movements of the SARS-CoV-2 glycoprotein, negative selection preserved its inter-domain structure throughout evolution in different hosts and inter-species transmissions.
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Affiliation(s)
- Massimiliano S. Tagliamonte
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, 5000 Monastir, Tunisia;
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
- Institute for Biological Systems, National Research Council, Via Salaria, Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Elisa Sangiovanni
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | | | - Marco Salemi
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
| | - Carla Mavian
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
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6
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Baruah C, Devi P, Sharma DK. Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus. Biomed Res Int 2020; 2020:7234961. [PMID: 33102591 PMCID: PMC7576348 DOI: 10.1155/2020/7234961] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a single-stranded RNA genome that encodes 14 open reading frames (ORFs), eight of which encode accessory proteins that allow the virus to infect the host and promote virulence. The genome expresses around 29 structural and nonstructural protein products. The accessory proteins of SARS-CoV-2 are not essential for virus replication but do affect viral release, stability, and pathogenesis and finally contribute to virulence. This paper has attempted the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per residue) quality estimates verified the structures as high quality, which may be attributed to structure-based drug design targets. Tunnel analysis revealed the presence of 1-2 highly active tunneling sites, perhaps which will able to provide certain inputs for advanced structure-based drug design or to formulate potential vaccines in the absence of a complete experimental structure. The evolutionary analysis of both proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus. The whole-genome phylogeny indicates that only the new bat coronavirus followed by pangolin coronaviruses has a close evolutionary relationship with the novel SARS-CoV-2.
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Affiliation(s)
- Chittaranjan Baruah
- Bioinformatics Laboratory (DBT-Star College), P.G. Department of Zoology, Darrang College, Tezpur, 784 001 Assam, India
| | | | - Dhirendra K. Sharma
- School of Biological Sciences, University of Science and Technology, Meghalaya, Baridua-793101, India
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7
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Lasso G, Honig B, Shapira SD. A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. Cell Syst 2020; 12:82-91.e3. [PMID: 33053371 PMCID: PMC7552982 DOI: 10.1016/j.cels.2020.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/03/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022]
Abstract
Viruses deploy genetically encoded strategies to coopt host machinery and support viral replicative cycles. Here, we use protein structure similarity to scan for molecular mimicry, manifested by structural similarity between viral and endogenous host proteins, across thousands of cataloged viruses and hosts spanning broad ecological niches and taxonomic range, including bacteria, plants and fungi, invertebrates, and vertebrates. This survey identified over 6,000,000 instances of structural mimicry; more than 70% of viral mimics cannot be discerned through protein sequence alone. We demonstrate that the manner and degree to which viruses exploit molecular mimicry varies by genome size and nucleic acid type and identify 158 human proteins that are mimicked by coronaviruses, providing clues about cellular processes driving pathogenesis. Our observations point to molecular mimicry as a pervasive strategy employed by viruses and indicate that the protein structure space used by a given virus is dictated by the host proteome. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Gorka Lasso
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA; Zuckerman Mind Brain Behavior Institute, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University, New York, NY, USA
| | - Sagi D Shapira
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.
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8
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Hussain A, Hasan A, Nejadi Babadaei MM, Bloukh SH, Chowdhury MEH, Sharifi M, Haghighat S, Falahati M. Targeting SARS-CoV2 Spike Protein Receptor Binding Domain by Therapeutic Antibodies. Biomed Pharmacother 2020; 130:110559. [PMID: 32768882 PMCID: PMC7395593 DOI: 10.1016/j.biopha.2020.110559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/09/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
As the number of people infected with the newly identified 2019 novel coronavirus (SARS-CoV2) is continuously increasing every day, development of potential therapeutic platforms is vital. Based on the comparatively high similarity of receptor-binding domain (RBD) in SARS-CoV2 and SARS-CoV, it seems crucial to assay the cross-reactivity of anti-SARS-CoV monoclonal antibodies (mAbs) with SARS-CoV2 spike (S)-protein. Indeed, developing mAbs targeting SARS-CoV2 S-protein RBD could show novel applications for rapid and sensitive development of potential epitope-specific vaccines (ESV). Herein, we present an overview on the discovery of new CoV followed by some explanation on the SARS-CoV2 S-protein RBD site. Furthermore, we surveyed the novel therapeutic mAbs for targeting S-protein RBD such as S230, 80R, F26G18, F26G19, CR3014, CR3022, M396, and S230.15. Afterwards, the mechanism of interaction of RBD and different mAbs were explained and it was suggested that one of the SARS-CoV-specific human mAbs, namely CR3022, could show the highest binding affinity with SARS-CoV2 S-protein RBD. Finally, some ongoing challenges and future prospects for rapid and sensitive advancement of therapeutic mAbs targeting S-protein RBD were discussed. In conclusion, it may be proposed that this review may pave the way for recognition of RBD and different mAbs to develop potential therapeutic ESV.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antibody Affinity
- Antigen-Antibody Reactions
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Betacoronavirus/immunology
- Binding Sites, Antibody
- COVID-19
- COVID-19 Vaccines
- Coronavirus/chemistry
- Coronavirus/immunology
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Epitopes/immunology
- Humans
- Models, Molecular
- Pandemics
- Phylogeny
- Pneumonia, Viral/immunology
- Protein Binding
- Protein Conformation
- Protein Domains
- SARS-CoV-2
- Sequence Alignment
- Sequence Homology, Amino Acid
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Vaccines/immunology
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Affiliation(s)
- Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha, 2713, Qatar; Biomedical Research Center, Qatar University, Doha, 2713, Qatar.
| | - Mohammad Mahdi Nejadi Babadaei
- Department of Molecular Genetics, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Samir Haj Bloukh
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, PO Box 346, Ajman, United Arab Emirates
| | | | - Majid Sharifi
- Department of Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Setareh Haghighat
- Department of Microbiology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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9
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Frick DN, Virdi RS, Vuksanovic N, Dahal N, Silvaggi NR. Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3. Biochemistry 2020; 59:2608-2615. [PMID: 32578982 PMCID: PMC7341687 DOI: 10.1021/acs.biochem.0c00309] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [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: 04/16/2020] [Revised: 06/22/2020] [Indexed: 12/21/2022]
Abstract
The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the proteins encoded by SARS-CoV-2 that is most different, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodomain differ from those observed in other coronaviruses, biochemical and structural data reveal that the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta coronaviruses and a potential therapeutic target.
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Affiliation(s)
- David N. Frick
- Department of Chemistry & Biochemistry, The University of Wisconsin- Milwaukee, Milwaukee, WI 53217
| | - Rajdeep S. Virdi
- Department of Chemistry & Biochemistry, The University of Wisconsin- Milwaukee, Milwaukee, WI 53217
| | - Nemanja Vuksanovic
- Department of Chemistry & Biochemistry, The University of Wisconsin- Milwaukee, Milwaukee, WI 53217
| | - Narayan Dahal
- Department of Physics, The University of Wisconsin- Milwaukee, Milwaukee, WI 53217
| | - Nicholas R. Silvaggi
- Department of Chemistry & Biochemistry, The University of Wisconsin- Milwaukee, Milwaukee, WI 53217
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10
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Tan Y, Schneider T, Leong M, Aravind L, Zhang D. Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis of SARS-CoV-2-Related Viruses. mBio 2020; 11:e00760-20. [PMID: 32471829 PMCID: PMC7267882 DOI: 10.1128/mbio.00760-20] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [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: 03/28/2020] [Accepted: 05/08/2020] [Indexed: 12/17/2022] Open
Abstract
A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was recently identified as the causative agent for the coronavirus disease 2019 (COVID-19) outbreak that has generated a global health crisis. We use a combination of genomic analysis and sensitive profile-based sequence and structure analysis to understand the potential pathogenesis determinants of this virus. As a result, we identify several fast-evolving genomic regions that might be at the interface of virus-host interactions, corresponding to the receptor binding domain of the Spike protein, the three tandem Macro fold domains in ORF1a, and the uncharacterized protein ORF8. Further, we show that ORF8 and several other proteins from alpha- and beta-CoVs belong to novel families of immunoglobulin (Ig) proteins. Among them, ORF8 is distinguished by being rapidly evolving, possessing a unique insert, and having a hypervariable position among SARS-CoV-2 genomes in its predicted ligand-binding groove. We also uncover numerous Ig domain proteins from several unrelated metazoan viruses, which are distinct in sequence and structure but share comparable architectures to those of the CoV Ig domain proteins. Hence, we propose that SARS-CoV-2 ORF8 and other previously unidentified CoV Ig domain proteins fall under the umbrella of a widespread strategy of deployment of Ig domain proteins in animal viruses as pathogenicity factors that modulate host immunity. The rapid evolution of the ORF8 Ig domain proteins points to a potential evolutionary arms race between viruses and hosts, likely arising from immune pressure, and suggests a role in transmission between distinct host species.IMPORTANCE The ongoing COVID-19 pandemic strongly emphasizes the need for a more complete understanding of the biology and pathogenesis of its causative agent SARS-CoV-2. Despite intense scrutiny, several proteins encoded by the genomes of SARS-CoV-2 and other SARS-like coronaviruses remain enigmatic. Moreover, the high infectivity and severity of SARS-CoV-2 in certain individuals make wet-lab studies currently challenging. In this study, we used a series of computational strategies to identify several fast-evolving regions of SARS-CoV-2 proteins which are potentially under host immune pressure. Most notably, the hitherto-uncharacterized protein encoded by ORF8 is one of them. Using sensitive sequence and structural analysis methods, we show that ORF8 and several other proteins from alpha- and beta-coronavirus comprise novel families of immunoglobulin domain proteins, which might function as potential immune modulators to delay or attenuate the host immune response against the viruses.
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Affiliation(s)
- Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Theresa Schneider
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Matthew Leong
- School of Medicine, Saint Louis University, St. Louis, Missouri, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
- Program of Bioinformatics and Computational Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
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11
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Abstract
A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) recently emerged and is rapidly spreading in humans, causing COVID-191,2. A key to tackling this pandemic is to understand the receptor recognition mechanism of the virus, which regulates its infectivity, pathogenesis and host range. SARS-CoV-2 and SARS-CoV recognize the same receptor-angiotensin-converting enzyme 2 (ACE2)-in humans3,4. Here we determined the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 (engineered to facilitate crystallization) in complex with ACE2. In comparison with the SARS-CoV RBD, an ACE2-binding ridge in SARS-CoV-2 RBD has a more compact conformation; moreover, several residue changes in the SARS-CoV-2 RBD stabilize two virus-binding hotspots at the RBD-ACE2 interface. These structural features of SARS-CoV-2 RBD increase its ACE2-binding affinity. Additionally, we show that RaTG13, a bat coronavirus that is closely related to SARS-CoV-2, also uses human ACE2 as its receptor. The differences among SARS-CoV-2, SARS-CoV and RaTG13 in ACE2 recognition shed light on the potential animal-to-human transmission of SARS-CoV-2. This study provides guidance for intervention strategies that target receptor recognition by SARS-CoV-2.
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MESH Headings
- Angiotensin-Converting Enzyme 2
- Animals
- Betacoronavirus/chemistry
- Betacoronavirus/drug effects
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- China/epidemiology
- Chiroptera/virology
- Coronavirus/chemistry
- Coronavirus/isolation & purification
- Coronavirus Infections/drug therapy
- Coronavirus Infections/epidemiology
- Coronavirus Infections/transmission
- Coronavirus Infections/virology
- Crystallization
- Crystallography, X-Ray
- Disease Reservoirs/virology
- Eutheria/virology
- Humans
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/transmission
- Pneumonia, Viral/virology
- Protein Binding
- Protein Domains
- Protein Stability
- Receptors, Virus/chemistry
- Receptors, Virus/metabolism
- Severe acute respiratory syndrome-related coronavirus/chemistry
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Zoonoses/epidemiology
- Zoonoses/transmission
- Zoonoses/virology
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Affiliation(s)
- Jian Shang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Gang Ye
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Yushun Wan
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Chuming Luo
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Qibin Geng
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Ashley Auerbach
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA.
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12
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Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu NH, Nitsche A, Müller MA, Drosten C, Pöhlmann S. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 2020. [PMID: 32142651 DOI: 10.1016/j.cell.2020.02.052,] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The recent emergence of the novel, pathogenic SARS-coronavirus 2 (SARS-CoV-2) in China and its rapid national and international spread pose a global health emergency. Cell entry of coronaviruses depends on binding of the viral spike (S) proteins to cellular receptors and on S protein priming by host cell proteases. Unravelling which cellular factors are used by SARS-CoV-2 for entry might provide insights into viral transmission and reveal therapeutic targets. Here, we demonstrate that SARS-CoV-2 uses the SARS-CoV receptor ACE2 for entry and the serine protease TMPRSS2 for S protein priming. A TMPRSS2 inhibitor approved for clinical use blocked entry and might constitute a treatment option. Finally, we show that the sera from convalescent SARS patients cross-neutralized SARS-2-S-driven entry. Our results reveal important commonalities between SARS-CoV-2 and SARS-CoV infection and identify a potential target for antiviral intervention.
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Affiliation(s)
- Markus Hoffmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany.
| | - Hannah Kleine-Weber
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany
| | - Simon Schroeder
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Nadine Krüger
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany; Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | - Sandra Erichsen
- Institute for Biomechanics, BG Unfallklinik Murnau, Murnau, Germany; Institute for Biomechanics, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Tobias S Schiergens
- Biobank of the Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Georg Herrler
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Nai-Huei Wu
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Andreas Nitsche
- Robert Koch Institute, ZBS 1 Highly Pathogenic Viruses, WHO Collaborating Centre for Emerging Infections and Biological Threats, Berlin, Germany
| | - Marcel A Müller
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Centre for Infection Research, associated partner Charité, Berlin, Germany; Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Centre for Infection Research, associated partner Charité, Berlin, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany.
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13
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Abstract
BACKGROUND Coronaviruses (CoVs) primarily cause enzootic infections in birds and mammals but, in the last few decades, have shown to be capable of infecting humans as well. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and, more recently, Middle-East respiratory syndrome (MERS) has demonstrated the lethality of CoVs when they cross the species barrier and infect humans. A renewed interest in coronaviral research has led to the discovery of several novel human CoVs and since then much progress has been made in understanding the CoV life cycle. The CoV envelope (E) protein is a small, integral membrane protein involved in several aspects of the virus' life cycle, such as assembly, budding, envelope formation, and pathogenesis. Recent studies have expanded on its structural motifs and topology, its functions as an ion-channelling viroporin, and its interactions with both other CoV proteins and host cell proteins. MAIN BODY This review aims to establish the current knowledge on CoV E by highlighting the recent progress that has been made and comparing it to previous knowledge. It also compares E to other viral proteins of a similar nature to speculate the relevance of these new findings. Good progress has been made but much still remains unknown and this review has identified some gaps in the current knowledge and made suggestions for consideration in future research. CONCLUSIONS The most progress has been made on SARS-CoV E, highlighting specific structural requirements for its functions in the CoV life cycle as well as mechanisms behind its pathogenesis. Data shows that E is involved in critical aspects of the viral life cycle and that CoVs lacking E make promising vaccine candidates. The high mortality rate of certain CoVs, along with their ease of transmission, underpins the need for more research into CoV molecular biology which can aid in the production of effective anti-coronaviral agents for both human CoVs and enzootic CoVs.
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Affiliation(s)
- Dewald Schoeman
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - Burtram C Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa.
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14
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Han X, Qi J, Song H, Wang Q, Zhang Y, Wu Y, Lu G, Yuen KY, Shi Y, Gao GF. Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike protein. Virology 2017; 507:101-109. [PMID: 28432925 PMCID: PMC7111649 DOI: 10.1016/j.virol.2017.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/10/2017] [Accepted: 04/15/2017] [Indexed: 02/05/2023]
Abstract
Accumulating evidence indicates that MERS-CoV originated from bat coronaviruses (BatCoVs). Previously, we demonstrated that both MERS-CoV and BatCoV HKU4 use CD26 as a receptor, but how the BatCoVs evolved to bind CD26 is an intriguing question. Here, we solved the crystal structure of the S1 subunit C-terminal domain of HKU5 (HKU5-CTD), another BatCoV that is phylogenetically related to MERS-CoV but cannot bind to CD26. We observed that the conserved core subdomain and those of other betacoronaviruses (betaCoVs) have a similar topology of the external subdomain, indicating the same ancestor of lineage C betaCoVs. However, two deletions in two respective loops located in HKU5-CTD result in conformational variations in CD26-binding interface and are responsible for the non-binding of HKU5-CTD to CD26. Combined with sequence variation in the HKU5-CTD receptor binding interface, we propose the necessity for surveilling the mutation in BatCoV HKU5 spike protein in case of bat-to-human interspecies transmission.
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Affiliation(s)
- Xue Han
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Song
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yanfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Pokfulam 999077, Hong Kong Special Administration Region; Department of Microbiology, The University of Hong Kong, Pokfulam 999077, Hong Kong Special Administration Region; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China; Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
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15
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Iinuma Y. [Middle East Respiratory Syndrome (MERS)]. Rinsho Byori 2016; 64:1044-1051. [PMID: 30609457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Middle East respiratory syndrome (MERS) is an emerging infectious disease of growing global importance, which has caused severe acute respiratory disease in more than 1,700 people, resulting in almost 600 deaths. MERS is caused by a novel betacoronavirus (MERS-CoV). All cases of MERS have been linked through travel to or residence in countries in or near the Arabian Peninsula. Dromedary camels are considered natu- ral reservoirs for MERS-CoV. MERS-CoV is mainly transmitted from infected dromedary camels to human beings, and it is transmitted among human beings by droplets, contact, and perhaps airborne spread. Both community-acquired and hospital-acquired cases have been reported with little human-to-human transmis- sion reported in the community. The largest known outbreak of MERS outside the Arabian Peninsula oc- curred in the Republic of Korea in 2015, with 186 cases. The outbreak was associated with a traveler re- turning from the Arabian Peninsula. Clinical features of MERS range from asymptomatic or mild disease to acute respiratory distress syndrome and multi-organ failure resulting in death, especially in individuals with underlying comorbidities. MERS is suspected in the presence of febrile acute respiratory illness and close contact with MERS-CoV, and can be confirmed by the detection of viral nucleic acid through RT-PCR or se- rology. No specific drug treatment exists for MERS; however, the neutralizing antibodies, ribavirin and interferon have been shown to be potentially useful anti-MERS-CoV drugs. Rigorous infection prevention and control measures with droplet and contact precautions are crucial to prevent the spread in health-care facilities. [Review].
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16
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Kirchdoerfer RN, Cottrell CA, Wang N, Pallesen J, Yassine HM, Turner HL, Corbett KS, Graham BS, McLellan JS, Ward AB. Pre-fusion structure of a human coronavirus spike protein. Nature 2016; 531:118-21. [PMID: 26935699 PMCID: PMC4860016 DOI: 10.1038/nature17200] [Citation(s) in RCA: 525] [Impact Index Per Article: 65.6] [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: 01/18/2016] [Accepted: 02/05/2016] [Indexed: 02/07/2023]
Abstract
HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. Cell tropism and host range is determined in part by the coronavirus spike (S) protein, which binds cellular receptors and mediates membrane fusion. As the largest known class I fusion protein, its size and extensive glycosylation have hindered structural studies of the full ectodomain, thus preventing a molecular understanding of its function and limiting development of effective interventions. Here we present the 4.0 Å resolution structure of the trimeric HKU1 S protein determined using single-particle cryo-electron microscopy. In the pre-fusion conformation, the receptor-binding subunits, S1, rest above the fusion-mediating subunits, S2, preventing their conformational rearrangement. Surprisingly, the S1 C-terminal domains are interdigitated and form extensive quaternary interactions that occlude surfaces known in other coronaviruses to bind protein receptors. These features, along with the location of the two protease sites known to be important for coronavirus entry, provide a structural basis to support a model of membrane fusion mediated by progressive S protein destabilization through receptor binding and proteolytic cleavage. These studies should also serve as a foundation for the structure-based design of betacoronavirus vaccine immunogens.
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Affiliation(s)
- Robert N. Kirchdoerfer
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
| | - Nianshuang Wang
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, 03755 New Hampshire USA
| | - Jesper Pallesen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
| | - Hadi M. Yassine
- Viral Pathogenesis Laboratory, National Institute of Allergy and Infectious Diseases, Building 40, Room 2502, 40 Convent Drive, Bethesda, 20892 Maryland USA
- Present Address: † Present address: Biomedical Research Center, Qatar University, QU-NRC, Zone 5, Room D130, Doha, Qatar.,
| | - Hannah L. Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
| | - Kizzmekia S. Corbett
- Viral Pathogenesis Laboratory, National Institute of Allergy and Infectious Diseases, Building 40, Room 2502, 40 Convent Drive, Bethesda, 20892 Maryland USA
| | - Barney S. Graham
- Viral Pathogenesis Laboratory, National Institute of Allergy and Infectious Diseases, Building 40, Room 2502, 40 Convent Drive, Bethesda, 20892 Maryland USA
| | - Jason S. McLellan
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, 03755 New Hampshire USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037 California USA
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17
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Stanley M, Mayr J, Huber W, Vlasak R, Streicher H. Synthesis and inhibitory activity of sialic acid derivatives targeted at viral sialate-O-acetylesterases. Eur J Med Chem 2011; 46:2852-60. [PMID: 21524502 PMCID: PMC7111470 DOI: 10.1016/j.ejmech.2011.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 03/25/2011] [Accepted: 04/02/2011] [Indexed: 11/18/2022]
Abstract
A series of sialosides modified at the 4- and 9-hydroxy group were synthesised and tested for inhibition of the viral haemagglutinin-esterase activity from various Orthomyxoviruses and Coronaviruses. While no inhibition of the sialate-4-O-acetylesterases from mouse hepatitis virus strain S or sialodacryoadenitis virus was found, a 9-O-methyl derivative displayed inhibitory activity against recombinant sialate-9-O-acetylesterase from influenza C virus.
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Affiliation(s)
- Mathew Stanley
- Department of Chemistry and Biochemistry, University of Sussex, Brighton, BN1 9QG, UK
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18
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Zhao M, Zhang TY, Zhou WM, Zhao GX, Zhang LL, Gao JM, Tan WJ. [Expression and purification of different segments from HCoV-NL63 nucleocapsid protein and their application in detection of antibodies]. Bing Du Xue Bao 2011; 27:244-249. [PMID: 21774250] [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] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Prokaryotic expression plasmids carrying N-terminal(1-163aa) and C-terminal(141-306aa) gene of HCoV-NL63 nucleocapsid protein were constructed with pET-30a(+) vector. Consequently, we prepared two purified proteins, Np and Cp, respectively, and established a Western blotting-based line assay (WBLA) for detection of antibodies against HCoV-NL63 using three purified proteins: Np , Cp and Nf, a full-length HCoV-NL63 nucleocapsid protein as previously reported. We detected anti-HCoV-NL63 antibodies among 50 sera samples collected from adult for health-examination by WBLA. The results showed that: 25 (50%), 27 (54%), 36 (72%) of 50 sera were indentified as anti-HCoV-NL63 antibody positive when the antigen was from Nf, Np and Cp, respectively. Among these sera with positive anti-HCoV-NL63 antibody,Cp showed highest antibody positive rate in WBLA,and consistent rates of detection were 64% between Nf and Np, 54% between Nf and Cp, 54% between Np and Cp. Our study provides the foundation for development of HCoV-NL63 serological detection reagents and an experimental tool for immunological research of HCoV-NL63 infection.
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Affiliation(s)
- Min Zhao
- Institute of Medical Virology, Wenzhou Medical College, Wenzhou 325000, China
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19
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Abstract
Coronavirus envelope (E) proteins are small (approximately 75- to 110-amino-acid) membrane proteins that have a short hydrophilic amino terminus, a relatively long hydrophobic membrane domain, and a long hydrophilic carboxy-terminal domain. The protein is a minor virion structural component that plays an important, not fully understood role in virus production. It was recently demonstrated that the protein forms ion channels. We investigated the importance of the hydrophobic domain of the mouse hepatitis coronavirus (MHV) A59 E protein. Alanine scanning insertion mutagenesis was used to examine the effect of disruption of the domain on virus production in the context of the virus genome by using a MHV A59 infectious clone. Mutant viruses exhibited smaller plaque phenotypes, and virus production was significantly crippled. Analysis of recovered viruses suggested that the structure of the presumed alpha-helical structure and positioning of polar hydrophilic residues within the predicted transmembrane domain are important for virus production. Generation of viruses with restored wild-type helical pitch resulted in increased virus production, but some exhibited decreased virus release. Viruses with the restored helical pitch were more sensitive to treatment with the ion channel inhibitor hexamethylene amiloride than were the more crippled parental viruses with the single alanine insertions, suggesting that disruption of the transmembrane domain affects the functional activity of the protein. Overall the results indicate that the transmembrane domain plays a crucial role during biogenesis of virions.
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Affiliation(s)
- Ye Ye
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5401, USA
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20
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Zheng Q, Deng Y, Liu J, van der Hoek L, Berkhout B, Lu M. Core structure of S2 from the human coronavirus NL63 spike glycoprotein. Biochemistry 2006; 45:15205-15. [PMID: 17176042 DOI: 10.1021/bi061686w] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human coronavirus NL63 (HCoV-NL63) has recently been identified as a causative agent of acute respiratory tract illnesses in infants and young children. The HCoV-NL63 spike (S) protein mediates virion attachment to cells and subsequent fusion of the viral and cellular membranes. This viral entry process is a primary target for vaccine and drug development. HCoV-NL63 S is expressed as a single-chain glycoprotein and consists of an N-terminal receptor-binding domain (S1) and a C-terminal transmembrane fusion domain (S2). The latter contains two highly conserved heptad-repeat (HR) sequences that are each extended by 14 amino acids relative to those of the SARS coronavirus or the prototypic murine coronavirus, mouse hepatitis virus. Limited proteolysis studies of the HCoV-NL63 S2 fusion core identify an alpha-helical domain composed of a trimer of the HR segments N57 and C42. The crystal structure of this complex reveals three C42 helices entwined in an oblique and antiparallel manner around a central triple-stranded coiled coil formed by three N57 helices. The overall geometry comprises distinctive high-affinity conformations of interacting cross-sectional layers of the six helices. As a result, this structure is unusually stable, with an apparent melting temperature of 78 degrees C in the presence of the denaturant guanidine hydrochloride at 5 M concentration. The extended HR regions may therefore be required to prime the group 1 S glycoproteins for their fusion-activating conformational changes during viral entry. Our results provide an initial basis for understanding an intriguing interplay between the presence or absence of proteolytic maturation among the coronavirus groups and the membrane fusion activity of their S glycoproteins. This study also suggests a potential strategy for the development of improved HCoV-NL63 fusion inhibitors.
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Affiliation(s)
- Qi Zheng
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA
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21
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Zúñiga S, Sola I, Moreno JL, Sabella P, Plana-Durán J, Enjuanes L. Coronavirus nucleocapsid protein is an RNA chaperone. Virology 2006; 357:215-27. [PMID: 16979208 PMCID: PMC7111943 DOI: 10.1016/j.virol.2006.07.046] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Revised: 07/11/2006] [Accepted: 07/29/2006] [Indexed: 01/19/2023]
Abstract
RNA chaperones are nonspecific nucleic acid binding proteins with long disordered regions that help RNA molecules to adopt its functional conformation. Coronavirus nucleoproteins (N) are nonspecific RNA-binding proteins with long disordered regions. Therefore, we investigated whether transmissible gastroenteritis coronavirus (TGEV) N protein was an RNA chaperone. Purified N protein enhanced hammerhead ribozyme self-cleavage and nucleic acids annealing, which are properties that define RNA chaperones. In contrast, another RNA-binding protein, PTB, did not show these activities. N protein chaperone activity was blocked by specific monoclonal antibodies. Therefore, it was concluded that TGEV N protein is an RNA chaperone. In addition, we have shown that purified severe acute respiratory syndrome (SARS)-CoV N protein also has RNA chaperone activity. In silico predictions of disordered domains showed a similar pattern for all coronavirus N proteins evaluated. Altogether, these data led us to suggest that all coronavirus N proteins might be RNA chaperones.
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Affiliation(s)
- Sonia Zúñiga
- Centro Nacional de Biotecnología, CSIC, Department of Molecular and Cell Biology, Campus Universidad Autónoma, Darwin 3, Cantoblanco, 28049 Madrid, Spain
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Pyrc K, Bosch BJ, Berkhout B, Jebbink MF, Dijkman R, Rottier P, van der Hoek L. Inhibition of human coronavirus NL63 infection at early stages of the replication cycle. Antimicrob Agents Chemother 2006; 50:2000-8. [PMID: 16723558 PMCID: PMC1479111 DOI: 10.1128/aac.01598-05] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human coronavirus NL63 (HCoV-NL63), a recently discovered member of the Coronaviridae family, has spread worldwide and is associated with acute respiratory illness in young children and elderly and immunocompromised persons. Further analysis of HCoV-NL63 pathogenicity seems warranted, in particular because the virus uses the same cellular receptor as severe acute respiratory syndrome-associated coronavirus. As there is currently no HCoV-NL63-specific and effective vaccine or drug therapy available, we evaluated several existing antiviral drugs and new synthetic compounds as inhibitors of HCoV-NL63, targeting multiple stages of the replication cycle. Of the 28 compounds that we tested, 6 potently inhibited HCoV-NL63 at early steps of the replication cycle. Intravenous immunoglobulins, heptad repeat 2 peptide, small interfering RNA1 (siRNA1), siRNA2, beta-D-N(4)-hydroxycytidine, and 6-azauridine showed 50% inhibitory concentrations of 125 microg/ml, 2 microM, 5 nM, 3 nM, 400 nM, and 32 nM, respectively, and low 50% cytotoxicity concentrations (>10 mg/ml, >40 microM, >200 nM, >200 nM, >100 microM, and 80 microM, respectively). These agents may be investigated further for the treatment of coronavirus infections.
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Affiliation(s)
- Krzysztof Pyrc
- Department of Human Retrovirology, University of Amsterdam, The Netherlands.
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23
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Jayaram H, Fan H, Bowman BR, Ooi A, Jayaram J, Collisson EW, Lescar J, Prasad BVV. X-ray structures of the N- and C-terminal domains of a coronavirus nucleocapsid protein: implications for nucleocapsid formation. J Virol 2006; 80:6612-20. [PMID: 16775348 PMCID: PMC1488953 DOI: 10.1128/jvi.00157-06] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [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: 01/07/2023] Open
Abstract
Coronaviruses cause a variety of respiratory and enteric diseases in animals and humans including severe acute respiratory syndrome. In these enveloped viruses, the filamentous nucleocapsid is formed by the association of nucleocapsid (N) protein with single-stranded viral RNA. The N protein is a highly immunogenic phosphoprotein also implicated in viral genome replication and in modulating cell signaling pathways. We describe the structure of the two proteolytically resistant domains of the N protein from infectious bronchitis virus (IBV), a prototype coronavirus. These domains are located at its N- and C-terminal ends (NTD and CTD, respectively). The NTD of the IBV Gray strain at 1.3-A resolution exhibits a U-shaped structure, with two arms rich in basic residues, providing a module for specific interaction with RNA. The CTD forms a tightly intertwined dimer with an intermolecular four-stranded central beta-sheet platform flanked by alpha helices, indicating that the basic building block for coronavirus nucleocapsid formation is a dimeric assembly of N protein. The variety of quaternary arrangements of the NTD and CTD revealed by the analysis of the different crystal forms delineates possible interfaces that could be used for the formation of a flexible filamentous ribonucleocapsid. The striking similarity between the dimeric structure of CTD and the nucleocapsid-forming domain of a distantly related arterivirus indicates a conserved mechanism of nucleocapsid formation for these two viral families.
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Affiliation(s)
- Hariharan Jayaram
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030-3498, USA
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24
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Perlman S, Holmes KV. Validation of Coronavirus E Proteins Ion Channels as Targets for Antiviral Drugs. Advances in Experimental Medicine and Biology 2006; 581:573-8. [PMID: 17037600 PMCID: PMC7124025 DOI: 10.1007/978-0-387-33012-9_104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Stanley Perlman
- Department of Pediatrics, University of Iowa, 52242 Iowa City, IA USA
| | - Kathryn V. Holmes
- Department of Microbiology, University of Colorado Health Sciences Center at Fitzsimons, 80045-8333 Aurora, CO USA
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25
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Ma G, Feng Y, Gao F, Wang J, Liu C, Li Y. Biochemical and biophysical characterization of the transmissible gastroenteritis coronavirus fusion core. Biochem Biophys Res Commun 2005; 337:1301-7. [PMID: 16236266 PMCID: PMC7092864 DOI: 10.1016/j.bbrc.2005.09.189] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Accepted: 09/30/2005] [Indexed: 11/25/2022]
Abstract
Transmissible gastroenteritis coronavirus (TGEV) is one of the most destructive agents, responsible for the enteric infections that are lethal for suckling piglets, causing enormous economic loss to the porcine fostering industry every year. Although it has been known that TGEV spiker protein is essential for the viral entry for many years, the detail knowledge of the TGEV fusion protein core is still very limited. Here, we report that TGEV fusion core (HR1-SGGRGG-HR2), in vitro expressed in GST prokaryotic expression system, shares the typical properties of the trimer of coiled-coil heterodimer (six α-helix bundle), which has been confirmed by a combined series of biochemical and biophysical evidences including size exclusion chromatography (gel-filtration), chemical crossing, and circular diagram. The 3D homologous structure model presents its most likely structure, extremely similar to those of the coronaviruses documented. Taken together, TGEV spiker protein belongs to the class I fusion protein, characterized by the existence of two heptad-repeat (HR) regions, HR1 and HR2, and the present knowledge about the truncated TGEV fusion protein core may facilitate in the design of the small molecule or polypeptide drugs targeting the membrane fusion between TGEV and its host.
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Affiliation(s)
- Guangpeng Ma
- Department of Preventive Veterinary, College of Veterinary Medicine, Northeast Agriculture University, 150030 Harbin, PR China
| | - Youjun Feng
- Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
- Graduate School of the Chinese Academy of Sciences, PR China
| | - Feng Gao
- Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
- China Agricultural University, Beijing 100094, PR China
| | - Jinzi Wang
- China Agricultural University, Beijing 100094, PR China
| | - Cheng Liu
- China Agricultural University, Beijing 100094, PR China
| | - Yijing Li
- Department of Preventive Veterinary, College of Veterinary Medicine, Northeast Agriculture University, 150030 Harbin, PR China
- Corresponding author. Fax: +86 0451 5113336.
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26
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Qiu M, Wang J, Wang H, Chen Z, Dai E, Guo Z, Wang X, Pang X, Fan B, Wen J, Wang J, Yang R. Use of the COOH portion of the nucleocapsid protein in an antigen-capturing enzyme-linked immunosorbent assay for specific and sensitive detection of severe acute respiratory syndrome coronavirus. Clin Diagn Lab Immunol 2005; 12:474-6. [PMID: 15753261 PMCID: PMC1065208 DOI: 10.1128/cdli.12.3.474-476.2005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antibody detection with a recombinant COOH portion of the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid (N) protein, N13 (amino acids 221 to 422), was demonstrated to be more specific and sensitive than that with the full-length N protein, and an N13-based antigen-capturing enzyme-linked immunosorbent assay providing a convenient and specific test for serodiagnosis and epidemiological study of SARS was developed.
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Affiliation(s)
- Maofeng Qiu
- Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, No. 20, Dongdajie, Fengtai District, Beijing 100071, People's Republic of China
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27
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Stock I. [Coronaviruses. Causes of SARS and other infections]. Med Monatsschr Pharm 2004; 27:4-12. [PMID: 14752927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Affiliation(s)
- Ingo Stock
- Institut für Medizinische Mikrobiologie und Immunologie, Pharmazeutische Mikrobiologie, Universität Bonn, Meckenheimer Allee 168, 53115 Bonn.
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28
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Eickmann M, Becker S, Klenk HD, Doerr HW, Stadler K, Censini S, Guidotti S, Masignani V, Scarselli M, Mora M, Donati C, Han JH, Song HC, Abrignani S, Covacci A, Rappuoli R. Phylogeny of the SARS coronavirus. Science 2003; 302:1504-5. [PMID: 14645828 DOI: 10.1126/science.302.5650.1504b] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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29
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Gao F, Ou HY, Chen LL, Zheng WX, Zhang CT. Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS-CoV genomes. FEBS Lett 2003; 553:451-6. [PMID: 14572668 PMCID: PMC7232748 DOI: 10.1016/s0014-5793(03)01091-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Recently, we have developed a coronavirus-specific gene-finding system, ZCURVE_CoV 1.0. In this paper, the system is further improved by taking the prediction of cleavage sites of viral proteinases in polyproteins into account. The cleavage sites of the 3C-like proteinase and papain-like proteinase are highly conserved. Based on the method of traditional positional weight matrix trained by the peptides around cleavage sites, the present method also sufficiently considers the length conservation of non-structural proteins cleaved by the 3C-like proteinase and papain-like proteinase to reduce the false positive prediction rate. The improved system, ZCURVE_CoV 2.0, has been run for each of the 24 completely sequenced coronavirus genomes in GenBank. Consequently, all the non-structural proteins in the 24 genomes are accurately predicted. Compared with known annotations, the performance of the present method is satisfactory. The software ZCURVE_CoV 2.0 is freely available at http://tubic.tju.edu.cn/sars/.
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Affiliation(s)
- Feng Gao
- Department of Physics, Tianjin University, Tianjin 300072, PR China
| | - Hong-Yu Ou
- Department of Physics, Tianjin University, Tianjin 300072, PR China
| | - Ling-Ling Chen
- Department of Physics, Tianjin University, Tianjin 300072, PR China
- Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049, PR China
| | - Wen-Xin Zheng
- Department of Physics, Tianjin University, Tianjin 300072, PR China
| | - Chun-Ting Zhang
- Department of Physics, Tianjin University, Tianjin 300072, PR China
- Corresponding author. Fax: (86)-22-2740 2697
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Abstract
In this study, we analyzed the amino acid pairs affected by mutations in two spike proteins from human coronavirus strains 229E and OC43 by means of random analysis in order to gain some insight into the possible mutations in the spike protein from SARS-CoV. The results demonstrate that the randomly unpredictable amino acid pairs are more sensitive to the mutations. The larger is the difference between actual and predicted frequencies, the higher is the chance of mutation occurring. The effect induced by mutations is to reduce the difference between actual and predicted frequencies. The amino acid pairs whose actual frequencies are larger than their predicted frequencies are more likely to be targeted by mutations, whereas the amino acid pairs whose actual frequencies are smaller than their predicted frequencies are more likely to be formed after mutations. These findings are identical to our several recent studies, i.e. the mutations represent a process of degeneration inducing human diseases.
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Affiliation(s)
- Guang Wu
- DreamSciTech Consulting Co. Ltd., 301, Building 12, Nanyou A-zone, Jainnan Road, CN-518054, Shenzhen, PR China.
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31
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Tan K, Zelus BD, Meijers R, Liu JH, Bergelson JM, Duke N, Zhang R, Joachimiak A, Holmes KV, Wang JH. Crystal structure of murine sCEACAM1a[1,4]: a coronavirus receptor in the CEA family. EMBO J 2002; 21:2076-86. [PMID: 11980704 PMCID: PMC125375 DOI: 10.1093/emboj/21.9.2076] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [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] [Indexed: 01/07/2023] Open
Abstract
CEACAM1 is a member of the carcinoembryonic antigen (CEA) family. Isoforms of murine CEACAM1 serve as receptors for mouse hepatitis virus (MHV), a murine coronavirus. Here we report the crystal structure of soluble murine sCEACAM1a[1,4], which is composed of two Ig-like domains and has MHV neutralizing activity. Its N-terminal domain has a uniquely folded CC' loop that encompasses key virus-binding residues. This is the first atomic structure of any member of the CEA family, and provides a prototypic architecture for functional exploration of CEA family members. We discuss the structural basis of virus receptor activities of murine CEACAM1 proteins, binding of Neisseria to human CEACAM1, and other homophilic and heterophilic interactions of CEA family members.
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Affiliation(s)
- Kemin Tan
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Bruce D. Zelus
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Rob Meijers
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Jin-huan Liu
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Jeffrey M. Bergelson
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Norma Duke
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Rongguang Zhang
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Andrzej Joachimiak
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Kathryn V. Holmes
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
| | - Jia-huai Wang
- Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, Departments of Medicine, Pediatrics, Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Corresponding authors e-mail: or
K.Tan, B.D.Zelus and R.Meijers contributed equally to this work
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Abstract
Many enteric viruses are difficult or impossible to propagate in tissue culture. Coronaviruses and toroviruses are large, enveloped, plus-strand RNA viruses in the order Nidovirales that cause enteric disease in young pigs, cows, dogs, mice, cats and horses. Two different serogroups of mammalian coronaviruses cause frequent respiratory infections in humans, and coronaviruses and toroviruses have been implicated in human diarrhoeal disease by immunoelectron microscopy. However, there is as yet no consensus about the importance of these enveloped viruses in human diarrhoea, and little is known about their genetic variability. The large spike (S) glycoprotein is an important determinant of species specificity, tissue tropism and virulence of coronavirus infection. To infect enterocytes, both S glycoproteins and the viral envelope must resist degradation by proteases, low and high pH, and bile salts. One specific site on the S glycoprotein of bovine coronavirus must be cleaved by an intracellular protease or trypsin to activate viral infectivity and cell fusion. S glycoprotein binds to specific receptors on the apical membranes of enterocytes, and can undergo a temperature-dependent, receptor-mediated conformational change that leads to fusion of the viral envelope with host membranes to initiate infection. Analysing spike-receptor interactions may lead to new ways to propagate these enteric viruses as well as new strategies for development of novel antiviral drugs.
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Affiliation(s)
- K V Holmes
- Department of Microbiology, B-175, University of Colorado Health Sciences Center, 4200 East 9th Avenue, Denver, CO 20862, USA
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33
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Raamsman MJ, Locker JK, de Hooge A, de Vries AA, Griffiths G, Vennema H, Rottier PJ. Characterization of the coronavirus mouse hepatitis virus strain A59 small membrane protein E. J Virol 2000; 74:2333-42. [PMID: 10666264 PMCID: PMC111715 DOI: 10.1128/jvi.74.5.2333-2342.2000] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.7] [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: 06/23/1999] [Accepted: 12/02/1999] [Indexed: 02/07/2023] Open
Abstract
The small envelope (E) protein has recently been shown to play an essential role in the assembly of coronaviruses. Expression studies revealed that for formation of the viral envelope, actually only the E protein and the membrane (M) protein are required. Since little is known about this generally low-abundance virion component, we have characterized the E protein of mouse hepatitis virus strain A59 (MHV-A59), an 83-residue polypeptide. Using an antiserum to the hydrophilic carboxy terminus of this otherwise hydrophobic protein, we found that the E protein was synthesized in infected cells with similar kinetics as the other viral structural proteins. The protein appeared to be quite stable both during infection and when expressed individually using a vaccinia virus expression system. Consistent with the lack of a predicted cleavage site, the protein was found to become integrated in membranes without involvement of a cleaved signal peptide, nor were any other modifications of the polypeptide observed. Immunofluorescence analysis of cells expressing the E protein demonstrated that the hydrophilic tail is exposed on the cytoplasmic side. Accordingly, this domain of the protein could not be detected on the outside of virions but appeared to be inside, where it was protected from proteolytic degradation. The results lead to a topological model in which the polypeptide is buried within the membrane, spanning the lipid bilayer once, possibly twice, and exposing only its carboxy-terminal domain. Finally, electron microscopic studies demonstrated that expression of the E protein in cells induced the formation of characteristic membrane structures also observed in MHV-A59-infected cells, apparently consisting of masses of tubular, smooth, convoluted membranes. As judged by their colabeling with antibodies to E and to Rab-1, a marker for the intermediate compartment and endoplasmic reticulum, the E protein accumulates in and induces curvature into these pre-Golgi membranes where coronaviruses have been shown earlier to assemble by budding.
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Affiliation(s)
- M J Raamsman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Institute of Virology, and Institute of Biomembranes, Utrecht University, 3584 CL Utrecht, The Netherlands
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Gómez N, Wigdorovitz A, Castañón S, Gil F, Ordás R, Borca MV, Escribano JM. Oral immunogenicity of the plant derived spike protein from swine-transmissible gastroenteritis coronavirus. Arch Virol 2000; 145:1725-32. [PMID: 11003480 PMCID: PMC7086604 DOI: 10.1007/s007050070087] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Transgenic plants represent an inexpensive alternative to classical fermentation systems for production of recombinant subunit vaccines. Transgenic potato plants were created that express the N-terminal domain of the glycoprotein S (N-gS) from Transmissible gastroenteritis coronavirus (TGEV), containing the major antigenic sites of the protein. Extracts from potato tubers expressing N-gS were inoculated intraperitoneally to mice, and the vaccinated mice developed serum IgG specific for TGEV. Furthermore, when potato tubers expressing N-gS were fed directly to mice, they developed serum antibodies specific for gS protein, demonstrating the oral immunogenicity of the plant derived spike protein from TGEV.
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Affiliation(s)
- N Gómez
- Departamento de Mejora Genética y Biotecnologí INIA, Madrid, Spain
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Abstract
A reverse transcriptase, polymerase chain reaction (RT-PCR) procedure was used to amplify a segment of the genome of turkey coronavirus (TCV) spanning portions of the matrix and nucleocapsid (MN) protein genes (approximately 1.1 kb). The MN gene region of three epidemiologically distinct TCV strains (Minnesota, NC95, Indiana) was amplified, cloned into pUC19, and sequenced. TCV MN gene sequences were compared with published sequences of other avian and mammalian coronaviruses. A high degree of similarity (>90%) was observed between the nucleotide, matrix protein, and nucleocapsid protein sequences of TCV strains and published sequences of infectious bronchitis virus (IBV). The matrix and nucleocapsid protein sequences of TCV had limited homology (<30%) with MN sequences of mammalian coronaviruses. These results demonstrate a close genetic relationship between the avian coronaviruses, IBV and TCV.
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Affiliation(s)
| | | | | | - James S. Guy
- *James S. Guy, North Carolina State University, College of Veterinary Medicine, 4700 Hillsborough Street, Raleigh, NC 27606 (USA), Tel. +1 919 829 4287, Fax +1 919 829 4455, E-Mail
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Chagnon F, Lamarre A, Lachance C, Krakowski M, Owens T, Laliberté JF, Talbot PJ. Characterization of the expression and immunogenicity of the ns4b protein of human coronavirus 229E. Can J Microbiol 1998; 44:1012-7. [PMID: 9933919 DOI: 10.1139/cjm-44-10-1012] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequencing of complementary DNAs prepared from various coronaviruses has revealed open reading frames encoding putative proteins that are yet to be characterized and are so far only described as nonstructural (ns). As a first step in the elucidation of its function, we characterized the expression and immunogenicity of the ns4b gene product from strain 229E of human coronavirus (HCV-229E), a respiratory virus with a neurotropic potential. The gene was cloned and expressed in bacteria. A fusion protein of ns4b with maltose-binding protein was injected into rabbits to generate specific antibodies that were used to demonstrate the expression of ns4b in HCV-229E-infected cells using flow cytometry. Given a previously reported contiguous five amino acid shared region between ns4b and myelin basic protein, a purified recombinant histidine-tagged ns4b protein and (or) human myelin basic protein were injected into mice to evaluate whether myelin-viral protein cross-reactive antibody responses could be generated. Each immunogen induced specific but not cross-reactive antibodies. We conclude that ns4b is expressed in infected cells and is immunogenic, although this does not involve amino acids shared with a self protein, at least in the experimental conditions used.
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Affiliation(s)
- F Chagnon
- Laboratory of Neuroimmunovirology and Human Health Research Center, Institut Armand-Frappier, Université du Québec, Laval, Canada
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Kasai H, Morita E, Hatakeyama K, Sugiyama K. Characterization of haemagglutinin-esterase protein (HE) of murine corona virus DVIM by monoclonal antibodies. Arch Virol 1998; 143:1941-8. [PMID: 9856082 PMCID: PMC7086726 DOI: 10.1007/s007050050431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We analyzed the characteristics of seven monoclonal antibodies (mAbs) raised against purified HE (hemagglutinin-esterase) glycoprotein of the murine coronavirus DVIM (diarrhea virus of infant mice). Immunocrossreaction of these mAbs with JHM and/or MHV-S suggest that antigenic epitopes of HE of DVIM are similar to those of JHM and/or MHV-S. Four mAbs (1b4, 3a28, 4c19, 10b7), designated as group A mAbs, strongly inhibited both HA and AE activities. On the other hand, three mAbs (5a3, 6a6, 13a4), referred to as group B, had a comparatively weak HA inhibition activity. These results indicate that the antigenic epitopes of this glycoprotein can be classified into at least two groups and that the functional sites of HA and AE activities are similar but not identical. Neutralizing activity was shown in group A mAbs exclusively, suggesting that the ratio of HA and/or AE activities may play important roles in the cell fusion activity of DVIM-infected cells.
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Affiliation(s)
- H Kasai
- Department of Biology, Faculty of Science, Hirosaki University, Japan
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Shchetinina VN, Panchenko LA, Volianskiĭ IL. [The structure and immunobiological properties of coronavirus proteins]. Mikrobiol Z 1995; 57:98-112. [PMID: 7655661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The survey includes data concerning structural proteins of coronaviruses obtained for the last ten years. It elucidates such problems as the proteins organization in the virion, heterogeneity of their composition, structure and biological properties, antigenic and immunobiological properties, prospects of creation of specific immunogenic anticoronavirus, prophylactic and diagnostic preparations.
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Oleszak EL, Perlman S, Parr R, Collisson EW, Leibowitz JL. Molecular mimicry between S peplomer proteins of coronaviruses (MHV, BCV, TGEV and IBV) and Fc receptor. Adv Exp Med Biol 1994; 342:183-8. [PMID: 8209728 DOI: 10.1007/978-1-4615-2996-5_29] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In previous studies we have demonstrated molecular mimicry between the S peplomer protein of Mouse Hepatitis Virus (MHV) and Fc gamma Receptor (Fc gamma R) of IgG. Rabbit IgG, but not its F(ab')2 fragments, monoclonal rat and mouse IgG and the rat 2.4G2 anti-mouse Fc gamma R monoclonal antibody (mab) immunoprecipitated natural and recombinant MHV S protein. On the basis of a number of criteria, MHV S peplomer protein exhibits Fc IgG binding ability. We report here a molecular mimicry between the S peplomer protein of Bovine Coronavirus (BCV) and Fc gamma R. BCV S peplomer protein which belongs to the same antigenic subgroup as MHV also binds Fc portion of rabbit IgG and is immunoprecipitated by the 2.4G2 anti-Fc gamma R mab. In contrast, Transmissible Gastroenteritis Coronavirus (TGEV) and Infectious Bronchitis Virus (IBV) S peplomer proteins which represent two distinct antigenic subgroups of Coronaviridae do not bind rabbit IgG and do not react with anti-Fc gamma R mab. However, homologous swine IgG, but not its F(ab')2 fragments, immunoprecipitated from TGEV-infected cells a polypeptide chain with molecular mass of 195 kDa, identical to that immunoprecipitated by the T36 mab anti-TGEV S peplomer protein.
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Affiliation(s)
- E L Oleszak
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center Medical School at Houston
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Utiger A, Rosskopf M, Guscetti F, Ackermann M. Preliminary characterization of a monoclonal antibody specific for a viral 27 kD glycoprotein family synthesized in porcine epidemic diarrhoea virus infected cells. Adv Exp Med Biol 1994; 342:197-202. [PMID: 8209730 DOI: 10.1007/978-1-4615-2996-5_31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We describe a new monoclonal antibody No. 204 (mcAb 204) which recognized a family of four polypeptides, consisting of a 27kD, a 24/23kD double band and a 19kD protein present within PEDV infected cell lysates. These proteins were identified by immunoprecipitation as well as by staining of immunoblots. In infected Vero cell cultures, the synthesis of the 27kD protein was initiated between 6 and 8 hours post inoculation. The 24/23kD double band and the 19kD protein were only detectable later. At least the 27 and the 24/23kD proteins were apparently glycosylated and present in purified virions. Pulse-chase as well as solubilization experiments indicated that the faster migrating bands represented processed products of the 27kD glycoprotein. The nature of the processing is not known at present. We suggest that the 27kD protein family may represent the integral membrane protein M of PEDV. Since this protein is highly abundant in virions as well as in infected cells, and since mcAb 204 is able to react with its antigen under various conditions, this monoclonal antibody may be useful to further studies of the M-protein of PEDV. In addition, it may provide a useful tool for routine diagnosis.
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Affiliation(s)
- A Utiger
- Institute for Virology, Vet.-med. Faculty, University of Zürich
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Abstract
Coronaviruses (CV) infect a variety of livestock, poultry and companion animals. They belong to at least five antigenic groups. CV cause localized infections of the respiratory and/or intestinal tracts, with the exception of feline infectious peritonitis virus (FIPV) and hemagglutinating encephalomyelitis (HEV) which cause systemic infections. The enteropathogenic CV infect the villous enterocytes resulting in villous atrophy leading to malabsorptive diarrhea. Several CV (bovine CV-BCV, porcine respiratory CV-PRCV, infectious bronchitis virus-IBV) cause respiratory disease. Current evidence indicates that protection against enteric and respiratory CV infections is mediated by passive or active immunity at the primary site of CV replication. Maternal vaccination approaches to induce passive immunity include the use of inactivated and modified live viral vaccines. Modified live viruses and a Ts mutant CV (FIPV) are also used as oral or intranasal vaccines to induce active mucosal immunity. The success of these vaccines in the field is often compromised by a number of potential problems. Coronaviruses are spherical, enveloped viruses, ranging from 80-160 nm in diameter and containing a positive-stranded RNA genome. They possess prominent surface spikes and some species display a fringe of smaller surface projections believed to be the hemagglutinin (HE). Coronaviruses possess 3 to 4 structural proteins: the spike (S) glycoprotein (150-200 kDa), the integral membrane glycoprotein (M; 20-30 kDa) and the nucleocapsid phosphoprotein (N; 43-50 kDa). A subset of CV (BCV, HEV, turkey CV) possess a third glycoprotein on the virion surface, the HE (60-65 kDa). These proteins can be quantitated using pooled monoclonal antibodies (mAb) to distinct epitopes of each protein in ELISA. Most research has focused on the S protein as a candidate antigen for CV vaccines since it induces virus neutralizing (VN) antibodies. However the HE protein stimulates the production of VN and HE inhibiting antibodies and the M protein induces antibodies that neutralize virus in the presence of complement. Attempts to correlate in vitro VN antibody activity with in vivo protection have shown that the passive transfer of VN mAb to the S or HE protein conferred passive protection against CV challenge in some studies, but not others. Additional research has implicated a possible role for other CV proteins in immunity. Studies of mAb to the M protein of transmissible gastroenteritis (TGEV) have provided evidence for a direct role of the M protein in the induction of alpha IFN by porcine blood leukocytes. The potential significance of this phenomenon to immunity to TGEV is unclear.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- L J Saif
- Ohio Agricultural Research and Development Center, Ohio State University, Wooster 44691
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Goncharuk EI, Shevtsova ZV, Rumel' NB, Fedorinov VV. [The properties of simian coronavirus]. Vopr Virusol 1993; 38:126-9. [PMID: 8073751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Properties of 20 coronavirus (CV) isolates obtained from spontaneously infected Papio hamadryas and rhesus monkeys were investigated. Two of them were selected as simian CV prototype strains-CVRM 281 (rhesus monkey) and CVP 250 (Papio hamadryas), and can be offered as candidates to the Coronaviridae family. They are closely related to each other, but differ in some biological properties and polypeptides. These strains belong to the 2nd antigen group of mammalian CV with the prototype strain HCV OC 43 but differ from the latter. The strain CVRM 281 induces experimental CV infection which can be used as a model for investigations of some obscure aspects of human infection. The properties of these viruses suggest their usefulness for diagnostic purposes.
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