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López-Muñoz AD, Santos JJS, Yewdell JW. Cell surface nucleocapsid protein expression: A betacoronavirus immunomodulatory strategy. Proc Natl Acad Sci U S A 2023; 120:e2304087120. [PMID: 37399385 PMCID: PMC10334784 DOI: 10.1073/pnas.2304087120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 06/08/2023] [Indexed: 07/05/2023] Open
Abstract
We recently reported that SARS-CoV-2 nucleocapsid (N) protein is abundantly expressed on the surface of both infected and neighboring uninfected cells, where it enables activation of Fc receptor-bearing immune cells with anti-N antibodies (Abs) and inhibits leukocyte chemotaxis by binding chemokines (CHKs). Here, we extend these findings to N from the common cold human coronavirus (HCoV)-OC43, which is also robustly expressed on the surface of infected and noninfected cells by binding heparan sulfate/heparin (HS/H). HCoV-OC43 N binds with high affinity to the same set of 11 human CHKs as SARS-CoV-2 N, but also to a nonoverlapping set of six cytokines. As with SARS-CoV-2 N, HCoV-OC43 N inhibits CXCL12β-mediated leukocyte migration in chemotaxis assays, as do all highly pathogenic and common cold HCoV N proteins. Together, our findings indicate that cell surface HCoV N plays important evolutionarily conserved roles in manipulating host innate immunity and as a target for adaptive immunity.
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Affiliation(s)
- Alberto Domingo López-Muñoz
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases National Institutes of Health, Bethesda, MD20892
| | - Jefferson J. S. Santos
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases National Institutes of Health, Bethesda, MD20892
| | - Jonathan W. Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases National Institutes of Health, Bethesda, MD20892
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2
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Vidal LEL, Figueira-Mansur J, Jurgilas PB, Argondizzo APC, Pestana CP, Martins FO, da Silva Junior HC, Miguez M, Loureiro BO, Marques CDFS, Trinta KS, da Silva LBR, de Mello MB, da Silva ED, Bastos RC, Esteves G. Process development and characterization of recombinant nucleocapsid protein for its application on COVID-19 diagnosis. Protein Expr Purif 2023; 207:106263. [PMID: 36921810 PMCID: PMC10012136 DOI: 10.1016/j.pep.2023.106263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023]
Abstract
COVID-19 pandemic was caused by the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2). The nucleocapsid (N) protein from Sars-CoV-2 is a highly immunogenic antigen and responsible for genome packing. Serological assays are important tools to detect previous exposure to SARS-CoV-2, complement epidemiological studies, vaccine evaluation and also in COVID-19 surveillance. SARS-CoV-2 N (r2N) protein was produced in Escherichia coli, characterized, and the immunological performance was evaluated by enzyme-linked immunosorbent assay (ELISA) and beads-based array immunoassay. r2N protein oligomers were evidenced when it is associated to nucleic acid. Benzonase treatment reduced host nucleic acid associated to r2N protein, but crosslinking assay still demonstrates the presence of higher-order oligomers. Nevertheless, after RNase treatment the higher-order oligomers reduced, and dimer form increased, suggesting RNA contributes to the oligomer formation. Structural analysis revealed nucleic acid did not interfere with the thermal stability of the recombinant protein. Interestingly, nucleic acid was able to prevent r2N protein aggregation even with increasing temperature while the protein benzonase treated begin aggregation process above 55 °C. In immunological characterization, ELISA performed with 233 serum samples presented a sensitivity of 97.44% (95% Confidence Interval, CI, 91.04%, 99.69%) and a specificity of 98.71% (95% CI, 95.42%, 99.84%) while beads-based array immunoassay carried out with 217 samples showed 100% sensitivity and 98.6% specificity. The results exhibited an excellent immunological performance of r2N protein in serologic assays showing that, even in presence of nucleic acid, it can be used as a component of an immunoassay for the sensitive and specific detection of SARS-CoV-2 antibodies.
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Affiliation(s)
- Luãnna Elisa Liebscher Vidal
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil.
| | - Janaina Figueira-Mansur
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Patrícia Barbosa Jurgilas
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Ana Paula Correa Argondizzo
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Cristiane Pinheiro Pestana
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Fernanda Otaviano Martins
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Haroldo Cid da Silva Junior
- Immunological Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Mariana Miguez
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Bernardo Oliveira Loureiro
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Christiane de Fátima Silva Marques
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Karen Soares Trinta
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Leila Botelho Rodrigues da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Marcelle Bral de Mello
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Edimilson Domingos da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Renata Chagas Bastos
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Gabriela Esteves
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
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López-Muñoz AD, Santos JJ, Yewdell JW. Cell Surface Nucleocapsid Protein Expression: A Betacoronavirus Immunomodulatory Strategy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529952. [PMID: 36993159 PMCID: PMC10054960 DOI: 10.1101/2023.02.24.529952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
We recently reported that SARS-CoV-2 Nucleocapsid (N) protein is abundantly expressed on the surface of both infected and neighboring uninfected cells, where it enables activation of Fc receptor-bearing immune cells with anti-N antibodies (Abs) and inhibits leukocyte chemotaxis by binding chemokines (CHKs). Here, we extend these findings to N from the seasonal human coronavirus (HCoV)-OC43, which is also robustly expressed on the surface of infected and non-infected cells by binding heparan-sulfate/heparin (HS/H). HCoV-OC43 N binds with high affinity to the same set of 11 human CHKs as SARS-CoV-2 N, but also to a non-overlapping set of 6 cytokines (CKs). As with SARS-CoV-2 N, HCoV-OC43 N inhibits CXCL12β-mediated leukocyte migration in chemotaxis assays, as do all highly pathogenic and endemic HCoV N proteins. Together, our findings indicate that cell surface HCoV N plays important evolutionary conserved roles in manipulating host innate immunity and as a target for adaptive immunity.
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4
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Kim MI, Lee C. Human Coronavirus OC43 as a Low-Risk Model to Study COVID-19. Viruses 2023; 15:v15020578. [PMID: 36851792 PMCID: PMC9965565 DOI: 10.3390/v15020578] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had irreversible and devastating impacts on every aspect of human life. To better prepare for the next similar pandemic, a clear understanding of coronavirus biology is a prerequisite. Nevertheless, the high-risk nature of the causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), requires the use of a cumbersome biosafety level-3 (BSL-3) confinement facility. To facilitate the development of preventive and therapeutic measures against SARS-CoV-2, one of the endemic strains of low-risk coronaviruses has gained attention as a useful research alternative: human coronavirus OC43 (HCoV-OC43). In this review, its history, classification, and clinical manifestations are first summarized. The characteristics of its viral genomes, genes, and evolution process are then further explained. In addition, the host factors necessary to support the life cycle of HCoV-OC43 and the innate, as well as adaptive, immunological responses to HCoV-OC43 infection are discussed. Finally, the development of in vitro and in vivo systems to study HCoV-OC43 and its application to the discovery of potential antivirals for COVID-19 by using HCoV-OC43 models are also presented. This review should serve as a concise guide for those who wish to use HCoV-OC43 to study coronaviruses in a low-risk research setting.
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Zhang B, Tian J, Zhang Q, Xie Y, Wang K, Qiu S, Lu K, Liu Y. Comparing the Nucleocapsid Proteins of Human Coronaviruses: Structure, Immunoregulation, Vaccine, and Targeted Drug. Front Mol Biosci 2022; 9:761173. [PMID: 35573742 PMCID: PMC9099148 DOI: 10.3389/fmolb.2022.761173] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/28/2022] [Indexed: 01/08/2023] Open
Abstract
The seven pathogenic human coronaviruses (HCoVs) include HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1, which usually cause mild upper respiratory tract diseases, and SARS-CoV, MERS-CoV, and SARS-CoV-2, which cause a severe acute respiratory syndrome. The nucleocapsid (N) protein, as the dominant structural protein from coronaviruses that bind to the genomic RNA, participates in various vital activities after virus invasion and will probably become a promising target of antiviral drug design. Therefore, a comprehensive literature review of human coronavirus’ pathogenic mechanism and therapeutic strategies is necessary for the control of the pandemic. Here, we give a systematic summary of the structures, immunoregulation, and potential vaccines and targeted drugs of the HCoVs N protein. First, we provide a general introduction to the fundamental structures and molecular function of N protein. Next, we outline the N protein mediated immune regulation and pathogenesis mechanism. Finally, we comprehensively summarize the development of potential N protein-targeted drugs and candidate vaccines to treat coronavirus disease 2019 (COVID-19). We believe this review provides insight into the virulence and transmission of SARS-CoV-2 as well as support for further study on epidemic control of COVID-19.
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Affiliation(s)
- Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
| | - Junjie Tian
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Qintao Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Yan Xie
- School of Public Health, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Shuyi Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Keyu Lu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
| | - Yang Liu
- School of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- *Correspondence: Yang Liu, ; Keyu Lu, ; Bo Zhang,
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Xu C, Katyal N, Nesterova T, Perilla JR. Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations. J Chem Phys 2021; 153:155102. [PMID: 33092380 DOI: 10.1063/5.0021491] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ebola virus (EBOV) is a human pathogen with the ability to cause hemorrhagic fever and bleeding diathesis in hosts. The life cycle of EBOV depends on its nucleocapsid. The Ebola nucleocapsid consists of a helical assembly of nucleoproteins (NPs) encapsidating single-stranded viral RNA (ssRNA). Knowledge of the molecular determinants of Ebola nucleocapsid stability is essential for the development of therapeutics against EBOV. However, large degrees of freedom associated with the Ebola nucleocapsid helical assembly pose a computational challenge, thereby limiting the previous simulation studies to the level of monomers. In the present work, we have performed all atom molecular dynamics (MD) simulations of the helical assembly of EBOV nucleoproteins in the absence and presence of ssRNA. We found that ssRNA is essential for maintaining structural integrity of the nucleocapsid. Other molecular determinants observed to stabilize the nucleocapsid include NP-RNA and NP-NP interactions and ion distributions. Additionally, the structural and dynamical behavior of the nucleocapsid monomer depends on its position in the helical assembly. NP monomers present on the longitudinal edges of the helical tube are more exposed, flexible, and have weaker NP-NP interactions than those residing in the center. This work provides key structural features stabilizing the nucleocapsid that may serve as therapeutic targets.
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Affiliation(s)
- Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Nidhi Katyal
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Tanya Nesterova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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7
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Zinzula L, Basquin J, Bohn S, Beck F, Klumpe S, Pfeifer G, Nagy I, Bracher A, Hartl FU, Baumeister W. High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2. Biochem Biophys Res Commun 2021; 538:54-62. [PMID: 33039147 PMCID: PMC7532810 DOI: 10.1016/j.bbrc.2020.09.131] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022]
Abstract
Unprecedented by number of casualties and socio-economic burden occurring worldwide, the coronavirus disease 2019 (Covid-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the worst health crisis of this century. In order to develop adequate countermeasures against Covid-19, identification and structural characterization of suitable antiviral targets within the SARS-CoV-2 protein repertoire is urgently needed. The nucleocapsid phosphoprotein (N) is a multifunctional and highly immunogenic determinant of virulence and pathogenicity, whose main functions consist in oligomerizing and packaging the single-stranded RNA (ssRNA) viral genome. Here we report the structural and biophysical characterization of the SARS-CoV-2 N C-terminal domain (CTD), on which both N homo-oligomerization and ssRNA binding depend. Crystal structures solved at 1.44 Å and 1.36 Å resolution describe a rhombus-shape N CTD dimer, which stably exists in solution as validated by size-exclusion chromatography coupled to multi-angle light scattering and analytical ultracentrifugation. Differential scanning fluorimetry revealed moderate thermal stability and a tendency towards conformational change. Microscale thermophoresis demonstrated binding to a 7-bp SARS-CoV-2 genomic ssRNA fragment at micromolar affinity. Furthermore, a low-resolution preliminary model of the full-length SARS-CoV N in complex with ssRNA, obtained by cryo-electron microscopy, provides an initial understanding of self-associating and RNA binding functions exerted by the SARS-CoV-2 N.
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Affiliation(s)
- Luca Zinzula
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany,Corresponding authors
| | - Jerome Basquin
- The Max-Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Stefan Bohn
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany,The Max-Planck Institute of Biochemistry, Department of Cellular Machines and Signaling, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Florian Beck
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Sven Klumpe
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Günter Pfeifer
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - István Nagy
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Andreas Bracher
- The Max-Planck Institute of Biochemistry, Department of Cellular Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - F. Ulrich Hartl
- The Max-Planck Institute of Biochemistry, Department of Cellular Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Baumeister
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152, Martinsried, Germany
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Gan Y, Tan F, Yi R, Zhou X, Li C, Zhao X. Research Progress on Coronavirus Prevention and Control in Animal-Source Foods. J Multidiscip Healthc 2020; 13:743-751. [PMID: 32801737 PMCID: PMC7414935 DOI: 10.2147/jmdh.s265059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 11/23/2022] Open
Abstract
Coronaviruses (CoVs) are common pathogens that can infect both animals and humans, thereby posing a threat to global public health. CoV infection mostly occurs during winter and spring in temperate countries; the virus has high transmission efficiency and may have severe infection outcomes. The recent SARS-CoV-2 outbreak exhibited transboundary transmission due to international transportation, trade, and economic exchange. Animal hosts provide a persistent source for CoVs and their recombination. Domestic camels have been shown to be one of the hosts of CoVs, while livestock, poultry and other warm-blooded animals may act as intermediate hosts for CoVs. This paper outlines the biological and epidemiological characteristics and diagnosis of CoVs and describes the origin, transmission route, animal-source food risk, and control measures for CoVs. Such knowledge can be used to prevent CoVs from harming consumers through animal-sourced foods and can help to prevent new zoonoses from occurring. This work will provide a reference for strengthening the controls on the production process in meat production companies, thereby improving food safety.
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Affiliation(s)
- Yi Gan
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
| | - Fang Tan
- Department of Public Health, Our Lady of Fatima University, Valenzuela, Philippines
| | - Ruokun Yi
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
| | - Xianrong Zhou
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
| | - Chong Li
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
| | - Xin Zhao
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
- Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People’s Republic of China
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An in vivo cell-based assay for investigating the specific interaction between the SARS-CoV N-protein and its viral RNA packaging sequence. Biochem Biophys Res Commun 2019; 520:499-506. [PMID: 31594639 PMCID: PMC7092827 DOI: 10.1016/j.bbrc.2019.09.115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/26/2019] [Indexed: 01/25/2023]
Abstract
The SARS-CoV nucleocapsid (N) protein serves multiple functions in viral replication, transcription, and assembly of the viral genome complex. Coronaviruses specifically package genomic RNA into assembled virions, and in SARS-CoV, it is reported that this process is driven by an interaction between the N-protein and a packaging signal encoded within the viral RNA. While recent studies have uncovered the sequence of this packaging signal, little is known about the specific interaction between the N-protein and the packaging signal sequence, and the mechanisms by which this interaction drives viral genome packaging. In this study, we developed a novel in vivo cell-based assay for examining this interaction between the N-protein and packaging signal RNA for SARS-CoV, as well as other viruses within the coronaviridae family. Our results demonstrate that the N-protein specifically recognizes the SARS-CoV packaging signal with greater affinity compared to signals from other coronaviruses or non-coronavirus species. We also use deletion mapping to identify a 151-nt region within the packaging signal sequence that is critical for N-protein-RNA binding, and conversely, we show that both the N-terminal and C-terminal domains of the N protein are necessary for recognizing the packaging RNA. These results describe, for the first time, in vivo evidence for an interaction between the SARS-CoV N-protein and its packaging signal RNA, and demonstrate the feasibility of using this cell-based assay to further probe viral RNA-protein interactions in future studies.
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10
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Lo CY, Tsai TL, Lin CN, Lin CH, Wu HY. Interaction of coronavirus nucleocapsid protein with the 5'- and 3'-ends of the coronavirus genome is involved in genome circularization and negative-strand RNA synthesis. FEBS J 2019; 286:3222-3239. [PMID: 31034708 PMCID: PMC7164124 DOI: 10.1111/febs.14863] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/21/2019] [Accepted: 04/25/2019] [Indexed: 12/28/2022]
Abstract
Synthesis of the negative‐strand ((−)‐strand) counterpart is the first step of coronavirus (CoV) replication; however, the detailed mechanism of the early event and the factors involved remain to be determined. Here, using bovine coronavirus (BCoV)‐defective interfering (DI) RNA, we showed that (a) a poly(A) tail with a length of 15 nucleotides (nt) was sufficient to initiate efficient (−)‐strand RNA synthesis and (b) substitution of the poly(A) tail with poly(U), (C) or (G) only slightly decreased the efficiency of (−)‐strand synthesis. The findings indicate that in addition to the poly(A) tail, other factors acting in trans may also participate in (−)‐strand synthesis. The BCoV nucleocapsid (N) protein, an RNA‐binding protein, was therefore tested as a candidate. Based on dissociation constant (Kd) values, it was found that the binding affinity between N protein, but not poly(A)‐binding protein, and the 3′‐terminal 55 nt plus a poly(A), poly(U), poly(C) or poly(G) tail correlates with the efficiency of (−)‐strand synthesis. Such an association was also evidenced by the binding affinity between the N protein and 5′‐ and 3′‐terminal cis‐acting elements important for (−)‐strand synthesis. Further analysis demonstrated that N protein can act as a bridge to facilitate interaction between the 5′‐ and 3′‐ends of the CoV genome, leading to circularization of the genome. Together, the current study extends our understanding of the mechanism of CoV (−)‐strand RNA synthesis through involvement of N protein and genome circularization and thus may explain why the addition of N protein in trans is required for efficient CoV replication.
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Affiliation(s)
- Chen-Yu Lo
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Tsung-Lin Tsai
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chao-Nan Lin
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, Pingtung, Taiwan
| | - Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
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11
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Leon-Icaza SA, Zeng M, Rosas-Taraco AG. microRNAs in viral acute respiratory infections: immune regulation, biomarkers, therapy, and vaccines. EXRNA 2019; 1:1. [PMID: 34171007 PMCID: PMC7149109 DOI: 10.1186/s41544-018-0004-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 12/27/2018] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are single-stranded RNAs of 17-24 nt. These molecules regulate gene expression at the post-transcriptional level and are differentially expressed in viral acute respiratory infections (ARIs), which are responsible for high morbidity and mortality around the world. In recent years, miRNAs have been studied in order to discover anti-viral ARI drug targets as well as biomarkers for diagnosis, severity, and prognosis. This review presents an analysis of the regulatory response to viral ARIs of miRNAs, including their participation in the innate immune response, their utility as biomarkers, and their potential for future therapies and vaccine development.
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Affiliation(s)
- Stephen A. Leon-Icaza
- 0000 0001 2203 0321grid.411455.0Department of Immunology, Faculty of Medicine, Universidad Autónoma de Nuevo León, Monterrey, NL Mexico ,grid.449768.0Center of Emphasis in Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905-2827 USA
| | - Mingtao Zeng
- grid.449768.0Center of Emphasis in Infectious Diseases, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905-2827 USA
| | - Adrian G. Rosas-Taraco
- 0000 0001 2203 0321grid.411455.0Department of Immunology, Faculty of Medicine, Universidad Autónoma de Nuevo León, Monterrey, NL Mexico
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12
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Chang CK, Jeyachandran S, Hu NJ, Liu CL, Lin SY, Wang YS, Chang YM, Hou MH. Structure-based virtual screening and experimental validation of the discovery of inhibitors targeted towards the human coronavirus nucleocapsid protein. MOLECULAR BIOSYSTEMS 2016; 12:59-66. [DOI: 10.1039/c5mb00582e] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nucleocapsid protein (NP), an essential RNA-binding viral protein in human coronavirus (CoV)-infected cells, is an antiviral target for drug discovery.
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Affiliation(s)
- Chung-ke Chang
- Institute of Biomedical Science
- Academia Sinica
- Nangang
- Taiwan
| | - Sivakamavalli Jeyachandran
- Institute of Genomics and Bioinformatics and Institute of Life Sciences
- National Chung Hsing University
- Taichung 40254
- Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry
- National Chung Hsing University
- Taichung 40254
- Taiwan
| | - Chia-Ling Liu
- Institute of Genomics and Bioinformatics and Institute of Life Sciences
- National Chung Hsing University
- Taichung 40254
- Taiwan
| | - Shing-Yen Lin
- Institute of Genomics and Bioinformatics and Institute of Life Sciences
- National Chung Hsing University
- Taichung 40254
- Taiwan
| | - Yong-Sheng Wang
- Institute of Genomics and Bioinformatics and Institute of Life Sciences
- National Chung Hsing University
- Taichung 40254
- Taiwan
| | - Yu-Ming Chang
- Institute of Biological Chemistry
- Academia Sinica
- Taipei 11529
- Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics and Institute of Life Sciences
- National Chung Hsing University
- Taichung 40254
- Taiwan
- Institute of Biochemistry
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13
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Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discov Today 2015; 21:562-72. [PMID: 26691874 PMCID: PMC7108309 DOI: 10.1016/j.drudis.2015.11.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/11/2015] [Accepted: 11/30/2015] [Indexed: 12/18/2022]
Abstract
Coronavirus nucleocapsid proteins are appealing drug targets against coronavirus-induced diseases. A variety of compounds targeting the coronavirus nucleocapsid protein have been developed. Many of these compounds show potential antiviral activity.
The advent of severe acute respiratory syndrome (SARS) in the 21st century and the recent outbreak of Middle-East respiratory syndrome (MERS) highlight the importance of coronaviruses (CoVs) as human pathogens, emphasizing the need for development of novel antiviral strategies to combat acute respiratory infections caused by CoVs. Recent studies suggest that nucleocapsid (N) proteins from coronaviruses and other viruses can be useful antiviral drug targets against viral infections. This review aims to provide readers with a concise survey of the structural features of coronavirus N proteins and how these features provide insights into structure-based development of therapeutics against coronaviruses. We will also present our latest results on MERS-CoV N protein and its potential as an antiviral drug target.
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14
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Wang YS, Chang CK, Hou MH. Crystallographic analysis of the N-terminal domain of Middle East respiratory syndrome coronavirus nucleocapsid protein. Acta Crystallogr F Struct Biol Commun 2015; 71:977-80. [PMID: 26249685 PMCID: PMC4528927 DOI: 10.1107/s2053230x15010146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/26/2015] [Indexed: 02/23/2023] Open
Abstract
The N-terminal domain of the nucleocapsid protein from Middle East respiratory syndrome coronavirus (MERS-CoV NP-NTD) contains many positively charged residues and has been identified to be responsible for RNA binding during ribonucleocapsid formation by the virus. In this study, the crystallization and crystallographic analysis of MERS-CoV NP-NTD (amino acids 39-165), with a molecular weight of 14.7 kDa, are reported. MERS-CoV NP-NTD was crystallized at 293 K using PEG 3350 as a precipitant and a 94.5% complete native data set was collected from a cooled crystal at 77 K to 2.63 Å resolution with an overall Rmerge of 9.6%. The crystals were monoclinic and belonged to space group P21, with unit-cell parameters a = 35.60, b = 109.64, c = 91.99 Å, β = 101.22°. The asymmetric unit contained four MERS-CoV NP-NTD molecules.
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Affiliation(s)
- Yong-Sheng Wang
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hon Hou
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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15
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Rusnati M, Chiodelli P, Bugatti A, Urbinati C. Bridging the past and the future of virology: surface plasmon resonance as a powerful tool to investigate virus/host interactions. Crit Rev Microbiol 2013; 41:238-60. [PMID: 24059853 DOI: 10.3109/1040841x.2013.826177] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Despite decades of antiviral drug research and development, viruses still remain a top global healthcare problem. Compared to eukaryotic cells, viruses are composed by a limited numbers of proteins that, nevertheless, set up multiple interactions with cellular components, allowing the virus to take control of the infected cell. Each virus/host interaction can be considered as a therapeutical target for new antiviral drugs but, unfortunately, the systematic study of a so huge number of interactions is time-consuming and expensive, calling for models overcoming these drawbacks. Surface plasmon resonance (SPR) is a label-free optical technique to study biomolecular interactions in real time by detecting reflected light from a prism-gold film interface. Launched 20 years ago, SPR has become a nearly irreplaceable technology for the study of biomolecular interactions. Accordingly, SPR is increasingly used in the field of virology, spanning from the study of biological interactions to the identification of putative antiviral drugs. From the literature available, SPR emerges as an ideal link between conventional biological experimentation and system biology studies functional to the identification of highly connected viral or host proteins that act as nodal points in virus life cycle and thus considerable as therapeutical targets for the development of innovative antiviral strategies.
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Affiliation(s)
- Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia , Brescia , Italy
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16
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The cellular interactome of the coronavirus infectious bronchitis virus nucleocapsid protein and functional implications for virus biology. J Virol 2013; 87:9486-500. [PMID: 23637410 DOI: 10.1128/jvi.00321-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The coronavirus nucleocapsid (N) protein plays a multifunctional role in the virus life cycle, from regulation of replication and transcription and genome packaging to modulation of host cell processes. These functions are likely to be facilitated by interactions with host cell proteins. The potential interactome of the infectious bronchitis virus (IBV) N protein was mapped using stable isotope labeling with amino acids in cell culture (SILAC) coupled to a green fluorescent protein-nanotrap pulldown methodology and liquid chromatography-tandem mass spectrometry. The addition of the SILAC label allowed discrimination of proteins that were likely to specifically bind to the N protein over background binding. Overall, 142 cellular proteins were selected as potentially binding to the N protein, many as part of larger possible complexes. These included ribosomal proteins, nucleolar proteins, translation initiation factors, helicases, and hnRNPs. The association of selected cellular proteins with IBV N protein was confirmed by immunoblotting, cosedimentation, and confocal microscopy. Further, the localization of selected proteins in IBV-infected cells as well as their activity during virus infection was assessed by small interfering RNA-mediated depletion, demonstrating the functional importance of cellular proteins in the biology of IBV. This interactome not only confirms previous observations made with other coronavirus and IBV N proteins with both overexpressed proteins and infectious virus but also provides novel data that can be exploited to understand the interaction between the virus and the host cell.
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17
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Chen IJ, Yuann JMP, Chang YM, Lin SY, Zhao J, Perlman S, Shen YY, Huang TH, Hou MH. Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1054-62. [PMID: 23501675 PMCID: PMC3774783 DOI: 10.1016/j.bbapap.2013.03.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 02/06/2013] [Accepted: 03/05/2013] [Indexed: 02/04/2023]
Abstract
Human coronavirus OC43 (HCoV-OC43) is a causative agent of the common cold. The nucleocapsid (N) protein, which is a major structural protein of CoVs, binds to the viral RNA genome to form the virion core and results in the formation of the ribonucleoprotein (RNP) complex. We have solved the crystal structure of the N-terminal domain of HCoV-OC43 N protein (N-NTD) (residues 58 to 195) to a resolution of 2.0Å. The HCoV-OC43 N-NTD is a single domain protein composed of a five-stranded β-sheet core and a long extended loop, similar to that observed in the structures of N-NTDs from other coronaviruses. The positively charged loop of the HCoV-OC43 N-NTD contains a structurally well-conserved positively charged residue, R106. To assess the role of R106 in RNA binding, we undertook a series of site-directed mutagenesis experiments and docking simulations to characterize the interaction between R106 and RNA. The results show that R106 plays an important role in the interaction between the N protein and RNA. In addition, we showed that, in cells transfected with plasmids that encoded the mutant (R106A) N protein and infected with virus, the level of the matrix protein gene was decreased by 7-fold compared to cells that were transfected with the wild-type N protein. This finding suggests that R106, by enhancing binding of the N protein to viral RNA plays a critical role in the viral replication. The results also indicate that the strength of N protein/RNA interactions is critical for HCoV-OC43 replication.
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Affiliation(s)
- I-Jung Chen
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
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18
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Šípová H, Homola J. Surface plasmon resonance sensing of nucleic acids: a review. Anal Chim Acta 2013; 773:9-23. [PMID: 23561902 DOI: 10.1016/j.aca.2012.12.040] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 12/12/2022]
Abstract
Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.
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Affiliation(s)
- Hana Šípová
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic
| | - Jiří Homola
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic.
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19
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Lo YS, Lin SY, Wang SM, Wang CT, Chiu YL, Huang TH, Hou MH. Oligomerization of the carboxyl terminal domain of the human coronavirus 229E nucleocapsid protein. FEBS Lett 2012. [PMID: 23178926 PMCID: PMC7089611 DOI: 10.1016/j.febslet.2012.11.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
N and N bind by cross‐linking study (View Interaction: 1, 2, 3, 4) ► The role of the C‐terminal tail of the HCoV‐229E N protein in oligomerization. ► A correlation between oligomerization and thermostability. ► The C‐terminal tail peptide interferes with the oligomerization. ► The development of drugs to disrupt the oligomerization of the viral N protein.
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Affiliation(s)
- Yu-Sheng Lo
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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20
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Liang FY, Lin LC, Ying TH, Yao CW, Tang TK, Chen YW, Hou MH. Immunoreactivity characterisation of the three structural regions of the human coronavirus OC43 nucleocapsid protein by Western blot: implications for the diagnosis of coronavirus infection. J Virol Methods 2012; 187:413-20. [PMID: 23174159 PMCID: PMC7112824 DOI: 10.1016/j.jviromet.2012.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 10/15/2012] [Accepted: 11/08/2012] [Indexed: 01/25/2023]
Abstract
Previous studies have reported that a prokaryotic-expressed recombinant nucleocapsid protein (NP) is a suitable reagent for the epidemiological screening of coronavirus infection. In this study, soluble recombinant human coronavirus OC43 (HCoV-OC43) NP was produced to examine the antigenicity of the HCoV-OC43 NP of betacoronavirus. Using the purified recombinant NP as an antigen, a polyclonal antibody from rabbit serum with specificity for HCoV-OC43 NP was generated; this antibody reacts specifically with HCoV-OC43 NP and does not cross-react with other human CoV NPs (including those of SARS-CoV and HCoV-229E) by Western blot. Sera from 26 young adults, 17 middle-aged and elderly patients with respiratory infection, and 15 cord blood samples were also tested. Strong reactivity to the NPs of HCoV-OC43 was observed in 96%, 82%, and 93% of the serum samples from the young adults, respiratory patients, and cord blood samples, respectively. To identify the immunoreactivities of the three structural regions of the NP that are recognised by the rabbit polyclonal antibody and human serum, the antigenicities of three protein fragments, including the N-terminal domain (aa 1-173), the central-linker region (aa 174-300), and the C-terminal domain (aa 301-448), were evaluated by Western blot. The rabbit polyclonal antibody demonstrated greater immunoreactivity to the central-linker region and the C-terminal domain than to the N-terminal domain. Three different patterns for the immunoreactivities of the three structural regions of HCoV-OC43 NP were observed in human serum, suggesting variability in the immune responses that occur during HCoV-OC43 infection in humans. The central-linker region of the NP appeared to be the most highly immunoreactive region for all three patterns observed. The goal of this study was to offer insight into the design of diagnostic tools for HCoV infection.
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Affiliation(s)
- Fang-Ying Liang
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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21
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Kuo SM, Kao HW, Hou MH, Wang CH, Lin SH, Su HL. Evolution of infectious bronchitis virus in Taiwan: positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity. Vet Microbiol 2012; 162:408-418. [PMID: 23159091 PMCID: PMC7117379 DOI: 10.1016/j.vetmic.2012.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 10/15/2012] [Accepted: 10/17/2012] [Indexed: 12/04/2022]
Abstract
RNA recombination has been shown to underlie the sporadic emergence of new variants of coronavirus, including the infectious bronchitis virus (IBV), a highly contagious avian pathogen. We have demonstrated that RNA recombination can give rise to a new viral population, supported by the finding that most isolated Taiwanese (TW) IBVs, similar to Chinese (CH) IBVs, exhibit a genetic rearrangement with the American (US) IBV at the 5’ end of the nucleocapsid (N) gene. Here, we further show that positive selection has occurred at two sites within the putative crossover region of the N-terminal domain (NTD) of the TW IBV N protein. Based on the crystal structure of the NTD, the stereographic positions of both predicted selected sites do not fall close to the RNA-binding groove. Surprisingly, converting either of the two residues to the amino acid present in most CH IBVs resulted in significantly reduced affinity of the N protein for the synthetic RNA repeats of the viral transcriptional regulatory sequence. These results suggest that modulating the amino acid residue at either selected site may alter the conformation of the N protein and affect the viral RNA–N interaction. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein.
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Affiliation(s)
- Shu-Ming Kuo
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Hsiao-Wei Kao
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ching-Ho Wang
- School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Siou-Hong Lin
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Hong-Lin Su
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan; Department of Physical Therapy, Graduate Institute of Rehabilitation Science, China Medical University, Taichung, Taiwan.
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22
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Chang YM, Chen CKM, Chang YC, Jeng WY, Hou MH, Wang AHJ. Functional studies of ssDNA binding ability of MarR family protein TcaR from Staphylococcus epidermidis. PLoS One 2012; 7:e45665. [PMID: 23029170 PMCID: PMC3448645 DOI: 10.1371/journal.pone.0045665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 08/20/2012] [Indexed: 01/21/2023] Open
Abstract
The negative transcription regulator of the ica locus, TcaR, regulates proteins involved in the biosynthesis of poly-N-acetylglucosamine (PNAG). Absence of TcaR increases PNAG production and promotes biofilm formation in Staphylococci. Previously, the 3D structure of TcaR in its apo form and its complex structure with several antibiotics have been analyzed. However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA). Here we show by electrophoretic mobility shift assay (EMSA), electron microscopy (EM), circular dichroism (CD), and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA), thereby identifying a new role in MarR family proteins. Moreover, we show that TcaR preferentially binds 33-mer ssDNA over double-stranded DNA and inhibits viral ssDNA replication. In contrast, such ssDNA binding properties were not observed for other MarR family protein and TetR family protein, suggesting that the results from our studies are not an artifact due to simple charge interactions between TcaR and ssDNA. Overall, these results suggest a novel role for TcaR in regulation of DNA replication. We anticipate that the results of this work will extend our understanding of MarR family protein and broaden the development of new therapeutic strategies for Staphylococci.
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Affiliation(s)
- Yu-Ming Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Yuan-Chih Chang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Yih Jeng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Hon Hou
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
| | - Andrew H. -J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan
- * E-mail:
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23
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The coronavirus nucleocapsid protein is dynamically associated with the replication-transcription complexes. J Virol 2010; 84:11575-9. [PMID: 20739524 DOI: 10.1128/jvi.00569-10] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The coronavirus nucleocapsid (N) protein is a virion structural protein. It also functions, however, in an unknown way in viral replication and localizes to the viral replication-transcription complexes (RTCs). Here we investigated, using recombinant murine coronaviruses expressing green fluorescent protein (GFP)-tagged versions of the N protein, the dynamics of its interactions with the RTCs and the domain(s) involved. Using fluorescent recovery after photobleaching, we showed that the N protein, unlike the nonstructural protein 2, is dynamically associated with the RTCs. Recruitment of the N protein to the RTCs requires the C-terminal N2b domain, which interacts with other N proteins in an RNA-independent manner.
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24
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Chen IJ, Chou CC, Liu CL, Lee CC, Kan LS, Hou MH. Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of human coronavirus OC43 nucleocapsid protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:815-8. [PMID: 20606281 PMCID: PMC2898469 DOI: 10.1107/s1744309110017616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Accepted: 05/13/2010] [Indexed: 11/25/2022]
Abstract
The N-terminal domain of nucleocapsid protein from human coronavirus OC43 (HCoV-OC43 N-NTD) mostly contains positively charged residues and has been identified as being responsible for RNA binding during ribonucleocapsid formation in the coronavirus. In this study, the crystallization and preliminary crystallographic analysis of HCoV-OC43 N-NTD (amino acids 58-195) with a molecular weight of 20 kDa are reported. HCoV-OC43 N-NTD was crystallized at 293 K using PEG 1500 as a precipitant and a 99.9% complete native data set was collected to 1.7 A resolution at 100 K with an overall R(merge) of 5.0%. The crystals belonged to the hexagonal space group P6(5), with unit-cell parameters a = 81.57, c = 42.87 A. Solvent-content calculations suggest that there is likely to be one subunit of N-NTD in the asymmetric unit.
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Affiliation(s)
- I-Jung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
| | - Chia-Cheng Chou
- National Synchrotron Radiation Research Center, Hsinchu 300, Taiwan
| | - Chia-Ling Liu
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Lou-Sing Kan
- Institute of Bioengineering, Tatung University, Taipei 104, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hon Hou
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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