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Ker DS, Jenkins HT, Greive SJ, Antson AA. CryoEM structure of the Nipah virus nucleocapsid assembly. PLoS Pathog 2021; 17:e1009740. [PMID: 34270629 PMCID: PMC8318291 DOI: 10.1371/journal.ppat.1009740] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/28/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we report the first cryoEM structure for a Henipavirus RNA-bound nucleocapsid assembly, at 3.5 Å resolution. The helical assembly is stabilised by previously undefined N- and C-terminal segments, contributing to subunit-subunit interactions. RNA is wrapped around the nucleocapsid protein assembly with a periodicity of six nucleotides per protomer, in the “3-bases-in, 3-bases-out” conformation, with protein plasticity enabling non-sequence specific interactions. The structure reveals commonalities in RNA binding pockets and in the conformation of bound RNA, not only with members of the Paramyxoviridae family, but also with the evolutionarily distant Filoviridae Ebola virus. Significant structural differences with other Paramyxoviridae members are also observed, particularly in the position and length of the exposed α-helix, residues 123–139, which may serve as a valuable epitope for surveillance and diagnostics. Nipah virus is a highly pathogenic RNA virus which, along with the closely related Hendra virus, emerged relatively recently. Due to ~40% mortality rate and evidence of animal-to-human as well as human-to-human transmission, development of antivirals against the Nipah and henipaviral disease is particularly urgent. In common with other single-stranded RNA viruses, including Ebola and coronaviruses, the nucleocapsid assembly of the Nipah virus safeguards the viral genome, protecting it from degradation and facilitating its encapsidation and storage inside the virion. Here, we used cryo-electron microscopy to determine accurate three-dimensional structure for several different assemblies of the Nipah virus nucleocapsid protein, in particular a detailed structure for the complex of this protein with RNA. This structural information is important for understanding detailed molecular interactions driving and stabilizing the nucleocapsid assembly formation that are of fundamental importance for understanding similar processes in a large group of ssRNA viruses. Apart from highlighting structural similarities and differences with nucleocapsid proteins of other viruses of the Paramyxoviridae family, these data will inform the development of new antiviral approaches for the henipaviruses.
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Affiliation(s)
- De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
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Balamurugan V, Varghese B, SowjanyaKumari S, Vinod Kumar K, Muthuchelvan D, Nagalingam M, Hemadri D, Roy P, Shome BR. Avidin-Biotin recombinant nucleoprotein competitive ELISA for the detection of peste des petits ruminants virus antibodies in sheep and goats. J Virol Methods 2021; 295:114213. [PMID: 34119607 DOI: 10.1016/j.jviromet.2021.114213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/08/2021] [Indexed: 01/21/2023]
Abstract
The present study describes the development of a truncated recombinant peste des petits ruminants virus (PPRV) nucleoprotein (rPPRV-NPN) and its polyclonal antibodies-based immuno-diagnostic assay, Avidin-Biotin (AB) recombinant nucleoprotein competitive ELISA (ABrC-ELISA) for the detection of PPRV antibodies in the sheep and goats. The PPRV N-terminal immunogenic region (1-266 aa) of nucleoprotein (NPN) coding sequence was amplified and cloned into the pETite vector. The rPPRV-NPN with a molecular weight of ∼ 30 kDa was expressed in E. coli, purified, and characterized by SDS-PAGE and immunoblot using standard PPRV specific sera. The Ni-NTA affinity-purified rPPRV-NPN as coating antigen and its hyperimmune serum as competitive antibodies raised in guinea pigs were evaluated as diagnostic reagents in ABrC-ELISA using the known standard panel of sera. The threshold (cut-off) Percentage Inhibition (PI) value was determined as 45 (mean ± 3 SD) based on the reactivity of the known sheep and goats sera to PPRV antibodies [negative (n = 140) and positive (n = 98)] and the assay had a sensitivity of 97 % (95 % Confidence Interval (CI): 91.3-99.4 %) and specificity of 100 % (95 % CI: 97.4-100 %) with an excellent Area under curve (AUC) of 0.997 (95 % CI: 0.99-1.0). On evaluation of diagnostic performance of the assay using the sheep and goats sera (n = 391) from vaccinated, infected, and non-vaccinated animals, the ABrC-ELISA showed the relative diagnostic sensitivity of 95.88 % (95 % CI: 92.56-98.01 %) & 98.77 % (95 % CI: 96.43-99.74 %) and diagnostic specificity of 97.97 % (95 % CI: 94.19-99.58 %) & 90.54 % (95 % CI: 84.64-94.73 %) against indigenous PPR competitive ELISA kit & IDvet Screen® PPR Competition kit, respectively. The study showed that ABrC-ELISA is rapid, sensitive, and specific and can be a better alternative assay for the detection of the PPRV antibodies in the sera of small ruminants for serosurveillance / seromonitoring of PPR not only at the eradication and post-eradication phases in the disease-controlled endemic countries but also in the PPR non-endemic countries.
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Affiliation(s)
- V Balamurugan
- Indian Council of Agricultural Research -National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), Yelahanka, Bengaluru, 560 064, Karnataka, India.
| | - Bibitha Varghese
- Indian Council of Agricultural Research -National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), Yelahanka, Bengaluru, 560 064, Karnataka, India
| | - S SowjanyaKumari
- Indian Council of Agricultural Research -National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), Yelahanka, Bengaluru, 560 064, Karnataka, India
| | - K Vinod Kumar
- Indian Council of Agricultural Research -National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), Yelahanka, Bengaluru, 560 064, Karnataka, India
| | - D Muthuchelvan
- Division of Virology, ICAR-Indian Veterinary Research Institute, Campus Mukteswar-263 138, Nainital, Uttarakhand, India
| | - M Nagalingam
- Indian Council of Agricultural Research -National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), Yelahanka, Bengaluru, 560 064, Karnataka, India
| | - D Hemadri
- Indian Council of Agricultural Research -National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), Yelahanka, Bengaluru, 560 064, Karnataka, India
| | - Parimal Roy
- Centre for Animal Health Studies, TANUVAS, Madhavaram Milk Colony, Chennai, 600 051, Tamil Nadu, India
| | - B R Shome
- Indian Council of Agricultural Research -National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), Yelahanka, Bengaluru, 560 064, Karnataka, India
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Roy R, Mishra A, Poddar S, Nayak D, Kar P. Investigating the mechanism of recognition and structural dynamics of nucleoprotein-RNA complex from Peste des petits ruminants virus via Gaussian accelerated molecular dynamics simulations. J Biomol Struct Dyn 2020; 40:2302-2315. [DOI: 10.1080/07391102.2020.1838327] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Rajarshi Roy
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Anurag Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Sayan Poddar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Debasis Nayak
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Parimal Kar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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Influence of mutation in nucleoprotein of Peste-des-petits-ruminants virus (PPRV) isolated from 2016 Indian outbreak. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Yi L, Cao Z, Tong M, Cheng Y, Yang Y, Li S, Wang J, Lin P, Sun Y, Zhang M, Cheng S. Identification of a novel linear B-cell epitope using a monoclonal antibody against the carboxy terminus of the canine distemper virus nucleoprotein and sequence analysis of the identified epitope in different CDV isolates. Virol J 2017; 14:187. [PMID: 28962633 PMCID: PMC5622507 DOI: 10.1186/s12985-017-0858-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Nucleoprotein (NP) is the most abundant and highly immunogenic protein in canine distemper virus (CDV), playing an important role in CDV viral replication and assembly. RESULTS In this study, a specific monoclonal antibody, named C8, was produced against the NP protein C terminal (amino acids 401-523). A linear N protein epitope was identified by subjecting a series of partially overlapping synthesized peptides to enzyme-linked immunosorbent assay (ELISA) analysis.The results indicated that 444GDKYPIHFNDER455 was the minimal linear epitope that could be recognized by mAb C8. Sequence alignments demonstrated that this linear epitope is less conserved among three CDV genotypes. We next analyzed the level of conservation of the defined epitope in19 Chinese CDV clinical isolates, and it has one site variation in amino acid among these CDV isolations. 2 isolates have the amino acid mutations F451L, while one has P448Ssubstitution.Phylogenetic analysis showed the two isolates with F451Lsubstitution had a closer relationship in a virulent strain ZJ-7, so the epitope may be a significant tag associated with virus virulence. CONCLUSION This collection of mAb along with defined linear epitope may provide useful reagents for investigations of NP protein function and the development of CDV specific diagnostics.
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Affiliation(s)
- Li Yi
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - Zhigang Cao
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Mingwei Tong
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuening Cheng
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yong Yang
- Key Lab of Zoonosis Research, Ministry of Education Institute of Zoonosis, Jilin University, Changchun, China
| | - Shuang Li
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jianke Wang
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Peng Lin
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yaru Sun
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Miao Zhang
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shipeng Cheng
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China.
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Zhang GR, Zeng JY, Zhu YM, Dong SJ, Zhu S, Yu RS, Duoji C, Lei ZH, Li Z. Development of an Indirect ELISA with Artificially Synthesized N Protein of PPR Virus. Intervirology 2012; 55:12-20. [DOI: 10.1159/000322220] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 10/14/2010] [Indexed: 11/19/2022] Open
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Yadav V, Balamurugan V, Bhanuprakash V, Sen A, Bhanot V, Venkatesan G, Riyesh T, Singh R. Expression of Peste des petits ruminants virus nucleocapsid protein in prokaryotic system and its potential use as a diagnostic antigen or immunogen. J Virol Methods 2009; 162:56-63. [DOI: 10.1016/j.jviromet.2009.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 07/10/2009] [Accepted: 07/21/2009] [Indexed: 11/16/2022]
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