Unraveling the Assembly Mechanism of SADS-CoV Virus Nucleocapsid Protein: Insights from RNA Binding, Dimerization, and Epitope Diversity Profiling

Overview

Journal J Virol

Publisher American Society for Microbiology

Date 2024 Jul 31

PMID 39082816

Authors

Ying Zhang

Fang Wu

Yongyue Han

Yuzhe Wu

Liqiu Huang

Yuanwei Huang

Di Yan

Xiwen Jiang

Jingyun Ma

Wei Xu

Affiliations

Soon will be listed here.

Abstract

Importance: SADS-CoV is a porcine coronavirus that originated from a bat HKU2-related coronavirus. It causes devastating swine diseases and poses a high risk of spillover to humans. The coronavirus N protein, as the most abundant viral protein in infected cells, likely plays a key role in viral assembly and replication. However, the structure and function of this protein remain unclear. Therefore, this study employed a combination of biochemistry and X-ray crystallography to uncover distinct structural domains in the N protein, including RNA-binding domains, two disordered domains, and dimerization domains. Additionally, we made the novel discovery that the disordered domain elicited a significant antibody response. These findings provide new insights into the structure and functions of the SADS-CoV N protein, which have important implications for future studies on SADS-CoV diagnosis, as well as the development of vaccines and anti-viral drugs.

Citing Articles

Swine Acute Diarrhea Syndrome Coronavirus: An Overview of Virus Structure and Virus-Host Interactions.

Baek S, Park J Animals (Basel). 2025; 15(2).

PMID: 39858149 PMC: 11758606. DOI: 10.3390/ani15020149.

References

Klein S, Cortese M, Winter S, Wachsmuth-Melm M, Neufeldt C, Cerikan B . SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat Commun. 2020; 11(1):5885. PMC: 7676268. DOI: 10.1038/s41467-020-19619-7. View

Chang C, Hsu Y, Chang Y, Chao F, Wu M, Huang Y . Multiple nucleic acid binding sites and intrinsic disorder of severe acute respiratory syndrome coronavirus nucleocapsid protein: implications for ribonucleocapsid protein packaging. J Virol. 2008; 83(5):2255-64. PMC: 2643731. DOI: 10.1128/JVI.02001-08. View

Jack A, Ferro L, Trnka M, Wehri E, Nadgir A, Nguyenla X . SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. PLoS Biol. 2021; 19(10):e3001425. PMC: 8553124. DOI: 10.1371/journal.pbio.3001425. View

Savastano A, de Opakua A, Rankovic M, Zweckstetter M . Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates. Nat Commun. 2020; 11(1):6041. PMC: 7699647. DOI: 10.1038/s41467-020-19843-1. View

Mishra P, Verma N, Rao C, Uversky V, Nandi C . Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis. Prog Mol Biol Transl Sci. 2020; 174:1-78. PMC: 7129803. DOI: 10.1016/bs.pmbts.2020.03.001. View

Chen C, Chang C, Chang Y, Sue S, Bai H, Riang L . Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA. J Mol Biol. 2007; 368(4):1075-86. PMC: 7094638. DOI: 10.1016/j.jmb.2007.02.069. View

Fan Y, Zhao K, Shi Z, Zhou P . Bat Coronaviruses in China. Viruses. 2019; 11(3). PMC: 6466186. DOI: 10.3390/v11030210. View

de Almeida M, Barbosa A, Bomfim C, Visnardi A, Vinces T, Ceroni A . Obtaining a high titer of polyclonal antibodies from rats to the SARS-CoV-2 nucleocapsid protein and its N- and C-terminal domains for diagnostic test development. J Immunol Methods. 2023; 522:113558. DOI: 10.1016/j.jim.2023.113558. View

Li K, Li H, Bi Z, Gu J, Gong W, Luo S . Complete Genome Sequence of a Novel Swine Acute Diarrhea Syndrome Coronavirus, CH/FJWT/2018, Isolated in Fujian, China, in 2018. Microbiol Resour Announc. 2018; 7(22). PMC: 6284080. DOI: 10.1128/MRA.01259-18. View

10.

Zuwala K, Golda A, Kabala W, Burmistrz M, Zdzalik M, Nowak P . The nucleocapsid protein of human coronavirus NL63. PLoS One. 2015; 10(2):e0117833. PMC: 4336326. DOI: 10.1371/journal.pone.0117833. View

11.

Gong L, Li J, Zhou Q, Xu Z, Chen L, Zhang Y . A New Bat-HKU2-like Coronavirus in Swine, China, 2017. Emerg Infect Dis. 2017; 23(9). PMC: 5572857. DOI: 10.3201/eid2309.170915. View

12.

Bonilauri P, Rugna G . Animal Coronaviruses and SARS-COV-2 in Animals, What Do We Actually Know?. Life (Basel). 2021; 11(2). PMC: 7914637. DOI: 10.3390/life11020123. View

13.

Wang S, Dai T, Qin Z, Pan T, Chu F, Lou L . Targeting liquid-liquid phase separation of SARS-CoV-2 nucleocapsid protein promotes innate antiviral immunity by elevating MAVS activity. Nat Cell Biol. 2021; 23(7):718-732. DOI: 10.1038/s41556-021-00710-0. View

14.

McBride R, Van Zyl M, Fielding B . The coronavirus nucleocapsid is a multifunctional protein. Viruses. 2014; 6(8):2991-3018. PMC: 4147684. DOI: 10.3390/v6082991. View

15.

Vkovski P, Kratzel A, Steiner S, Stalder H, Thiel V . Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol. 2020; 19(3):155-170. PMC: 7592455. DOI: 10.1038/s41579-020-00468-6. View

16.

Zhou P, Fan H, Lan T, Yang X, Shi W, Zhang W . Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature. 2018; 556(7700):255-258. PMC: 7094983. DOI: 10.1038/s41586-018-0010-9. View

17.

Zaki A, van Boheemen S, Bestebroer T, Osterhaus A, Fouchier R . Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012; 367(19):1814-20. DOI: 10.1056/NEJMoa1211721. View

18.

Bourassa L, Perchetti G, Phung Q, Lin M, Mills M, Roychoudhury P . A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. J Clin Virol. 2021; 141:104900. PMC: 8219478. DOI: 10.1016/j.jcv.2021.104900. View

19.

Clerc I, Sagar A, Barducci A, Sibille N, Bernado P, Cortes J . The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective. Comput Struct Biotechnol J. 2021; 19:3817-3828. PMC: 8273358. DOI: 10.1016/j.csbj.2021.06.031. View

20.

Wright P, Dyson H . Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol. 1999; 293(2):321-31. DOI: 10.1006/jmbi.1999.3110. View