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Journal of Virology, March 2009, p. 2255-2264, Vol. 83, No. 5
0022-538X/09/$08.00+0     doi:10.1128/JVI.02001-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Multiple Nucleic Acid Binding Sites and Intrinsic Disorder of Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein: Implications for Ribonucleocapsid Protein Packaging

Chung-Ke Chang,¹ Yen-Lan Hsu,¹ Yuan-Hsiang Chang,¹ Fa-An Chao,¹ Ming-Chya Wu,^2,3,4 Yu-Shan Huang,⁵ Chin-Kun Hu,^3,6 and Tai-Huang Huang^1,7*

Institute of Biomedical Sciences,¹ Institute of Physics, Academia Sinica, Taipei 11529,³ Research Center for Adaptive Data Analysis,² Department of Physics, National Central University, Chungli 32001,⁴ National Synchrotron Radiation Research Center, Hsinchu 30076,⁵ Center for Nonlinear and Complex Systems and Department of Physics, Chung Yuan Christian University, Chungli 32023,⁶ Department of Physics, National Taiwan Normal University, Taipei 10610, Taiwan, Republic of China⁷

Received 23 September 2008/ Accepted 24 November 2008

The nucleocapsid protein (N) of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genomic RNA and is crucial for viability. However, the RNA-binding mechanism is poorly understood. We have shown previously that the N protein contains two structural domains—the N-terminal domain (NTD; residues 45 to 181) and the C-terminal dimerization domain (CTD; residues 248 to 365)—flanked by long stretches of disordered regions accounting for almost half of the entire sequence. Small-angle X-ray scattering data show that the protein is in an extended conformation and that the two structural domains of the SARS-CoV N protein are far apart. Both the NTD and the CTD have been shown to bind RNA. Here we show that all disordered regions are also capable of binding to RNA. Constructs containing multiple RNA-binding regions showed Hill coefficients greater than 1, suggesting that the N protein binds to RNA cooperatively. The effect can be explained by the "coupled-allostery" model, devised to explain the allosteric effect in a multidomain regulatory system. Although the N proteins of different coronaviruses share very low sequence homology, the physicochemical features described above may be conserved across different groups of Coronaviridae. The current results underscore the important roles of multisite nucleic acid binding and intrinsic disorder in N protein function and RNP packaging.

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* Corresponding author. Mailing address: Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road, Nankang, Taipei 11529, Taiwan. Phone: 886-2-2652-3036. Fax: 886-2-2788-7641. E-mail: bmthh{at}ibms.sinica.edu.tw

Published ahead of print on 3 December 2008.

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Journal of Virology, March 2009, p. 2255-2264, Vol. 83, No. 5
0022-538X/09/$08.00+0     doi:10.1128/JVI.02001-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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