title: Multiple nucleic acid binding sites and intrinsic disorder of severe acute respiratory syndrome coronavirus nucleocapsid protein: implications for ribonucleocapsid protein packaging.
abstract: 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.
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, Republic of China.
authors.forename: Chung-Ke
authors.initials: CK
authors.lastname: Chang
authors.forename: Yen-Lan
authors.initials: YL
authors.lastname: Hsu
authors.forename: Yuan-Hsiang
authors.initials: YH
authors.lastname: Chang
authors.forename: Fa-An
authors.initials: FA
authors.lastname: Chao
authors.forename: Ming-Chya
authors.initials: MC
authors.lastname: Wu
authors.forename: Yu-Shan
authors.initials: YS
authors.lastname: Huang
authors.forename: Chin-Kun
authors.initials: CK
authors.lastname: Hu
authors.forename: Tai-Huang
authors.initials: TH
authors.lastname: Huang
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D000086462:Coronavirus Nucleocapsid Proteins; D024202:Electrophoretic Mobility Shift Assay; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D019590:Nucleocapsid Proteins / Q000737:chemistry* / Q000235:genetics; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012367:RNA, Viral / Q000378:metabolism; D012261:Ribonucleoproteins / Q000737:chemistry* / Q000235:genetics; D045473:Severe acute respiratory syndrome-related coronavirus / Q000737:chemistry* / Q000235:genetics; D053838:Scattering, Small Angle; D016415:Sequence Alignment; D014961:X-Ray Diffraction
chemical_list: D000086462:Coronavirus Nucleocapsid Proteins; D019590:Nucleocapsid Proteins; D012367:RNA, Viral; D012261:Ribonucleoproteins