Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. Nucleocapsid is an unit of vrial structure, consisting of a capsid with the enclosed nucleic acid; it is generally inside the cytoplasm. Depending on the virus, the nucleocapsid may correspond to a naked core or be surrounded by a membranous envelope.
In 2012, a novel coronavirus was identified as the causative agent of rapidly progressive acute respiratory infection in two men from the Middle East. In these enveloped viruses, the filamentous nucleocapsid is formed by the association of nucleocapsid (N) protein with single-stranded viral RNA (Figure 1). The nucleocapsid protein is a highly immunogenic phosphoprotein also implicated in viral genome replication and in modulating cell signaling pathways.
HIV-1 nucleocapsid protein (NC) is a small basic protein generated by the cleavage of the Gag structural polyprotein precusor by the viral protease during virus assembly in the infected cell. HIV-1 nucleocapsid possesses two copies of a highly conserved CCHC zinc finger (ZnF), flanked by basic residues. HIV-1 nucleocapsid and more generally retroviral nucleocapsid proteins are nucleic acid binding proteins possessing potent nucleic acid condensing and chaperoning activities. HIV-1 nucleocapsid functions in the early and late phases of virus replication. One of the salient feature of the nucleocapsid central globular domain is an hydrophobic plateau which appears to orchestrate the nucleocapsid functions, such as chaperoning the conversion of the genomic RNA into viral DNA by RT during the early phase, and driving the selection and dimerization of the genomic RNA at the initial stage of viral particle assembly. This ensures a bona fide trafficking of early GagNC-genomic RNA complexes to the plasma membrane of the infected cell and ultimately virion formation and budding.
IBV nucleocapsid is a prototype coronavirus nucleocapsid. The N-terminal domain (NTD) of the IBV Gray strain at 1.3-Å resolution exhibits a U-shaped structure, with two arms rich in basic residues, providing a module for specific interaction with RNA. The C-terminal domain (CTD) forms a tightly intertwined dimer with an intermolecular four-stranded central β-sheet platform flanked by α helices, indicating that the basic building block for coronavirus nucleocapsid formation is a dimeric assembly of nucleocapsid protein. During the virus life cycle, multiple copies of the nucleocapsid phosphoprotein (N) interact intimately with genomic and subgenomic RNA molecules and together with M, the most abundant envelope protein, participate in genome condensation and packaging. The N and M proteins interact via their C termini, leading to specific genome encapsidation in the budding viral particle. In addition to its structural role, the nucleocapsid protein is also implicated in other processes during infection including mRNA transcription, replication, and host cell modulation. The nucleocapsid protein is also an important diagnostic marker for coronavirus disease and a major immunogen that can prime protective immune responses.
Nucleocapsid protein is a most abundant protein of coronavirus. During virion assembly, N protein binds to viral RNA and leads to formation of the helical nucleocapsid. The abundance and high hydrophilicity of N protein are supposed to contribute to potent immunity after SARS infection. About a week after SARS onset, N protein-specific antibody may be detected and sustains for long time. The corresponding epitopes in N protein were summarized as Figure 2. N371-390 and N385-407 have a potent ability to react with the serum of 94-97% patients, suggesting the epitope site at the C-terminus of the N protein is likely to be located at codons 371-407. As other coronavirus, N protein of SARS virus is able to induce specific CTL by use of DNA vaccine. The epitopes for CTL induction remain unknown.
Figure 1. Nucleocapsid protein (N protein) in coronavirus virion structure. The genome RNA is complexed with the N protein to form a helical cased within the viral membrane, HE, hemagglutinin-esterase; S, spike; E, small membrane envelope; M, membrane are all transmembrane proteins.
Figure 2. Antigenic motifs of SARS nucleocapsid protein. Blank bar indicates stronger ability to induce antibody production. The number indicates amino acids of nucleocapsid protein.