The SARS-CoV-2 Nucleocapsid Protein and Its Role in Viral Structure, Biological Functions, and a Potential Target for Drug or Vaccine Mitigation

Abstract

The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the world is still expanding. Thus, there is an urgent need to better understand this novel virus and find a way to control its spread. Like other coronaviruses, the nucleocapsid (N) protein is one of the most crucial structural components of SARS-CoV-2. This protein shares 90% homology with the severe acute respiratory syndrome coronavirus N protein, implying functional significance. Based on the evolutionary conservation of the N protein in coronavirus, we reviewed the currently available knowledge regarding the SARS-CoV-2 N protein in terms of structure, biological functions, and clinical application as a drug target or vaccine candidate.

Keywords: SARS-CoV-2; biological function; nucleocapsid protein; structure; vaccine.

Figure 1

Structural overview of the SARS-CoV-2 N protein. (A,B) Schematic of the SARS-CoV-2 N protein modular organization. The three intrinsically disordered regions, including the N-arm, central Ser/Arg(SR)-rich flexible linker region (LKR) and C-tail, and the N-terminal domain (NTD) and C-terminal domain (CTD) are illustrated. (C) Electrostatic surface of the SARS-CoV-2 N-NTD (PDB ID 6YI3) and N-CTD (PDB ID 7CE0). Blue denotes positive charge potential, while red indicates negative charge potential. All structural figures were prepared using PyMOL.

Figure 2

The host cell’s innate immune processes involving the N protein. (A) N proteins act as viral suppressors of RNA interference (RNAi) in host cells. In the initiation step, the dsRNA in infected cells could be sequestrated by N proteins, which prevent the recognition and cleavage of viral dsRNA by Dicer. In addition, the N protein can suppress siRNA-induced RNA degradation in the effector step. (B) N proteins interact with RIG-I and repress RIG-mediated IFN-β production. N proteins can interact with RIG-I through the helicase domain of DExD/H-box helicases, which has ATPase activity and plays an important role in the binding of immunostimulatory RNAs. Therefore, SARS-CoV-2 N proteins suppress the IFN-β response by targeting the initial step of IFN activation. (C) N proteins antagonize type I IFN signaling by suppressing phosphorylation and nuclear translocation of signal transducer and activator of transcription 1 and 2 (STAT1 and STAT2). The binding of secreted type I IFN to their receptors on neighboring cells can trigger phosphorylation of pre-associated Janus kinase 1 (JAK1) and tyrosine kinase 2 (TYK2), which in turn phosphorylates the receptors. This leads to the recruitment and phosphorylation of STAT1 and 2. In SARS-CoV-2 infected cells, N proteins can interfere with the interactions of STAT1 with JAK1 and STAT2 with TYK2 by competitively binding to STAT1/STAT2 and in turn inhibit their phosphorylation. Therefore, N proteins further reduce the subsequent nuclear translocation of the IFN-stimulated gene factor 3 (ISGF3) transcription complex and inhibiting the expression of IFN stimulated genes (ISGs).

Figure 3

Sequences alignment of four CoVs N-NTD. Multiple sequence alignment of HCoV-OC43 (UniProtKB: P33469), SARS-CoV-2 (UniProtKB: P0DTC9), SARS-CoV (UniProtKB: P59595), MERS-CoV (UniProtKB: K9N4V7). The highly conserved residues were filled with colors. Red arrows indicate conserved RNA binding sites. Blue arrows and green arrow indicate conserved and mutant residues for the non-native interaction interface, respectively. HCoV-OC43, human coronavirus OC43; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SARS-CoV, severe acute respiratory syndrome coronavirus; MERS-CoV, Middle East respiratory syndrome coronavirus. (The fill color selected in this figure legend is the default setting of the BioEdit software.).