SARS-CoV-2 nucleocapsid protein variants have differential RNA chaperone activity

Area of Science:

• Virology
• Structural Biology
• Molecular Biology

Background:

• SARS-CoV-2 RNA genome features complex secondary structures.
• The nucleocapsid (N) protein packages viral RNA.
• RNA chaperones facilitate RNA folding and are characterized by non-specific RNA binding and intrinsically disordered regions (IDRs).

Purpose of the Study:

• To investigate the role of the SARS-CoV-2 nucleocapsid (N) protein as an RNA chaperone.
• To identify key regions and regulatory mechanisms governing N protein's RNA chaperone activity.

Main Methods:

• Characterization of N protein domains, including RNA-binding domain (RBD) and C-terminal domain (CTD), and intrinsically disordered regions (IDRs).
• Assessing chaperone activity of N protein variants and comparing Wuhan and Omicron BA.5 variants.
• Investigating the effect of phosphorylation on N protein chaperone activity.

Main Results:

• The N protein functions as an RNA chaperone, facilitating viral RNA folding.
• Amino acids 46-364 (RBD-IDR2-CTD) are crucial for N protein chaperone activity, with flanking IDRs modulating this function.
• Omicron BA.5 N protein exhibits reduced chaperone activity compared to the Wuhan variant.
• Mimicking cellular phosphorylation restored Omicron N protein's chaperone activity.

Conclusions:

• Intrinsically disordered regions (IDRs) are essential for the N protein's RNA chaperone mechanism.
• N protein phosphorylation is a key regulatory mechanism for its chaperone activity.
• Targeting RNA chaperoning offers a potential therapeutic strategy against RNA viruses.