A specific phosphorylation-dependent conformational switch of SARS-CoV-2 nucleoprotein inhibits RNA binding

• Published in: bioRxiv
• Main Authors: Botova, Maiia, Camacho-Zarco, Aldo R, Tognetti, Jacqueline, Luiza Mamigonian Bessa, Guseva, Serafima, Mikkola, Emmi, Salvi, Nicola, Maurin, Damien, Herrmann, Torsten, Blackledge, Martin
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 23.02.2024
• Subjects: Dimerization; Genomes; Phosphorylation; Ribonucleic acid; RNA; Severe acute respiratory syndrome coronavirus 2
• DOI: 10.1101/2024.02.22.579423

The nucleoprotein (N) of SARS-CoV-2 encapsidates the viral genome and is essential for viral function. The central disordered domain comprises a serine-arginine-rich domain (SR) that is hyperphosphorylated in infected cells. This modification is thought to regulate function of N, although mechanistic details remain unknown. We use time-resolved NMR to follow local and long-range structural changes occurring during hyperphosphorylation by the kinases SRPK1/GSK-3/CK1, thereby identifying a conformational switch that abolishes interaction with RNA. When 8 approximately uniformly-distributed sites are phosphorylated, the SR domain competitively binds the same interface as single-stranded RNA, resulting in RNA binding inhibition. Phosphorylation by PKA does not prevent RNA binding, indicating that the pattern resulting from the physiologically-relevant kinases is specific for inhibition. Long-range contacts between the RNA-binding, linker and dimerization domains are also abrogated, phenomena possibly related to genome packaging and unpackaging. This study provides insight into recruitment of specific host kinases to regulate viral function.Competing Interest StatementThe authors have declared no competing interest.