Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation

• Published in: The Journal of biological chemistry Vol. 298; no. 11; p. 102560
• Main Authors: Carlson, Christopher R., Adly, Armin N., Bi, Maxine, Howard, Conor J., Frost, Adam, Cheng, Yifan, Morgan, David O.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.11.2022; THE AUTHORS. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology
• Subjects: COVID-19 - genetics; Genomics; Humans; N protein; nucleocapsid; Nucleocapsid Proteins - metabolism; nucleosome; Phosphorylation; plus-stranded RNA virus; Ribonucleoproteins - metabolism; RNA binding protein; RNA virus; RNA, Viral - metabolism; SARS-CoV-2; SARS-CoV-2 - genetics; RTC; E; nt; CK1; M; N; nucleocapsid; CBP; SARS-CoV-2; S; GSK3; plus-stranded RNA virus; MHV; phosphorylation; SR; GraFix; RNA virus; N protein; RNA binding protein; EM; vRNP; Nsp; CTD; CTE; nucleosome; LH; SRPK; NTE; NTD
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1016/j.jbc.2022.102560

The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35 to 40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein–RNA and protein–protein interactions. Phosphorylation of N protein in its disordered serine/arginine region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.