Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures.

TitleDouble-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures.
Publication TypeJournal Article
Year of Publication2022
AuthorsRoden, CA, Dai, Y, Giannetti, CA, Seim, I, Lee, M, Sealfon, R, McLaughlin, GA, Boerneke, MA, Iserman, C, Wey, SA, Ekena, JL, Troyanskaya, OG, Weeks, KM, You, L, Chilkoti, A, Gladfelter, AS
JournalNucleic Acids Res
Volume50
Issue14
Pagination8168-8192
Date Published2022 Aug 12
ISSN1362-4962
KeywordsBinding Sites, Coronavirus Nucleocapsid Proteins, Phosphoproteins, RNA, Double-Stranded, RNA, Viral, RNA-Binding Proteins, SARS-CoV-2, Temperature
Abstract

<p>Nucleocapsid protein (N-protein) is required for multiple steps in betacoronaviruses replication. SARS-CoV-2-N-protein condenses with specific viral RNAs at particular temperatures making it a powerful model for deciphering RNA sequence specificity in condensates. We identify two separate and distinct double-stranded, RNA motifs (dsRNA stickers) that promote N-protein condensation. These dsRNA stickers are separately recognized by N-protein's two RNA binding domains (RBDs). RBD1 prefers structured RNA with sequences like the transcription-regulatory sequence (TRS). RBD2 prefers long stretches of dsRNA, independent of sequence. Thus, the two N-protein RBDs interact with distinct dsRNA stickers, and these interactions impart specific droplet physical properties that could support varied viral functions. Specifically, we find that addition of dsRNA lowers the condensation temperature dependent on RBD2 interactions and tunes translational repression. In contrast RBD1 sites are sequences critical for sub-genomic (sg) RNA generation and promote gRNA compression. The density of RBD1 binding motifs in proximity to TRS-L/B sequences is associated with levels of sub-genomic RNA generation. The switch to packaging is likely mediated by RBD1 interactions which generate particles that recapitulate the packaging unit of the virion. Thus, SARS-CoV-2 can achieve biochemical complexity, performing multiple functions in the same cytoplasm, with minimal protein components based on utilizing multiple distinct RNA motifs that control N-protein interactions.</p>

DOI10.1093/nar/gkac596
Alternate JournalNucleic Acids Res
PubMed ID35871289
PubMed Central IDPMC9371935
Grant ListR01 GM081506 / GM / NIGMS NIH HHS / United States
F32 GM128330 / GM / NIGMS NIH HHS / United States
K99 AI156640 / AI / NIAID NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States
R35 GM122532 / GM / NIGMS NIH HHS / United States
F32 GM136164 / GM / NIGMS NIH HHS / United States