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

Publication ,  Journal Article
Roden, CA; Dai, Y; Giannetti, CA; Seim, I; Lee, M; Sealfon, R; McLaughlin, GA; Boerneke, MA; Iserman, C; Wey, SA; Ekena, JL; Troyanskaya, OG ...
Published in: Nucleic Acids Res
August 12, 2022

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.

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Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

August 12, 2022

Volume

50

Issue

14

Start / End Page

8168 / 8192

Location

England

Related Subject Headings

  • Temperature
  • SARS-CoV-2
  • RNA-Binding Proteins
  • RNA, Viral
  • RNA, Double-Stranded
  • Phosphoproteins
  • Developmental Biology
  • Coronavirus Nucleocapsid Proteins
  • Binding Sites
  • 41 Environmental sciences
 

Citation

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Roden, C. A., Dai, Y., Giannetti, C. A., Seim, I., Lee, M., Sealfon, R., … Gladfelter, A. S. (2022). Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res, 50(14), 8168–8192. https://doi.org/10.1093/nar/gkac596
Roden, Christine A., Yifan Dai, Catherine A. Giannetti, Ian Seim, Myungwoon Lee, Rachel Sealfon, Grace A. McLaughlin, et al. “Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures.Nucleic Acids Res 50, no. 14 (August 12, 2022): 8168–92. https://doi.org/10.1093/nar/gkac596.
Roden CA, Dai Y, Giannetti CA, Seim I, Lee M, Sealfon R, et al. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res. 2022 Aug 12;50(14):8168–92.
Roden, Christine A., et al. “Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures.Nucleic Acids Res, vol. 50, no. 14, Aug. 2022, pp. 8168–92. Pubmed, doi:10.1093/nar/gkac596.
Roden 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. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res. 2022 Aug 12;50(14):8168–8192.
Journal cover image

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

August 12, 2022

Volume

50

Issue

14

Start / End Page

8168 / 8192

Location

England

Related Subject Headings

  • Temperature
  • SARS-CoV-2
  • RNA-Binding Proteins
  • RNA, Viral
  • RNA, Double-Stranded
  • Phosphoproteins
  • Developmental Biology
  • Coronavirus Nucleocapsid Proteins
  • Binding Sites
  • 41 Environmental sciences