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bioRxiv · 10.1101/2023.08.16.553581

Assembly of SARS-CoV-2 ribonucleosomes by truncated N* variant of the nucleocapsid protein

Adly, A.·Bi, M.·Carlson, C.·Syed, A. M.·Ciling, A.·Doudna, J.·Cheng, Y.·Morgan, D. O.
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Abstract

The Nucleocapsid (N) protein of SARS-CoV-2 compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein SR region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N* or {Delta}(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we show that {Delta}(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of {Delta}(1-209) vRNPs requires the leucine-rich helix (LH) of the central disordered region, and that the LH promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to {Delta}(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by SR phosphorylation.

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Adly, A., Bi, M., Carlson, C., Syed, A. M., Ciling, A., Doudna, J., Cheng, Y., Morgan, D. O.. 2023-08-17. Assembly of SARS-CoV-2 ribonucleosomes by truncated N* variant of the nucleocapsid protein. https://doi.org/10.1101/2023.08.16.553581

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