NMR Reveals Specific Tracts within the Intrinsically Disordered Regions of the SARS-CoV-2 Nucleocapsid Protein Involved in RNA Encountering

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Abstract
The SARS-CoV-2 nucleocapsid (N) protein is crucial for the highly organized packaging and transcription of the genomic RNA. Studying atomic details of the role of its intrinsically disordered regions (IDRs) in RNA recognition is challenging due to the absence of structure and to the repetitive nature of their primary sequence. IDRs are known to act in concert with the folded domains of N and here we use NMR spectroscopy to identify the priming events of N interacting with a regulatory SARS-CoV-2 RNA element. 13C-detected NMR experiments, acquired simultaneously to 1H detected ones, provide information on the two IDRs flanking the N-terminal RNA binding domain (NTD) within the N-terminal region of the protein (NTR, 1–248). We identify specific tracts of the IDRs that most rapidly sense and engage with RNA, and thus provide an atom-resolved picture of the interplay between the folded and disordered regions of N during RNA interaction.
Funding Information
  • Italian Ministry of University and Research (FISR2020IP_02112, 58503_DIPECC, SCHL2062/2-1, 2019/AS01)
  • Fondazione CR Firenze and with the support of the Italian government program “MIUR Dipartimenti di Eccellenza 2018–2022” (FISR2020IP_02112, 58503_DIPECC, SCHL2062/2-1, 2019/AS01)
  • German research council (DFG) (FISR2020IP_02112, 58503_DIPECC, SCHL2062/2-1, 2019/AS01)
  • Johanna Quandt Young Academy (FISR2020IP_02112, 58503_DIPECC, SCHL2062/2-1, 2019/AS01)

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