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

Letizia Pontoriero; Marco Schiavina; Sophie M Korn; Andreas Schlundt; Roberta Pierattelli; Isabella C Felli

doi:10.3390/biom12070929

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

Biomolecules. 2022 Jul 2;12(7):929. doi: 10.3390/biom12070929.

Authors

Letizia Pontoriero¹, Marco Schiavina¹, Sophie M Korn², Andreas Schlundt², Roberta Pierattelli¹, Isabella C Felli¹

Affiliations

¹ Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy.
² Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.

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.

Keywords: COVID-19; IDP; NMR; RNA; SARS-CoV-2.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Humans
Magnetic Resonance Spectroscopy
Protein Binding
RNA, Viral / metabolism
SARS-CoV-2*

Substances

RNA, Viral

Grants and funding

This work was funded in part by a grant from the Italian Ministry of University and Research (FISR2020IP_02112, ID-COVID), by Fondazione CR Firenze and with the support of the Italian government program “MIUR Dipartimenti di Eccellenza 2018–2022” (58503_DIPECC). This work was also supported by the Goethe Corona Funds, by the German Research Council (DFG) within CRC902 (“Molecular Principles of RNA-based regulation”) project part B18, through DFG grant number SCHL2062/2-1 to A.S., and by the Johanna Quandt Young Academy at Goethe through the financial support of A.S. (stipend number 2019/AS01).