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Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease

Meredith N Frazier1, Isha M Wilson1, Juno M Krahn2

  • 1Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.

Biorxiv : the Preprint Server for Biology
|March 9, 2022
PubMed

Insights

Coronaviruses use Nsp15 to cleave double-stranded RNA and evade immune sensors. New structures reveal Nsp15 uses a base-flipping mechanism to process both single- and double-stranded RNA effectively.

Area of Science:

  • Virology
  • Structural Biology
  • Immunology

Background:

  • Coronaviruses generate double-stranded (ds) RNA during replication, which can trigger host immune responses.
  • The viral Nsp15 endoribonuclease is crucial for coronaviruses to evade detection by host pattern recognition receptors like MDA5.
  • Previous structural studies of Nsp15 were limited to single-stranded (ss) RNA, hindering understanding of its dsRNA processing.

Approach:

  • Utilized cryo-electron microscopy (cryo-EM) to determine the structures of SARS-CoV-2 Nsp15 bound to a 52-nucleotide dsRNA molecule.
  • Performed site-directed mutagenesis and RNA cleavage assays to investigate the functional implications of the observed structures.
  • Analyzed the Nsp15 hexameric structure for dsRNA engagement across multiple protomers.

Key Points:

  • The hexameric Nsp15 forms a platform for binding dsRNA across multiple subunits.
  • A base-flipping mechanism was identified for orienting uridine within the active site for efficient cleavage.
  • Nsp15 demonstrates the ability to effectively cleave both single-stranded (ssRNA) and double-stranded (dsRNA) substrates.

Conclusions:

  • Nsp15 effectively cleaves dsRNA intermediates, aiding coronavirus immune evasion.
  • The structural and mechanistic insights provide a deeper understanding of Nsp15's role in viral replication.
  • Nsp15 is a versatile endoribonuclease capable of processing both single- and double-stranded RNA.

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