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SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome

Yann Tardivat1, Piotr Sosnowski1, Antonin Tidu1

  • 1Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France.

Nucleic Acids Research
|July 28, 2023
PubMed

Insights

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein NSP1 cleaves host and viral messenger RNAs (mRNAs) differently. These distinct cleavage patterns, mediated by NSP1

Area of Science:

  • Molecular Biology
  • Virology
  • Biochemistry

Background:

  • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes non-structural protein 1 (NSP1) to inhibit host cell translation.
  • NSP1 binds the ribosome's mRNA entry channel, hindering host mRNA translation.
  • Viral 5'-untranslated regions (UTRs) can evade NSP1-mediated inhibition.

Purpose of the Study:

  • To investigate the mechanism of NSP1-mediated mRNA cleavage.
  • To characterize the distinct cleavage patterns of host versus viral mRNAs by NSP1.
  • To identify the domains of NSP1 responsible for mRNA cleavage activity.

Main Methods:

  • Ribosome-bound mRNA cleavage assays.
  • Analysis of cleavage site specificity in host and SARS-CoV-2 RNAs.
  • Site-directed mutagenesis to assess NSP1 domains.
  • RNA structure probing (SL1 hairpin).

Main Results:

  • NSP1 induces distinct endonucleolytic cleavage patterns in host and viral 5'UTRs.
  • Host mRNAs are cleaved near the 5' cap (6-11 nt), independent of sequence.
  • SARS-CoV-2 RNAs exhibit sequence-specific cleavage at positions 45, 46, and 49 at high NSP1 concentrations.
  • The N-terminal domain of NSP1 is essential and sufficient for cleavage.
  • The SL1 hairpin protects viral RNA from degradation at low NSP1 concentrations.

Conclusions:

  • NSP1 employs differential mRNA cleavage strategies against host and viral RNAs.
  • Ribosome binding and specific RNA structures influence NSP1 cleavage activity.
  • NSP1's N-terminal domain contains the catalytic activity, unmasked by conformational changes.

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