The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression

Aaron S Mendez; Michael Ly; Angélica M González-Sánchez; Ella Hartenian; Nicholas T Ingolia; Jamie H Cate; Britt A Glaunsinger

doi:10.1016/j.celrep.2021.109841

The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression

Cell Rep. 2021 Oct 19;37(3):109841. doi: 10.1016/j.celrep.2021.109841. Epub 2021 Sep 30.

Authors

Aaron S Mendez¹, Michael Ly², Angélica M González-Sánchez³, Ella Hartenian², Nicholas T Ingolia⁴, Jamie H Cate⁵, Britt A Glaunsinger⁶

Affiliations

¹ Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
² Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
³ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Comparative Biochemistry Graduate Program, University of California, Berkeley, Berkeley, CA, USA.
⁴ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
⁵ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁶ Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, Berkeley, CA, USA. Electronic address: glaunsinger@berkeley.edu.

Abstract

Nonstructural protein 1 (nsp1) is a coronavirus (CoV) virulence factor that restricts cellular gene expression by inhibiting translation through blocking the mRNA entry channel of the 40S ribosomal subunit and by promoting mRNA degradation. We perform a detailed structure-guided mutational analysis of severe acute respiratory syndrome (SARS)-CoV-2 nsp1, revealing insights into how it coordinates these activities against host but not viral mRNA. We find that residues in the N-terminal and central regions of nsp1 not involved in docking into the 40S mRNA entry channel nonetheless stabilize its association with the ribosome and mRNA, both enhancing its restriction of host gene expression and enabling mRNA containing the SARS-CoV-2 leader sequence to escape translational repression. These data support a model in which viral mRNA binding functionally alters the association of nsp1 with the ribosome, which has implications for drug targeting and understanding how engineered or emerging mutations in SARS-CoV-2 nsp1 could attenuate the virus.

Keywords: RNA; SARS; SARS-CoV-2; coronavirus; nsp1; nuclease; ribosome; translation.

Publication types

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

MeSH terms

Anisotropy
COVID-19 / genetics*
COVID-19 / immunology
DNA Mutational Analysis
Female
Gene Expression Profiling
Gene Expression Regulation, Viral*
Green Fluorescent Proteins / metabolism
HEK293 Cells
Humans
Kinetics
Mutation
Phenotype
Point Mutation
Protein Biosynthesis
Protein Domains
RNA Stability
Ribosome Subunits, Small, Eukaryotic / metabolism
Ribosomes / metabolism
SARS-CoV-2 / genetics*
Viral Nonstructural Proteins / metabolism*

Substances

Viral Nonstructural Proteins
Green Fluorescent Proteins

Grants and funding

HHMI/Howard Hughes Medical Institute/United States