The SARS-unique domain (SUD) of SARS-CoV and SARS-CoV-2 interacts with human Paip1 to enhance viral RNA translation

EMBO J. 2021 Jun 1;40(11):e102277. doi: 10.15252/embj.2019102277. Epub 2021 Apr 20.

Abstract

The ongoing outbreak of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) demonstrates the continuous threat of emerging coronaviruses (CoVs) to public health. SARS-CoV-2 and SARS-CoV share an otherwise non-conserved part of non-structural protein 3 (Nsp3), therefore named as "SARS-unique domain" (SUD). We previously found a yeast-2-hybrid screen interaction of the SARS-CoV SUD with human poly(A)-binding protein (PABP)-interacting protein 1 (Paip1), a stimulator of protein translation. Here, we validate SARS-CoV SUD:Paip1 interaction by size-exclusion chromatography, split-yellow fluorescent protein, and co-immunoprecipitation assays, and confirm such interaction also between the corresponding domain of SARS-CoV-2 and Paip1. The three-dimensional structure of the N-terminal domain of SARS-CoV SUD ("macrodomain II", Mac2) in complex with the middle domain of Paip1, determined by X-ray crystallography and small-angle X-ray scattering, provides insights into the structural determinants of the complex formation. In cellulo, SUD enhances synthesis of viral but not host proteins via binding to Paip1 in pBAC-SARS-CoV replicon-transfected cells. We propose a possible mechanism for stimulation of viral translation by the SUD of SARS-CoV and SARS-CoV-2.

Keywords: coronavirus; eukaryotic translation initiation factors; macrodomain; protein synthesis; virus-host interactions.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins
  • Chromatography, Gel
  • Coronavirus Papain-Like Proteases / chemistry
  • Coronavirus Papain-Like Proteases / metabolism*
  • Crystallography, X-Ray
  • Gene Expression Regulation, Viral*
  • Genes, Reporter
  • HEK293 Cells
  • Humans
  • Immunoprecipitation
  • Luminescent Proteins
  • Models, Molecular
  • Peptide Initiation Factors / chemistry
  • Peptide Initiation Factors / metabolism*
  • Protein Binding
  • Protein Biosynthesis
  • Protein Conformation
  • Protein Domains
  • Protein Interaction Mapping
  • RNA, Viral / genetics
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism*
  • RNA-Dependent RNA Polymerase / chemistry
  • RNA-Dependent RNA Polymerase / metabolism*
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / metabolism
  • Ribosome Subunits / metabolism
  • SARS Virus / genetics
  • SARS Virus / physiology*
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / physiology*
  • Scattering, Small Angle
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Viral Nonstructural Proteins / chemistry
  • Viral Nonstructural Proteins / metabolism*
  • X-Ray Diffraction

Substances

  • Bacterial Proteins
  • Luminescent Proteins
  • PAIP1 protein, human
  • Peptide Initiation Factors
  • RNA, Viral
  • RNA-Binding Proteins
  • Recombinant Fusion Proteins
  • Viral Nonstructural Proteins
  • yellow fluorescent protein, Bacteria
  • Nsp3 protein, SARS-CoV
  • RNA-Dependent RNA Polymerase
  • Coronavirus Papain-Like Proteases
  • papain-like protease, SARS-CoV-2

Associated data

  • PDB/6YXJ