A genome-wide CRISPR screen identifies UFMylation and TRAMP-like complexes as host factors required for hepatitis A virus infection

Cell Rep. 2021 Mar 16;34(11):108859. doi: 10.1016/j.celrep.2021.108859.

Abstract

Hepatitis A virus (HAV) is a positive-sense RNA virus causing acute inflammation of the liver. Here, using a genome-scale CRISPR screen, we provide a comprehensive picture of the cellular factors that are exploited by HAV. We identify genes involved in sialic acid/ganglioside biosynthesis and members of the eukaryotic translation initiation factor complex, corroborating their putative roles for HAV. Additionally, we uncover all components of the cellular machinery for UFMylation, a ubiquitin-like protein modification. We show that HAV translation specifically depends on UFM1 conjugation of the ribosomal protein RPL26. Furthermore, we find that components related to the yeast Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex are required for viral translation independent of controlling viral poly(A) tails or RNA stability. Finally, we demonstrate that pharmacological inhibition of the TRAMP-like complex decreases HAV replication in hepatocyte cells and human liver organoids, thus providing a strategy for host-directed therapy of HAV infection.

Keywords: CRISPR screen; PAPD5; PAPD7; RPL26; TENT4; UFM1; UFMylation; ZCCHC14; hepatitis A virus; host factor.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / metabolism
  • Catalysis
  • Cell Line, Tumor
  • Chromosomal Proteins, Non-Histone / metabolism
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • DNA-Directed DNA Polymerase / metabolism
  • Genome, Human*
  • Hepatitis / metabolism
  • Hepatitis / virology*
  • Hepatitis A virus / physiology*
  • Hepatocytes / drug effects
  • Hepatocytes / metabolism
  • Hepatocytes / virology
  • Host-Pathogen Interactions* / drug effects
  • Humans
  • Multiprotein Complexes / metabolism*
  • Organoids / drug effects
  • Organoids / metabolism
  • Organoids / virology
  • Polyadenylation / drug effects
  • Protein Biosynthesis / drug effects
  • Proteins / metabolism*
  • RNA Nucleotidyltransferases / metabolism
  • RNA Stability / drug effects
  • RNA Stability / genetics
  • RNA, Viral / genetics
  • Ribosomal Proteins / metabolism
  • Saccharomyces cerevisiae
  • Small Molecule Libraries / pharmacology
  • Ubiquitination*
  • Virus Replication / drug effects

Substances

  • Antiviral Agents
  • Chromosomal Proteins, Non-Histone
  • Multiprotein Complexes
  • Proteins
  • RNA, Viral
  • RPL26 protein, human
  • Ribosomal Proteins
  • Small Molecule Libraries
  • UFM1 protein, human
  • RNA Nucleotidyltransferases
  • TENT4B protein, human
  • DNA-Directed DNA Polymerase
  • TENT4A protein, human