A CRISPR screen defines a signal peptide processing pathway required by flaviviruses

Nature. 2016 Jul 7;535(7610):164-8. doi: 10.1038/nature18625. Epub 2016 Jun 17.


Flaviviruses infect hundreds of millions of people annually, and no antiviral therapy is available. We performed a genome-wide CRISPR/Cas9-based screen to identify host genes that, when edited, resulted in reduced flavivirus infection. Here, we validated nine human genes required for flavivirus infectivity, and these were associated with endoplasmic reticulum functions including translocation, protein degradation, and N-linked glycosylation. In particular, a subset of endoplasmic reticulum-associated signal peptidase complex (SPCS) proteins was necessary for proper cleavage of the flavivirus structural proteins (prM and E) and secretion of viral particles. Loss of SPCS1 expression resulted in markedly reduced yield of all Flaviviridae family members tested (West Nile, Dengue, Zika, yellow fever, Japanese encephalitis, and hepatitis C viruses), but had little impact on alphavirus, bunyavirus, or rhabdovirus infection or the surface expression or secretion of diverse host proteins. We found that SPCS1 dependence could be bypassed by replacing the native prM protein leader sequences with a class I major histocompatibility complex (MHC) antigen leader sequence. Thus, SPCS1, either directly or indirectly via its interactions with unknown host proteins, preferentially promotes the processing of specific protein cargo, and Flaviviridae have a unique dependence on this signal peptide processing pathway. SPCS1 and other signal processing pathway members could represent pharmacological targets for inhibiting infection by the expanding number of flaviviruses of medical concern.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • Animals
  • CRISPR-Cas Systems / genetics*
  • Cell Line
  • Drosophila / cytology
  • Drosophila / genetics
  • Drosophila / virology
  • Drug Discovery
  • Endoplasmic Reticulum / metabolism
  • Female
  • Flavivirus / metabolism
  • Flavivirus / physiology*
  • Flavivirus Infections / genetics
  • Flavivirus Infections / virology
  • Genome, Human / genetics*
  • Glycosylation
  • Host-Derived Cellular Factors / genetics*
  • Host-Pathogen Interactions / genetics
  • Humans
  • Membrane Proteins / genetics
  • Molecular Targeted Therapy
  • Protein Sorting Signals / physiology*
  • Protein Transport / genetics
  • Proteolysis
  • Reproducibility of Results
  • Serine Endopeptidases / genetics
  • Species Specificity
  • Viral Proteins / chemistry
  • Viral Proteins / metabolism
  • Viral Structural Proteins / metabolism


  • Host-Derived Cellular Factors
  • Membrane Proteins
  • Protein Sorting Signals
  • Viral Proteins
  • Viral Structural Proteins
  • Serine Endopeptidases
  • type I signal peptidase