Epstein-barr virus encodes three bona fide ubiquitin-specific proteases

J Virol. 2008 Nov;82(21):10477-86. doi: 10.1128/JVI.01113-08. Epub 2008 Aug 20.


Manipulation of the ubiquitin proteasome system (UPS) is emerging as a common theme in viral pathogenesis. Some viruses have been shown to encode functional homologs of UPS enzymes, suggesting that a systematic identification of these products may provide new insights into virus-host cell interactions. Ubiquitin-specific proteases, collectively known as deubiquitinating enzymes (DUBs), regulate the activity of the UPS by hydrolyzing ubiquitin peptide or isopeptide bonds. The prediction of viral DUBs based on sequence similarity with known enzymes is hampered by the diversity of viral genomes. In this study sequence alignments, pattern searches, and hidden Markov models were developed for the conserved C- and H-boxes of the known DUB families and used to search the open reading frames (ORFs) of Epstein-Barr virus (EBV), a large gammaherpesvirus that has been implicated in the pathogenesis of a broad spectrum of human malignancies of lymphoid and epithelial cell origin. The searches identified a limited number of EBV ORFs that contain putative DUB catalytic domains. DUB activity was confirmed by functional assays and mutation analysis for three high scoring candidates, supporting the usefulness of this bioinformatics approach in predicting distant homologues of cellular enzymes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Substitution / genetics
  • Artificial Gene Fusion
  • Computational Biology
  • Conserved Sequence
  • Endopeptidases / genetics*
  • Endopeptidases / metabolism*
  • Genes, Reporter
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • Herpesvirus 4, Human / enzymology*
  • Herpesvirus 4, Human / genetics*
  • Mutagenesis, Site-Directed
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Ubiquitin-Specific Proteases
  • Viral Proteins / genetics*
  • Viral Proteins / metabolism*


  • Recombinant Fusion Proteins
  • Viral Proteins
  • Green Fluorescent Proteins
  • Endopeptidases
  • Ubiquitin-Specific Proteases