Discovering hidden viral piracy.
BACKGROUND
Viruses and developers of anti-inflammatory therapies share a common interest in proteins that manipulate the immune response. Large double-stranded DNA viruses acquire host proteins to evade host defense mechanisms. Hence, viral pirated proteins may have a therapeutic potential. Although dozens of viral piracy events have already been identified, we hypothesized that sequence divergence impedes the discovery of many others.


RESULTS
We developed a method to assess the number of viral/human homologs and discovered that at least 917 highly diverged homologs are hidden in low-similarity alignment hits that are usually ignored. However, these low-similarity homologs are masked by many false alignment hits. We therefore applied a filtering method to increase the proportion of viral/human homologous proteins. The homologous proteins we found may facilitate functional annotation of viral and human proteins. Furthermore, some of these proteins play a key role in immune modulation and are therefore therapeutic protein candidates.
Kim
Eddo
E
Compugen Ltd Tel Aviv 69512, Israel.
Kliger
Yossef
Y
D019295:Computational Biology / Q000379:methods*; D004266:DNA Virus Infections / Q000276:immunology*; D004267:DNA Viruses / Q000235:genetics*; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics*; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D015967:Gene Expression Regulation, Viral; D006801:Humans; D007107:Immune System / Q000821:virology; D021382:Protein Sorting Signals; D012328:RNA Viruses / Q000737:chemistry; D018121:Receptors, Cytokine / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry; D014779:Virus Replication
D004279:DNA, Viral; D021382:Protein Sorting Signals; D018121:Receptors, Cytokine; D014764:Viral Proteins