Mature Epstein-Barr virus (EBV) was purified from the culture medium of infected lymphocytes made functionally conditional for Zta activation of lytic replication by an in-frame fusion with a mutant estrogen receptor. Proteins in purified virus preparations were separated by gradient gel electrophoresis and trypsin-digested; peptides were then analyzed by tandem hydrophobic chromatography, tandem MS sequencing, and MS scans. Potential peptides were matched with EBV and human gene ORFs. Mature EBV was mostly composed of homologues of proteins previously found in a herpes virion. However, EBV homologues to herpes simplex virus capsid-associated or tegument components UL7 (BBRF2), UL14 (BGLF3), and EBV BFRF1 were not significantly detected. Instead, probable tegument components included the EBV and ␥-herpesvirus-encoded BLRF2, BRRF2, BDLF2 and BKRF4 proteins. Actin was also a major tegument protein, and cofilin, tubulin, heat shock protein 90, and heat shock protein 70 were substantial components. EBV envelope glycoprotein gp350 was highly abundant, followed by glycoprotein gH, intact and furincleaved gB, gM, gp42, gL, gp78, gp150, and gN. BILF1 (gp64) and proteins associated with latent EBV infection were not detected in virions.lymphocyte ͉ proteomics ͉ virion ͉ herpes virus T he experiments reported here determine the protein composition of mature enveloped Epstein-Barr (EB) virus (EBV). EBV protein composition has not been systematically studied since the proteins of purified enveloped and deenveloped EBV were initially displayed on polyacrylamide gels. Except for glycoproteins, EB virion protein annotations have usually been based on DNA sequence homology to a characterized herpesvirus ORF, with verification for EBV in specific instances.EBV is a ␥1-herpesvirus. The ␥1-and ␥2-herpesvirus genomes are mostly collinear and share smaller conserved gene clusters with ␣-and ␤-herpesvirus genomes. Herpesvirus family-conserved genes mostly encode proteins that are important for DNA replication, virus morphogenesis, or virion composition. Conserved herpesvirus genes are known to encode 5 capsid proteins, 5 envelope proteins, and 10 tegument proteins in at least one herpesvirus (1, 2). Accordingly, EBV BcLF1, BDLF1, BFRF3, BORF1, and BBRF1 ORFs are likely to encode the major, minor, and smallest capsid proteins (MCP, mCP, and sCP, respectively); the mCP-binding protein (mCPBP); and portal. Furthermore, the EBV BPLF1, BOLF1, BVRF1, BGLF1, BGLF4, BGLF2, BBRF2, BSRF1, BGLF3, and BBLF1 ORFs are likely to encode tegument proteins (3-5). EBV BNRF1 and BLRF2 probably encode ␥-herpesvirus-unique tegument proteins (Table 1) (6-8). The EBV homologues of gB (BALF4), gH (BXLF2), and gL (BKRF2) have been detected by specific antibodies in EB virions. Moreover, EBV BLLF1, BZLF2, and BDLF3 ORF-specific antibodies have detected EBV-unique gp350, gp42, and gp150 in the virus (Table 1) (9). EBV BMRF2-encoded protein may also be in virus envelopes because it has an RGD (arginine-glycine-aspartic acid) motif that may be a ligand for an int...

Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations1. Genome sequencing efforts have identified numerous germline mutations associated with cancer predisposition and large numbers of somatic genomic alterations2. However, it remains challenging to distinguish between background, or “passenger” and causal, or “driver” cancer mutations in these datasets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations3. To test the hypothesis that genomic variations and tumour viruses may cause cancer via related mechanisms, we systematically examined host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways that go awry in cancer, such as Notch signalling and apoptosis. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on par with their identification through functional genomics and large-scale cataloguing of tumour mutations. Together, these complementary approaches result in increased specificity for cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate prioritization of cancer-causing driver genes so as to advance understanding of the genetic basis of human cancer.