Identification of an Epstein-Barr virus-specific desoxyribonuclease gene using complementary DNA

Functional Implications of Epstein-Barr Virus Lytic Genes in Carcinogenesis

Epstein-Barr virus (EBV) is associated with a diverse range of tumors of both lymphoid and epithelial origin. Similar to other herpesviruses, EBV displays a bipartite life cycle consisting of latent and lytic phases. Current dogma indicates that the latent genes are key drivers in the pathogenesis of EBV-associated cancers, while the lytic genes are primarily responsible for viral transmission. In recent years, evidence has emerged to show that the EBV lytic phase also plays an important role in EBV tumorigenesis, and the expression of EBV lytic genes is frequently detected in tumor tissues and cell lines. The advent of next generation sequencing has allowed the comprehensive profiling of EBV gene expression, and this has revealed the consistent expression of several lytic genes across various types of EBV-associated cancers. In this review, we provide an overview of the functional implications of EBV lytic gene expression to the oncogenic process and discuss possible avenues for future investigations.

Epstein-Barr virus inactivates the transcriptome and disrupts the chromatin architecture of its host cell in the first phase of lytic reactivation

Epstein-Barr virus (EBV), a herpes virus also termed HHV 4 and the first identified human tumor virus, establishes a stable, long-term latent infection in human B cells, its preferred host. Upon induction of EBV's lytic phase, the latently infected cells turn into a virus factory, a process that is governed by EBV. In the lytic, productive phase, all herpes viruses ensure the efficient induction of all lytic viral genes to produce progeny, but certain of these genes also repress the ensuing antiviral responses of the virally infected host cells, regulate their apoptotic death or control the cellular transcriptome. We now find that EBV causes previously unknown massive and global alterations in the chromatin of its host cell upon induction of the viral lytic phase and prior to the onset of viral DNA replication. The viral initiator protein of the lytic cycle, BZLF1, binds to >105 binding sites with different sequence motifs in cellular chromatin in a concentration dependent manner implementing a binary molar switch probably to prevent noise-induced erroneous induction of EBV's lytic phase. Concomitant with DNA binding of BZLF1, silent chromatin opens locally as shown by ATAC-seq experiments, while previously wide-open cellular chromatin becomes inaccessible on a global scale within hours. While viral transcripts increase drastically, the induction of the lytic phase results in a massive reduction of cellular transcripts and a loss of chromatin-chromatin interactions of cellular promoters with their distal regulatory elements as shown in Capture-C experiments. Our data document that EBV's lytic cycle induces discrete early processes that disrupt the architecture of host cellular chromatin and repress the cellular epigenome and transcriptome likely supporting the efficient de novo synthesis of this herpes virus.

Epstein-Barr virus DNase (BGLF5) induces genomic instability in human epithelial cells

Epstein–Barr Virus (EBV) DNase (BGLF5) is an alkaline nuclease and has been suggested to be important in the viral life cycle. However, its effect on host cells remains unknown. Serological and histopathological studies implied that EBV DNase seems to be correlated with carcinogenesis. Therefore, we investigate the effect of EBV DNase on epithelial cells. Here, we report that expression of EBV DNase induces increased formation of micronucleus, an indicator of genomic instability, in human epithelial cells. We also demonstrate, using γH2AX formation and comet assay, that EBV DNase induces DNA damage. Furthermore, using host cell reactivation assay, we find that EBV DNase expression repressed damaged DNA repair in various epithelial cells. Western blot and quantitative PCR analyses reveal that expression of repair-related genes is reduced significantly in cells expressing EBV DNase. Host shut-off mutants eliminate shut-off expression of repair genes and repress damaged DNA repair, suggesting that shut-off function of BGLF5 contributes to repression of DNA repair. In addition, EBV DNase caused chromosomal aberrations and increased the microsatellite instability (MSI) and frequency of genetic mutation in human epithelial cells. Together, we propose that EBV DNase induces genomic instability in epithelial cells, which may be through induction of DNA damage and also repression of DNA repair, subsequently increases MSI and genetic mutations, and may contribute consequently to the carcinogenesis of human epithelial cells.

The Epstein-Barr virus protein kinase BGLF4 and the exonuclease BGLF5 have opposite effects on the regulation of viral protein production

The Epstein-Barr virus BGLF4 and BGLF5 genes encode a protein kinase and an alkaline exonuclease, respectively. Both proteins were previously found to regulate multiple steps of virus replication, including lytic DNA replication and primary egress. However, while inactivation of BGLF4 led to the downregulation of several viral proteins, the absence of BGLF5 had the opposite effect. Using recombinant viruses that lack both viral enzymes, we confirm and extend these initial observations, e.g., by showing that both BGLF4 and BGLF5 are required for proper phosphorylation of the DNA polymerase processivity factor BMRF1. We further found that neither BGLF4 nor BGLF5 is required for baseline viral protein production. Complementation with BGLF5 downregulated mRNA levels and translation of numerous viral genes, though to various degrees, whereas BGLF4 had the opposite effect. BGLF4 and BGLF5 influences on viral expression were most pronounced for BFRF1 and BFLF2, two proteins essential for nuclear egress. For most viral genes studied, cotransfection of BGLF4 and BGLF5 had only a marginal influence on their expression patterns, showing that BGLF4 antagonizes BGLF5-mediated viral gene shutoff. To be able to exert its functions on viral gene expression, BGLF4 must be able to escape BGLF5's shutoff activities. Indeed, we found that BGLF5 stimulated the BGLF4 gene's transcription through an as yet uncharacterized molecular mechanism. The BGLF4/BGLF5 enzyme pair builds a regulatory loop that allows fine-tuning of virus protein production, which is required for efficient viral replication.

The Epstein-Barr virus alkaline exonuclease BGLF5 serves pleiotropic functions in virus replication

The Epstein-Barr virus (EBV) alkaline exonuclease BGLF5 has previously been recognized to contribute to immune evasion by downregulating production of HLA molecules during virus replication. We have constructed a BGLF5-null virus mutant to determine BGLF5's functions during EBV viral replication. Quantification of virus production in permissive 293 cells carrying a DeltaBGLF5 genome identified a 17- to 21-fold reduction relative to complemented or wild-type controls. Detailed monitoring of DeltaBGLF5 replication evidenced an impaired virus nucleocapsid maturation, a reduced primary egress and a 1.4-fold reduction in total viral DNA synthesis. DeltaBGLF5 single-unit-length viral genomes were not only less abundant but also migrated faster than expected in gel electrophoresis. We concluded that BGLF5 pertained both to the generation and to the processing of viral linear genomes. DeltaBGLF5 phenotypic traits were reminiscent of those previously identified in a mutant devoid of UL12, BGLF5's homolog in herpes simplex virus type 1, and indeed UL12 was found to partially complement the DeltaBGLF5 phenotype. However, BGLF5-specific functions could also be identified; the nuclear membrane of replicating cells displayed images of reduplication and complex folding that could be completely corrected by BGLF5 but not UL12. Similar nuclear abnormalities were previously observed in cells transfected with BFLF2 and BFRF1, two viral proteins crucial for EBV nuclear egress. Interestingly, DeltaBGLF5 cells produced more BFLF2 than wild-type or complemented counterparts. The present study provides an overview of BGLF5's functions that will guide future molecular studies. We anticipate that the 293/DeltaBGLF5 cell line will be instrumental in such developments.

Activation of human herpesvirus 8 (HHV-8) thymidine kinase (TK) TATAA-less promoter by HHV-8 ORF50 gene product is SP1 dependent

Human herpesvirus 8 (HHV-8) is a newly discovered virus closely associated with Kaposi's sarcoma and primary effusion lymphomas. When they occur in patients with AIDS, these B-cell lymphomas frequently harbor another human herpesvirus, Epstein-Barr virus (EBV). To determine the molecular mechanisms of the regulation of early gene expression by the immediate-early gene products of HHV-8 and to assess possible molecular interactions between HHV-8 and EBV, we studied the regulation of the HHV-8 thymidine kinase (TK) promoter in cell lines harboring either or both viruses. The constitutive chloramphenicol acetyltransferase (CAT) activity of the TK promoter was low in all six cell lines tested. A putative immediate-early gene product of HHV-8 ORF50, which is a homolog of EBV BRLF1, was cloned into an expression vector and tested for its transactivating capacity. In the presence of 12-O-tetradecanoyl-phorbol-13-acetate (TPA), the CAT activity of the TK promoter was increased 7- to 720-fold by cotransfection with the ORF50 clone in EBV-producing cell lines (Ramos/AW, P3HR-1, and BC-1) but not in EBV-negative cell lines (BCBL-1 and Ramos), nor in the latently EBV-infected cell line Raji. The TK promoter contains three consensus SP1- and two AP1-binding sites. In electrophoretic mobility shift assays, the cellular factor SP1, but not AP1, was found to bind specifically to the TK promoter. To determine whether the increased CAT activity resulted from the interaction of SP1 with the ORF50 gene product, we introduced mutations into two SP1-binding sites. Both mutated SP1 sites had reduced SP1-binding activity and greatly decreased TK promoter responsiveness to ORF50 transactivation, suggesting that upregulation of TK promoter by ORF50 is SP1 dependent.

A major DNA binding protein encoded by BALF2 open reading frame of Epstein-Barr virus (EBV) forms a complex with other EBV DNA-binding proteins: DNAase, EA-D, and DNA polymerase

A major 135-kDa DNA binding protein (mDBP) encoded by the BALF2 open reading frame of Epstein-Barr Virus (EBV) is known to be an essential protein for the induction of the lytic cycle. The present investigation was carried out to know whether this protein forms a complex in vivo with other viral DNA binding proteins (DBP) involved in DNA replication: DNA polymerase, EA-D (diffused early antigen), and DNAase. Immunoprecipitation assays followed by mono- and two-dimensional electrophoresis showed that mDBP forms a complex with these three DBP. Other complexes were also found such as EA-D/DNAase, DNA polymerase/DNAase, and DNA polymerase/EA-D. The complexed forms already exist in the early stage of EBV cycle before DNA synthesis is induced in the EBV producer P3HR-1 cell line. The exonuclease activity encoded by DNAase was found to be inhibited when this enzyme complexed with mDBP, while the EBV DNA polymerase retained its activity in the complexed form with mDBP. Our results suggest that these complexes already present before DNA synthesis are necessary for EBV DNA synthesis.

Purified recombinant EBV desoxyribonuclease in serological diagnosis of nasopharyngeal carcinoma

To evaluate applications of highly purified recombinant EBV DNAase in the diagnosis and prognosis of NPC, we tested sera from patients with NPC, other EBV-associated diseases and EBV-seropositive and -seronegative healthy subjects by immunoblotting and DNAase inhibitory assay. The results were compared with those obtained by the conventional immunofluorescence assays against the EBV-specified early antigens and capsid antigens. The antigenic specificity of the immunoblotting assay for IgG antibody against the viral enzyme, but not that for the IgA antibody, was correlated with DNAase-inhibitory activity of the sera and their titers of IgG antibodies against the viral early antigens. Purified IgA as well as IgG from NPC sera inhibited enzyme activity with similar efficiency. The use of highly purified viral DNase has increased the sensitivity of detection of the corresponding antibodies by immunoblotting, with the IgG antibody being detected in all but one, and IgA antibody in all but 2, of the 174 NPC sera tested. The IgG antibody was also commonly detected in the other groups of control sera, while the IgA antibody was detected in about 10% of African Burkitt's lymphoma and Algerian Hodgkin's lymphoma patients and less than 3% of the other control subjects. These results suggest that IgA antibody against recombinant EBV DNAase may be useful in the diagnosis of NPC, but the level of this antibody did not appear to be related to clinical stages of this cancer.

Transcriptional expression of the viral genome in the Epstein-Barr virus-induced tamarin lymphoma and the corresponding lymphoblastoid tumour lines

Inoculation of the cottontop tamarin with Epstein-Barr virus (EBV) invariably gives rise to mono- or oligoclonal large cell lymphoma occurring at multiple sites, and which resembles to a certain extent B cell lymphoma that occurs in the immunodeficient patient. The viral transcriptional pattern in tamarin tumour biopsies and in the corresponding tumour cell lines was investigated by means of the synthesis of radioactive single-stranded cDNA. It was found that the EBV transcripts came mainly from the fragments BamH1-H, BamH1-S, BamH1-A and EcoR1-Dhet. Transcripts from a few other early or late genes, namely BARF1, BSLF1/BMLF1, BBLF-4, BLLF1 and BXLF2, were also detected in one of the three biopsies tested. It would be important to characterize the transcripts that originate from the region where viral latent expression has not previously been observed. Our results also revealed that there is a sharp increase in EBV transcription in the tumour cell lines derived from the tamarin lymphomas. Simultaneously, the copy number of the viral genome was found to be amplified. Such a significant change in viral activity might be indicative of a close virus-host cell interaction in vivo.

Antibody responses against polypeptide components of Epstein-Barr virus-induced early diffuse antigen in patients with connective tissue diseases

The specific humoral response against polypeptide components of Epstein-Barr virus (EBV), the induced early diffuse antigen (EA-D), in patients with connective tissue diseases, including systemic lupus erythematosus (SLE) and mixed connective tissue disease (MCTD), was investigated by using the immunoblotting technique. The EA(D)-positive sera from patients with infectious mononucleosis (IM), nasopharyngeal carcinoma (NPC), immunocompromised patients (renal transplant recipients and patients with AIDS) as well as the EA(D)-negative sera from patients with Burkitt's lymphoma and from clinically healthy subjects served as controls. Seven major antigenic polypeptides with molecular weights of 33 kDa, 35 kDa, 52 kDa, 54 kDa, 56 kDa, 58 kDa, and 134 kDa were detected reproducibly by the EA(D)-positive reference sera and, in particular, by each of the NPC sera tested. The EA(D)-positive sera from the other groups showed various combinations of detection patterns and few samples reacted with all the major EA(D) polypeptides. Seventy-three percent of sera from SLE and 47% of sera from MCTD were found to react with EA(D). Sixty-one percent of sera from SLE vs. 5% from MCTD detected all the EA(D) polypeptides. These results could either reflect perturbations of the immune response linked to the autoimmune disease or suggest a possible pathogenic role of EBV.

Molecular characterization of a cDNA clone encoding the Epstein-Barr virus (EBV) DNase

RNA from IdUrd-treated P3HR1 cells was used for the construction of a cDNA library and screened with B95-8 EBV DNA BamHI fragment B and G probes. One clone, BG9, containing a 1.7 kb cDNA insert was further studied. Complete DNA sequence analysis revealed that BG9 encompassed the B95-8 EBV DNA sequences from nucleotide 120,747 to nucleotide 122,412 and corresponded to the BGLF5 open reading frame of the EBV DNase gene. Comparison of the sequences of BG9 with that of published B95-8 EBV DNA indicated that there were 14 different bases which results in 7 amino acid residue changes. The product of in vitro transcription/translation of a subclone, pGEM-BG9, contained the EBV DNase activity and a 52 kDa protein was immunoprecipitated from the in vitro translation products using serum from a patient with nasopharyngeal carcinoma which contained a high level of anti-DNase activity. Northern hybridization of P3HR1 RNA with the BG9 probe revealed a complex pattern of transcription in this region. Subgenomic DNA fragments were then used to map these RNA species to the B95-8 EBV DNA sequence. The result of S1 nuclease analysis indicated that a DNase ORF containing transcript sized 2.0 kb is initiated at nucleotide 122,435 +/- 1 and terminated at nucleotide 120,741 of the EBV genome.

Chromatographic purification and characterization of EBV DNase from chemically induced lymphoid cells

Epstein-Barr virus-associated deoxyribonuclease (EBV-DNase) was purified to homogeneity, as determined by silver staining, sequential column chromatography, and FPLC from Raji and P3HR-1 cells treated with 12-O-tetradecanoyl-phorbol-13-acetate and sodium butyrate. This viral protein was immunogenic and elicited high neutralization titer sera in rabbits. By silver staining of SDS-PAGE, Western immunoblot, and radioimmunoprecipitation using NPC patient sera and both polyclonal and monoclonal antibodies, the EBV DNase was identified as a 58K protein. The potential presence of two EBV DNases was also discussed.

Purification and properties of Epstein-Barr virus DNase expressed in Escherichia coli

A cDNA corresponding to the BGLF5 open reading frame of the Epstein-Barr virus (EBV) genome and coding for an early DNase was inserted into the procaryotic expression vector pKK223-3. One bacterial clone producing the expected 52-kilodalton DNase was used as a source of EBV DNase. The 52-kilodalton Dnase was purified in the active form to near homogeneity by ammonium sulfate precipitation and successive chromatographies on phosphocellulose, DNA-cellulose, and gel filtration columns. The purified enzyme exhibited both exonuclease and endonuclease activities, an absolute requirement for divalent cations, an alkaline pH preference, and a typical residual activity in presence of 300 mM KCl. Moreover, the enzyme was specifically inhibited by human sera with high antibody titers to EBV early antigens. These properties are similar to those observed for EBV-induced DNase from lymphoblastoid cell extracts. In addition, the enzyme was recognized by both immunoglobulin G and A serum fractions from patients with nasopharyngeal carcinoma (NPC). From these results and previous studies which demonstrated the value of antibody titers to this viral DNase as an NPC marker, it appears that EBV-encoded DNase produced in a heterologous expression system could be used in the development of a specific and early NPC diagnosis test.

Relative rates of RNA synthesis across the genome of Epstein-Barr virus are highest near oriP and oriLyt

The rates of Epstein-Barr virus transcription were measured in isolated nuclei from marmoset and human lymphoblasts transformed in vitro. In B95-8, a marmoset B-lymphoid cell line, the most frequently transcribed viral genes are the EBERs (small nuclear RNAs) and BHLF-1 (encoding a lytic-phase gene product). The EBERs and BHLF-1 genes are separated by nearly 50 kilobase pairs on the Epstein-Barr virus genome and lie adjacent to (less than 300 base pairs from) oriP and oriLyt, respectively. oriP and oriLyt are putative origins of viral DNA replication, and each is associated with a transcriptional enhancer element. Among the human B-lymphoblastoid cell lines tested, only the transcription of EBERs predominates.

Relationship between nasopharyngeal carcinoma and high antibody titers to Epstein-Barr virus-specific thymidine kinase

Epstein-Barr virus (EBV) has long been implicated in nasopharyngeal carcinoma (NPC). Recent studies in our and other laboratories have shown a correlation between the disease and high antibody titers to EBV-specific DNase. These data led us to also examine serial sera from healthy adults and patients with infectious mononucleosis or NPC, for their capacity to neutralize the EBV-specific thymidine kinase (TK) activity from chemically induced EBV-carrying human lymphoblastoid cells. Our results were the following: (i) sera were found that efficiently blocked the EBV-specific TK activity of induced-Raji TK- cell extracts, but not the host-cell TK activity from EBV-negative BJAB cells; (ii) a relationship appeared between high levels of EBV-specific TK-neutralizing activity in sera and NPC pathology, even though in this preliminary study the degrees of EBV-induced TK-blocking activity detected in sera were not significantly correlated with EBV-specific antibody titers; (iii) the EBV-induced TK-neutralizing activity was found in the main IgG fraction derived from NPC sera. These data must be compared with other known antibody responses to EBV for their clinical interest in NPC control.

A human urine-derived interleukin 1 inhibitor. Homology with deoxyribonuclease I

We have previously reported that the urine of febrile humans contained large quantities of an inhibitor of IL-1-induced murine thymocyte proliferation that was a glycoprotein between 30 and 40 kD in size. In the present study this factor has been purified to homogeneity using a sequence of eight purification steps (ammonium sulfate precipitation, ion exchange chromatography, molecular sieve chromatography, hydrophobic affinity chromatography, hydroxylapatite chromatography, fast protein liquid chromatography, and two HPLC steps). SDS-PAGE analysis indicates that the purified material is a 38-kD molecule. Evidence based on a partial amino acid sequence analysis as well as enzyme studies indicates that this inhibitor is a type of human DNase I.

Altered expression of two Epstein-Barr virus early genes localized in BamHI-A in nonproducer Raji cells

The Epstein-Barr virus-carrying lymphoblastoid cell line Raji has two major genomic deletions and is incapable of virus production. Two cDNA clones, c70 and c55, were constructed from early mRNA of P3HR-1 cells and localized, respectively, in BALF-2 and BARF-1 open reading frames where one of the major genomic deletion in Raji cells is situated. These were used to search the different early viral transcripts in producer P3HR-1 and nonproducer Raji lines. c70 and c55 hybridized with their corresponding mRNAs only in producer lines. Analysis with in vitro-synthesized RNA probes showed quite a different transcriptional profile in Raji cells than in P3HR-1 cells. In the P3HR-1 line, BALF-2 encodes a 3.4-kilobase (kb) mRNA during the early phase and a 3.3-kb mRNA during the late phase, and in the Raji line, the probe corresponding to BALF-2 hybridized with three mRNAs of 5.0, 3.1, and 2.4 kb; in P3HR-1 cells, BARF-1 encodes a group of 3'-conterminal transcripts (0.8, 1.2, 1.7, 2.7, 3.2, and 5.0 kb) during both the early and late stages; in Raji cells, however, 0.8-, 1.2-, and 1.7-kb mRNAs are absent, the only mRNAs transcribed being upstream of the deletion and of 5.0, 2.6, and 2.0 kb in size. In vivo and in vitro experiments demonstrated that the BALF-2 open reading frame encodes an early 135-kilodalton (kDa) protein which possesses DNA-binding ability and can be recognized by a herpes simplex virus ICP-8 antiserum. The BARF-1 open reading frame encodes in vitro a 26- to 33-kDa early protein recognized by anti-EA serum. The proteins of both two genes expressed in psi AM 22b cells were localized in nuclei. According to their properties, both proteins, particularly the BALF-2-encoded 135-kDa DNA-binding protein, could play a role in virus replication.

The analysis of EBV proteins which are antigenic in vivo

We have used small random EBV B95-8 DNA fragments to generate a large genomic bank in a plasmid expression vector. This bank was screened with a pool of sera from individuals with IM thus allowing any EBV antigen which evoked an immune response in man to be identified. The characterization of four immunopositive clones obtained in this way is presented in this study. Three of these clones express viral ORF DNA sequences which are parts of larger ORFs in the BamH1 N(het), V and X regions of the B95-8 viral genome. cDNA cloning has been used to confirm that the cloned sequences from BamH1 N and V are expressed in cell culture and to identify the transcription units involved. The fourth clone expresses an ORF sequence located in the viral BamH1 F fragment in a region not previously recognized as having protein coding potential. The experimental design used here must reflect the situation in vivo and consequently these sequences must be expressed and be antigenic during IM.