Heterogeneity of Epstein-Barr virus. III. Comparison of a transforming and a nontransforming virus by partial denaturation mapping of their DNAs

Epithelial cell retention of transcriptionally active, P3HR-1-derived heterogeneous Epstein-Barr virus DNA with concurrent loss of parental virus

Deleted, rearranged, heterogeneous (het) Epstein-Barr virus (EBV) DNA with the distinctive capability of disrupting EBV latency has been reported in biopsy samples of EBV-associated tumors whose onset in immunocompetent hosts is characteristically preceded by an antibody response indicative of EBV reactivation. Using the EBV P3HR-1 strain, we have reproduced in long-term culture of SVK epithelial cells an unusual pattern of infection previously observed in a subset of tumor biopsy samples: the persistence of het DNA in the absence of the parental helper virus. Fluorescence in situ hybridization (FISH) of infected cell subclones indicated the retention of het DNA in an integrated form. Incorporation of an intact het DNA molecule was confirmed by PCR, using primers that framed junctions of the four rearranged EBV DNA segments comprising P3HR-1-derived het DNA. Structural analysis of EBV terminal repeats revealed a banding pattern consistent with the integration of het DNA as a concatemer. Linkage of concatemeric monomers was defined at a nucleotide level, and that junctional sequence was detected in cell-free P3HR-1 virion DNA, confirming that subgenomic het DNA was packaged into infectious particles in a concatemeric configuration. Stable integration into cells having lost the standard viral genome allowed the unambiguous designation of het DNA as the source for viral gene products potentially encoded by both. Continuous expression of the latency-to-lytic switch protein Zta and detection of the BALF4 gene product gB, known to expand the target cell range of standard virus when incorporated at augmented levels into infectious progeny, add to a presumption of het DNA-enhanced pathogenesis in diseases of EBV reactivation.

Points of recombination in Epstein-Barr virus (EBV) strain P3HR-1-derived heterogeneous DNA as indexes to EBV DNA recombinogenic events in vivo

Deletions and rearrangements in the genome of Epstein-Barr virus (EBV) strain P3HR-1 generate subgenomic infectious particles that, unlike defective interfering particles in other viral systems, enhance rather than restrict EBV replication in vitro. Reports of comparable heterogeneous (het) DNA in EBV-linked human diseases, based on detection of an abnormal juxtaposition of EBV DNA fragments BamHI W and BamHI Z that disrupts viral latency, prompted us to determine at the nucleotide level all remaining recombination joints formed by the four constituent segments of P3HR-1-derived het DNA. Guided by endonuclease restriction maps, we chose PCR primer pairs that approximated and framed junctions creating the unique BamHI M/B1 and E/S fusion fragments. Sequencing of PCR products revealed points of recombination that lacked regions of extensive homology between constituent fragments. Identical recombination junctions were detected by PCR in EBV-positive salivary samples from human immunodeficiency virus-infected donors, although the W/Z rearrangement that induces EBV reactivation was frequently found in the absence of the other two. In vitro infection of lymphoid cells similarly indicated that not all three het DNA rearrangements need to reside on a composite molecule. These results connote a precision in the recombination process that dictates both composition and regulation of gene segments altered by genomic rearrangement. Moreover, the apparent frequency of het DNA at sites of EBV replication in vivo is consistent with a likely contribution to the pathogenesis of EBV reactivation.

A defective, rearranged Epstein-Barr virus genome in EBER-negative and EBER-positive Hodgkin's disease

A ubiquitous herpesvirus that establishes life-long infection, the Epstein-Barr virus (EBV) has yielded little insight into how a single agent in general accord with its host can produce diverse pathologies ranging from oral hairy leukoplakia to nasopharyngeal carcinoma, from infectious mononucleosis to Hodgkin's disease (HD) and Burkitt's lymphoma. Its pathogenesis is further confounded by the less than total association of virus with histologically similar tumors. In other viral systems, defective (interfering) viral genomes are known to modulate outcome of infection, with either ameliorating or intensifying effects on disease processes initiated by prototype strains. To ascertain whether defective EBV genomes are present in HD, we examined paraffin-embedded tissue from 56 HD cases whose EBV status was first determined by cytohybridization for nonpolyadenylated EBV RNAs (EBERs). Using both standard polymerase chain reaction (PCR) and PCR in situ hybridization, we successfully amplified sequences that span abnormally juxtaposed BamHI W and Z fragments characteristic of defective heterogeneous (het) EBV DNA from 10 of 32 (31%) EBER-positive tumors. Of 24 EBER-negative HD, 8 yielded PCR products indicating presence of het EBV DNA. Two of these contained defective EBV in the apparent absence of the prototype virus. Of the 42 tumors analyzed for defective EBV by both PCR techniques, there was concordance of results in 38 (90%). Detection of defective EBV genomes with the potential to disrupt viral gene regulation suggests one mechanism for pathogenic diversity that may also account for loss of prototypic EBV from individual tumor cells.

Molecular virology of Epstein-Barr virus

Epstein-Barr virus (EBV) interacts with its host in three distinct ways in a highly regulated fashion: (i) EBV infects human B lymphocytes and induces proliferation of the infected cells, (ii) it enters into a latent phase in vivo that follows the proliferative phase, and (iii) it can be reactivated giving rise to the production of infectious progeny for reinfection of cells of the same type or transmission of the virus to another individual. In healthy people, these processes take place simultaneously in different anatomical and functional compartments and are linked to each other in a highly dynamic steady-state equilibrium. The development of a genetic system has paved the way for the dissection of those processes at a molecular level that can be studied in vitro, i.e. B-cell immortalization and the lytic cycle leading to production of infectious progeny. Polymerase chain reaction analyses coupled to fluorescent-activated cell sorting has on the other hand allowed a descriptive analysis of the virus-host interaction in peripheral blood cells as well as in tonsillar B cells in vivo. This paper is aimed at compiling our present knowledge on the process of B-cell immortalization in vitro as well as in vivo latency, and attempts to integrate this knowledge into the framework of the viral life cycle in vivo.

A replication function associated with the activation domain of the Epstein-Barr virus Zta transactivator

The Zta transactivator is crucial for both Epstein-Barr virus (EBV) lytic gene expression and lytic DNA replication. We have used a cotransfection-replication assay to examine the effect of mutations in the Zta activation domain (amino acids [aa] 1 to 167) on Zta replication activity. Deletion of Zta aa 25 to 86, which are critical for transcriptional activation of ori-Lyt, or aa 93 to 141 did not adversely affect replication of an ori-Lyt-containing target plasmid. However, removal of aa 2 to 25 (delta2-25) abolished replication activity. Within this subdomain, deletion of aa 2 to 10 (delta2-10) or mutation of codons 18 and 19 (m18/19) or 22 and 26 (m22/26) did not affect replication competency, while deletion of codons 13 to 19 (delta13-19) or mutation at codons 12 and 13 (m12/13) impaired Zta replication function. Each of the replication-negative Zta variants was capable of transactivating expression from both BHLF1 promoter-chloramphenicol acetyltransferase constructions and the BMRF1 promoter on endogenous EBV genomes in Raji cells with efficiency comparable to that of the wild-type polypeptide. Thus, a replication contribution of Zta was functionally separable from its transactivation activity and was supplied by the N-terminal region encompassing aa 11 to 25. Replication by a subset of the impaired Zta mutants was partially rescued upon the addition of Rta to the replication assay. The contribution of Rta mapped to domain II of the Rta activation domain and was specific for this region. A chimeric Rta-EBNA-2 transactivation domain fusion, which retains the DNA-binding and transactivation properties associated with wild-type Rta, failed to rescue replication-deficient Zta. Our data suggest that Rta may act as an ancillary replication factor in EBV ori-Lyt DNA synthesis by stabilizing Zta-replisome interactions.

A strategy for precision of genotyping of Epstein-Barr virus by polymerase chain reaction: application for studying Hodgkin's lymphoma

Previous studies on the genotyping of Epstein-Barr virus (EBV) have been based on the analysis of a single gene locus. The assignment of genotype of an isolate could easily be over-looked with this assay. Our strategy for precision of EBV genotyping has exploited the existence of two families of EBV strains (type A and B) that can be distinguished at three divergent gene loci (EBNA-2, EBNA-3C, and EBER). To precisely determine the genotype of EBV in Hodgkin's disease (HD), we designed primers and simultaneously analysed these three gene loci that distinguish type A and B viruses by the polymerase chain reaction (PCR) technique. The primers designed to amplify these three gene loci encompass either type-specific deletion sequences (EBNA-2 and EBNA-3C) or type-specific point mutations (EBER) that identify the virus strain based on the sizes of PCR-amplified products or the mobility shifts in single-strand conformation polymorphism (SSCP) analysis. The locations of point mutations were identified by direct sequencing of the PCR-amplified DNA. Fifteen EBV-infected cell lines were analysed and a good correlation between EBNA-2 and EBNA-3C typing results was found. In contrast, approximately 33% of the cell lines analysed maintained type A sequences in EBNA-2 and EBNA-3C genes while carrying type B sequences in the EBER region. Data obtained from analysis of cell lines served as a reference for studying HD samples. EBV DNA was detected in about 70% of HD. Among the EBV-positive samples, 56% were associated with type A virus, 13% with type B, and 31% with dual viral sequences.(ABSTRACT TRUNCATED AT 250 WORDS)

trans-acting requirements for replication of Epstein-Barr virus ori-Lyt

Epstein-Barr virus (EBV) utilizes a completely different mode of DNA replication during the lytic cycle than that employed during latency. The latency origin of replication, ori-P, which functions in the replication of the latent episomal form of the EBV genome, requires only a single virally encoded protein, EBNA-1, for its activity. During the lytic cycle, a separate origin, ori-Lyt, is utilized. Relatively little is known about the trans-acting proteins involved in ori-Lyt replication. We established a cotransfection-replication assay to identify EBV genes whose products are required for replication of ori-Lyt. In this assay, a BamHI-H plasmid containing ori-Lyt was replicated in Vero cells cotransfected with the BamHI-H target, the three EBV lytic-cycle transactivators Zta, Rta, and Mta, and the EBV genome provided in the form of a set of six overlapping cosmid clones. By removing individual cosmids from the cotransfection mixture, we found that only three of the six cosmids were necessary for ori-Lyt replication. Subcloning of the essential cosmids led to the identification of six EBV genes that encode replication proteins. These genes and their functions (either known or predicted on the basis of sequence comparison with herpes simplex virus) are BALF5, the DNA polymerase; BALF2, the single-stranded DNA-binding protein homolog; BMRF1, the DNA polymerase processivity factor; BSLF1 and BBLF4, the primase and helicase homologs; and BBLF2/3, a potential homolog of the third component of the helicase-primase complex. In addition, ori-Lyt replication in this cotransfection assay was also dependent on one or more genes provided by the EBV SalI-F fragment and on the three lytic-cycle transactivators Zta, Rta, and Mta.

Biochemical characterization of Epstein-Barr virus nuclear antigen 2A

The Epstein-Barr virus nuclear antigen 2A (EBNA-2A) was immunoprecipitated from latently Epstein-Barr virus-infected lymphocytes with a polyclonal serum raised against the EBNA-2A C terminus. The nucleus contained three subfractions of EBNA-2A which could be distinguished by their resistance to salt extraction: (i) a nucleoplasmatic fraction that was solubilized at 50 mM NaCl, (ii) a chromatin-associated fraction extractable at 1.5 M NaCl, and (iii) a nuclear matrix-associated fraction solubilized only by boiling with buffer containing 2% sodium dodecyl sulfate. The three subfractions were phosphorylated; it was demonstrated that the nucleoplasmatic and the chromatin-associated fractions were phosphorylated at serine and threonine residues. The half-life of the EBNA-2A protein was determined by cycloheximide treatment and by pulse-chase experiments and was found to be at least 24 h. The turnover of the phosphate residues bound to the two salt-soluble subfractions was determined to be approximately 6 to 9 h, suggesting a possible role of the phosphorylation in the regulation of the biological activity of EBNA-2A. Dephosphorylation of EBNA-2A resulted in an increased mobility of the protein during sodium dodecyl sulfate-polyacrylamide gel electrophoresis and indicated the presence of differentially phosphorylated subclasses of the protein. Analysis of EBNA-2A by sucrose gradient centrifugation revealed the existence of two subclasses of complexed molecules which exhibited sedimentation coefficients of approximately 13S and 34S.

An Epstein-Barr virus immortalization associated gene segment interferes specifically with the IFN-induced anti-proliferative response in human B-lymphoid cell lines

Immortalization of human B-lymphocytes by Epstein-Barr virus (EBV) is associated with a decreased anti-proliferative response to interferon (IFN). In the present investigation we show that the resistance to the anti-proliferative effect of IFN class I on certain EBV-carrying Burkitt lymphoma cell lines is connected to the presence of the EBNA-2 gene and parts of the EBNA-5 gene of the EBV genome. Transfection of the genomic segment comprising these open reading frames into an IFN-sensitive lymphoma cell line demonstrated that it is sufficient to make cells resistant towards the antiproliferative effect of IFN class I. Expression of the EBNA-2 gene seems to be correlated with the IFN-resistant phenotype. The antiviral function of IFN, as tested by inhibition by vesicular stomatitis virus (VSV) infection, and the IFN-receptor binding are not suppressed. The present results suggest that the neutralization of the anti-proliferative effect of IFN-alpha is involved in the EBV-mediated immortalization of B-cells and that the anti-proliferative action of IFN class I does not necessarily recruit the same mechanism as the antiviral effect.

Size and stability of the Epstein-Barr virus major internal repeat (IR-1) in Burkitt's lymphoma and lymphoblastoid cell lines

We have used field inversion gel electrophoresis to survey EBV strains for the size of the major internal repeat, IR-1, and estimate the number of 3.1-kb repeat units present. The B95-8 strain of EBV was estimated to contain 8.6 repeats. The repeat number varies considerably among naturally occurring isolates around a mean of six repeats. Some cell lines harbored multiple viral genomes with differing numbers of repeats and our results suggest that the repeat number in IR-1 is more likely to change during lytic replication than during latency. The Jijoye strain had 6.6 repeats and the Jijoye deletion mutant clone P3HR-1 retained 5.9 repeats setting the size of the P3HR-1 deletion at 6.8 kb. Thus, the nonimmortalizing mutant has retained all of the W1 and W2 exons of the immortalizing parent and has lost only the 3' unique exons of EBNA4 and all of EBNA2.

The transforming prototype of Epstein-Barr virus (B95-8) is also a lytic virus

The B95-8 isolate of the Epstein-Barr virus (EBV) has been described as a non-lytic transforming virus. We have performed experiments in order to determine if the B95-8 EBV is capable of super-infecting and replicating in EBV-genome-positive non-producer lymphoblastoid cells. Using concentrates of B95-8 EBV, prepared from 6 different B95-8 cell lines treated with 12-O-tetradecanoylphorbol-13-acetate (TPA), we demonstrated that virus concentrates could transform human or cotton-top tamarin B-lymphocytes and also lytically replicate in Raji cells, inducing EBV antigens and infectious virus. While the virus obtained from B95-8 super-infected Raji cells was able to transform cord-blood lymphocytes (CBLs) and super-infect Raji cells, transformation was abortive, with cell cultures only growing for up to 6 weeks. Transformation titers of the B95-8 virus concentrates ranged from 10(5) to greater than 10(8) transforming units/ml; early antigen (EA) induction ranged from 1% to 50% after superinfection of Raji cells, depending on the virus stock used, as determined by immunofluorescence. Southern blot analysis was carried out on the DNA prepared from B95-8 cells and virion DNA. The results were consistent with the published EcoRI restriction pattern for B95-8 EBV. The issue of whether the B95-8 cells produce virions with a dual biological phenotype or, rather, 2 biologically distinct viruses, is addressed.

Host cell-dependent regulation of growth transformation-associated Epstein-Barr virus antigens in somatic cell hybrids

We have analyzed the expression of the three major known growth transformation-associated Epstein-Barr virus (EBV) proteins, EBNA-1, EBNA-2, and latent membrane protein (LMP), in a series of somatic cell hybrids derived from the fusion of EBV-carrying Burkitt lymphoma (BL) lines with EBV-positive or EBV-negative B-cell lines. Independently of the cell phenotype, EBNA-1 was invariably coexpressed in all EBV-carrying hybrids. In hybrids between EBV-carrying, LMP-positive and LMP-negative Burkitt lymphoma lines, LMP was expressed, indicating positive control. Two EBV-negative lymphoma lines, Ramos and BJAB, differed in their ability to express LMP after B95-8 virus-induced conversion and after hybridization with Raji cells. BJAB was permissive while Ramos was nonpermissive for LMP, although both expressed EBNA-2. The EBNA-2-deleted P3HR-1 virus gave the same pattern of LMP expression in these two cells. Our findings indicate that the expression of EBNA-1, EBNA-2, and LMP is regulated by independent mechanisms.

Purification and characterization of the Epstein-Barr virus nuclear antigen 2 using monoclonal antipeptide antibodies

The Epstein-Barr virus (EBV) nuclear antigen 2 (EBNA-2) is the only one of the EBNA proteins to have been implicated as an EBV-encoded transforming protein. More detailed studies of this protein have been hampered by the lack of EBNA-2-specific monoclonal antibodies (MAbs) and of purified protein. To overcome these problems, we isolated 5 hybridomas producing MAbs reactive with an 18 residue synthetic peptide corresponding to the carboxyterminus of EBNA-2. Four of the 5 MAbs were specifically reactive with EBNA-2 in its denatured form on immunoblots. The 5th antibody (115E) was reactive with the native form of EBNA-2. By using a one-step immunoaffinity purification method with 115E cross-linked to protein-A-Sepharose, we purified EBNA-2 to homogeneity, i.e., more than 1,200-fold, from Burkitt lymphoma cell extracts. A major 32-kDa associated protein and a less abundant 17-kDa protein were co-purified with EBNA-2. Immunoprecipitation with 115E from 35S-methionine-labelled cell extracts showed that the 32-kDa protein co-precipitated with EBNA-2 from EBV-positive cells, but was not detectable in immunoprecipitates of EBV-negative cells. When the immunoprecipitates or the purified proteins were immunoblotted with EBV-immune sera, only EBNA-2 was reactive, indicating that the associated proteins are of cellular origin. Immunoprecipitation of cells labelled with 32P-orthophosphate showed that EBNA-2, but not the associated proteins, is a phosphoprotein. The expression level of EBNA-2 varied between different EBV-carrying cell lines, as measured by a 2-site ELISA based on antibody 115E. In indirect immunofluorescence, the 115E MAb gave an EBNA-2-specific characteristic granular staining pattern. These characteristics of EBNA-2 resemble those of other viral transforming proteins.

Amplification of Epstein-Barr virus (EBV) DNA by superinfection with a strain of EBV derived from nasopharyngeal carcinoma

Epstein-Barr virus (EBV) from a nasopharyngeal carcinoma (NPC) hybrid cell line (NPC-KT) lacking defective viral DNA molecules superinfected Raji cells and induced EBV early antigens (EA), as did virus from P3HR-1 cells, which contained defective molecules. The EBV polypeptides induced by NPC-KT appeared to be identical to those induced by P3HR-1 virus. The ability of NPC-KT virus to induce EA was enhanced more than 10-fold by treatment of superinfected cells with dimethyl sulfoxide; however, dimethyl sulfoxide treatment did not enhance superinfection by P3HR-1 virus. After infection, DNA synthesis of both the superinfecting NPC-KT virus and the resident Raji viral genome was induced. In addition to amplified Raji EBV episomal DNA, a fused terminal fragment of NPC-KT viral DNA was detected. The detection of fused terminal DNA fragments suggests that the superinfecting virion DNA either circularizes or polymerizes after superinfection and is possibly amplified through circular or concatenated replicative intermediates.

Monoclonal and polyclonal antibodies against Epstein-Barr virus nuclear antigen 5 (EBNA-5) detect multiple protein species in Burkitt's lymphoma and lymphoblastoid cell lines

The Epstein-Barr virus nuclear antigen 5 (EBNA-5) is encoded by highly spliced mRNA from the major IR1 (BamHI-W) repeat region of the virus genome. A mouse monoclonal antibody, JF186, has been raised against a synthetic 18-amino-acid peptide deduced from the EBNA-5 message of B95-8 and Raji cells. The antibody showed characteristic coarse nuclear granules by indirect immunofluorescence and revealed multiple EBNA-5 species by immunoblotting and immunoprecipitation. The B95-8 line itself and all B95-8 virus-carrying cells, whether lymphoblastoid cell lines or in vitro-converted sublines of Epstein-Barr virus (EBV)-negative Burkitt's lymphoma (BL) lines, were EBNA-5 positive. Among 36 cell lines carrying different EBV strains, only 10 expressed the B95-8-Raji-prototype EBNA-5 recognized by JF186; this was probably due to genetic variation in the epitope recognized by JF186, as shown for P3HR-1. Human antibodies, affinity purified against EBNA-5-JF186 immunoprecipitates, detected EBNA-5 in the majority of EBV-positive BL lines and in all lymphoblastoid cell lines containing the BL-derived viruses. Thus, EBNA-5 can be expressed by all virus isolates examined, but is down-regulated, together with other latent gene products, in a minority of BL lines which have a particular cellular phenotype. EBNA-5 was detected as a ladder of protein species of 20 to 130 kilodaltons (kDa), with a regular spacing of 6 to 8 kDa, consistent with the coding capacity of the combined BamHI-W 66- and 132-base-pair exons, together with shifts of 2 to 4 kDa, consistent with the size of the separate 66- and 132-base-pair exons. Multiple EBNA-5 proteins can be expressed by the single cell as shown by cloning of newly infected cells.

Two strains of Epstein-Barr virus (B95-8 and a P3HR-1 subclone) that lack defective genomes induce early antigen and cause abortive infection of Raji cells

The heterogeneity of Epstein-Barr virus (EBV) obtained from P3HR-1 cells has permitted derivation of a distinct subclone of P3HR-1 (L. Heston, M. Rabson, N. Brown, and G. Miller, Nature (London) 295:160-163, 1982). We have analyzed the biologic properties and genomic structure of this subclonal virus (clone 13) compared with those of parental P3HR-1 and B95-8 viruses. Synthesis of EBV compared with those of parental P3HR-1 and B95-8 viruses. Synthesis of EBV proteins in Raji cells superinfected with virus derived from P3HR-1, clone 13, and B95-8 was analyzed both by fluorography of radiolabeled proteins and by immunoblotting. Highly concentrated preparations of clone 13 and B95-8 virus induced most of the spectrum of EBV proteins in Raji cells with the exception of the 145,000-, 140,000-, and 110,000-molecular-weight proteins, which were either undetectable or reduced. Moreover, both clone 13 and B95-8 viruses also induced the same patterns of early antigen diffuse components as the parental P3HR-1 virus did. However, only P3HR-1 virus could induce EBV DNA synthesis in superinfected Raji cells, as determined both by buoyant density centrifugation and by in situ cytohybridization with biotinylated recombinant EBV DNA probes. Defective heterogeneous molecules present in P3HR-1 virus have been implicated in early antigen induction after superinfection of Raji cells. Therefore, Southern blots of clone 13, P3HR-1, and B95-8 viruses were hybridized to recombinant EBV fragments representing the sequences contained within the defective molecules in P3HR-1. The parental P3HR-1 contained the previously described defective molecules. No evidence for defective molecules was found in clone 13 or B95-8 viruses. These data indicate that concentrated preparations of both clone 13 and B95-8 viruses can induce abortive infection in Raji cells, but while the defective molecules are not needed for induction of early antigen diffuse components, they may be required for the induction of viral DNA synthesis.

Lymphoblastoid cell lines and Burkitt-lymphoma-derived cell lines differ in the expression of a second Epstein-Barr virus encoded nuclear antigen

Twenty-seven Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines and 27 EBV-carrying Burkitt-lymphoma-derived lines were analyzed for expression of the second EBV-encoded nuclear antigen (EBNA-2) by immunoblotting and anticomplement immunofluorescence with EBNA-2-specific sera. While all lymphoblastoid cell lines expressed EBNA-2, only 10 of the 27 BL lines were EBNA-2-positive. Comparison of the EBNA-2 coding BamHI W-, Y- and H-fragments of EBV-DNA in the different cell lines by restriction enzyme analysis suggests that EBNA-2 negativity is due either to sequence diversity or to a deletion in the BamHI WYH region.

An Epstein-Barr virus (EBV)-determined nuclear antigen (EBNA5) partly encoded by the transformation-associated Bam WYH region of EBV DNA: preferential expression in lymphoblastoid cell lines

Four peptides were synthesized on the basis of amino acid sequences deduced from a highly spliced transcript encoded by the Bam W, Y, and H fragments of the Epstein-Barr virus (EBV) genome [Bodescot, M., Chambraud, J. B., Farrell, P. J. & Perricaudet, M. (1984) EMBO J. 3, 1913-1917]. Rabbit antisera against three of the four peptides identified a nuclear polypeptide that varied between 22 and 70 kDa in molecular size. Four of 20 EBV-positive human sera contained antibodies against this polypeptide. Since this is the fifth EBV-determined nuclear antigen (EBNA) discovered in growth-transformed cells, it is designated EBNA5. The antigen was detected in virus nonproducer lines (less than 0.01% EBV early antigen expression) and is thus not dependent on the viral cycle. It was differentially expressed depending on the origin of the lines. All 10 lymphoblastoid cell lines tested expressed EBNA5, but it could not be detected in 10 of 11 EBV-carrying Burkitt lymphoma lines. Infection of tonsillar lymphocytes with the B95-8 strain of EBV induced six EBNA5-specific polypeptides that varied between 41 and 70 kDa in molecular size with regular increments of 6 kDa. This may be due to the fact that the EBNA5 coding sequence includes the Bam W internal repeat. Parallel infection of the EBV-negative Burkitt lymphoma line Ramos with the same viral substrain did not induce detectable levels of EBNA5, nor was this antigen present in permanently EBV-converted Ramos sublines. These findings imply that the expression of the viral genome varies among B cells having different phenotypes.

Palindromic structure and polypeptide expression of 36 kilobase pairs of heterogeneous Epstein-Barr virus (P3HR-1) DNA

Among the Epstein-Barr virions (EBV) produced by the P3HR-1 (HR-1) cell line are a defective subpopulation with rearranged viral DNA designated heterogeneous DNA (het DNA). These defective virions are responsible for the capacity of HR-1 virus to induce early antigen in Raji c cells and for trans activation of latent EBV in X50-7 cells. Virions with het DNA are independent replicons which pass horizontally from cell to cell rather than being partitioned vertically. We analyzed the structure and defined several polypeptide products of het DNA to understand these remarkable biologic properties. A 36-kilobase-pair (kbp) stretch of het DNA was cloned (as two EcoRI fragments of 20 and 16 kbp) from virions released from a cellular subclone of HR-1 cells. The unusual aspect of the 20-kbp fragment was the linkage of sequences of BamHI-M and BamHI-B', which are not adjacent on the standard EBV genome. The 16-kbp fragment was a palindrome in which at least two additional recombinations on each side of the palindrome had linked regions of the standard EBV genome which are not normally contiguous. The 20-kbp het DNA fragment was attached to at least one and possibly both ends of the 16-kbp het DNA fragment. We identified antigenic polypeptides produced in COS-1 cells after gene transfer of various cloned het DNA fragments. The 20-kbp fragment encoded a cytoplasmic antigen of about 95 kilodaltons (kDa). The 16-kbp fragment encoded antigens located in the nucleus, nuclear membrane, and cytoplasm. These were represented by several polypeptides, the most prominent of which were about 55, 52, and 36 kDa. The 36-kDa polypeptide was localized to a 2.7-kbp BamHI fragment which had homology to standard BamHI-W and BamHI-Z. Another polypeptide of 50 kDa found in the nucleus was mapped to the 7.1-kbp BamHI het DNA fragment which spans the EcoRI site linking the 20- and 16-kbp fragments of het DNA. Thus, HR-1 het DNA encodes several discrete polypeptide products, one or more of which could be responsible for the unusual biologic properties of the virus. The composition, regulation, and ultimately the expression of some of these products relative to standard EBV is probably altered by the genomic rearrangements of het DNA.

The Epstein-Barr virus determined nuclear antigen is composed of at least three different antigens

The EBV-determined nuclear antigen, EBNA, is the only known viral product to be regularly detected in all EBV-transformed cells. The anticomplement immunofluorescence (ACIF) staining detects an EBV-specific nuclear reaction that has recently been shown to be due to at least 2 different proteins, EBNA-1 and EBNA-2, encoded by different parts of the viral genome. We now report the existence of a third antigen of the EBNA complex, designated as EBNA-3. Serum from a patient with chronic infectious mononucleosis contained no detectable antibodies to EBNA-I and had only a low EBNA-2 antibody level. Nevertheless, it gave an EBV-specific nuclear reaction of normal intensity and stained EBNA-2-positive and EBNA-2-negative EBV-carrying lines equally well. Immunoblotting with the same serum identified a new EBV-specific nuclear protein of 143-157 kDa.

Mapping of genes in BamHI fragment M of Epstein-Barr virus DNA that may determine the fate of viral infection

We used nuclease digestion to map RNA transcripts encoded in the BamHI M fragment of the Epstein-Barr virus (EBV) genome (strain B95-8). Of the five RNAs, three are rightwardly transcribed, have different cap sites but common 3' termini, and are unspliced. The two remaining RNAs are leftwardly transcribed and are 5' and 3' coterminal. One of these transcripts is spliced, resulting in the removal of a small intron from the 5' region of this RNA. We have previously published data which indicated that the BamHI M region is the first actively transcribed region of the viral genome during the replicative cycle, suggesting that one or more genes in this region is important in the initiation of EBV replication. We have now mapped two large EcoRI restriction fragments which span approximately 75% of the P3HR-1 defective genome and which contain DNA from the BamHI M region of the standard genome. The data indicate that only the coding and 5' flanking sequences for the leftwardly transcribed RNAs are intact within the defective genome. Fewer than 500 bases coding for the 3'-most regions of the rightwardly transcribed RNAs are intact, and it is unlikely that these encode functional native polypeptides. Therefore, it seems that transcriptional activation of the BamHI M-region genes is not mediated directly by the rearrangement of M genes in defective P3HR-1 EBV.

Antibodies against synthetic peptides react with the second Epstein-Barr virus-associated nuclear antigen

Five peptides were synthesized on the basis of amino acid sequences predicted from the transformation-associated BamHI WYH region of the genome of the Epstein-Barr virus (EBV). Antisera to two peptides deduced from a 1.6-kb open reading frame in the BamHI H fragment identified an 87 000-dalton nuclear polypeptide that was present in EBV-carrying cell lines that expressed the second EBV-determined nuclear antigen (EBNA-2). This polypeptide was not detected in cell lines that carried EBV variants with a deleted BamHI WYH region or in EBV-negative cell lines. Three peptides deduced from the 1.6-kb open reading frame reacted with human EBNA-positive sera, but not with EBNA-negative sera. Following affinity purification with the peptides, two of the corresponding human antibodies also reacted with the 87 000-dalton polypeptide.

P3HR-1 Epstein-Barr virus with heterogeneous DNA is an independent replicon maintained by cell-to-cell spread

We present results of biological experiments which indicate that the subpopulation of Epstein-Barr virus strain P3HR-1 with heterogeneous (het) DNA consists of self-contained replicons which multiply alongside, but independently of, Epstein-Barr virus strain HR-1 containing standard DNA. When a population of HR-1 virions containing het DNA was introduced into X50-7 cells, the input heterogeneous DNA increased in abundance, as did the DNA of the endogenous virus of X50-7 cells. The input standard HR-1 viral DNA, however, was not amplified. When parental HR-1 cells or a cellular subclone containing het DNA were grown for several weeks in the presence of human serum with neutralizing antibody, the het DNA was lost from the culture; standard HR-1 DNA, however, was not affected by antiserum. Furthermore, virions containing het DNA could be serially propagated through cellular subclones of HR-1 cells which lack het DNA. After each serial passage, cells which acquired het DNA released virions with the ability to induce early antigens in Raji cells. These experiments define a novel in vitro life cycle of an Epstein-Barr virus variant which is maintained, not vertically by partitioning to daughter cells in cell division, but horizontally by cell-to-cell spread.

An EBNA-negative, EBV-genome-positive human lymphoblast cell line in which superinfecting EBV DNA is not maintained

A human B-lymphoid cell line, designated TG8, which does not express detectable levels of the EBV (Epstein-Barr virus)-associated nuclear antigen (EBNA), yet carries an average of one to two plasmid copies of the P3HR-1 EBV genome has been identified. TG8 can be superinfected by B95-8 EBV, resulting in up to 60-70% of the population becoming EBNA-positive and 20-30% of the incoming EBV genomes becoming circular by 48 hr postinfection. Neither EBNA expression nor the superinfecting viral DNA is maintained in the population. It is concluded that (1) superinfection of this EBV-genome-positive lymphoblast cell line leads to detectable EBNA expression and circularization of the incoming viral genome and (2) the incoming viral genome and detectable EBNA expression are selectively lost, whereas the endogenous viral plasmid DNA is maintained.

Epstein-Barr virus (P3HR-1) defective DNA codes for components of both the early antigen and viral capsid antigen complexes

A set of lambda phages containing overlapping fragments of Epstein-Barr virus (EBV) defective DNA has been cloned from P3HR-1-superinfected Raji cells. Mapping data obtained using these cloned DNA fragments confirmed the structure of P3HR-1 defective DNA previously deduced directly from virion DNA (M.-S. Cho, G. W. Bornkamm, and H. zur Hausen, 1984, J. Virol., in press). The ability of the cloned defective DNA fragments to induce EBV antigens in transfected baby hamster kidney (BHK) cells was tested using indirect immunofluorescence assays. Up to 5% of those cells receiving a defective DNA fragment BamHI-W'C' transiently expressed a de novo nuclear antigen which was identified as being a component of the EAD complex by its reactivity with characterized EBV-positive human sera. A 20-kb clone of P3HR-1 defective DNA (EcoRI-C1) was found to induce the synthesis of a component of the VCA complex. One percent of cells transfected with this clone showed cytoplasmic fluorescence when tested with either VCA+ human sera or EBV anti-VCA monoclonal antibody. Subcloning of the EcoRI-C1 fragment localized the VCA gene to a 4.1-kb segment which maps within the BamHI-A fragment of the standard genome. This segment contains a single large open reading frame of 2.6 kb (B. Barrell, A. Bankier, R. Baer, P. Biggin, P. Deininger, P. Farrell, T. Gibson, G. Hatfull, G. Hudson, S. Stachwell, and C. Sequin, 1984, Nature (London), in press). None of the defective DNA clones were capable of inducing EBV-specific nuclear antigens (EBNAs) which is consistent with the absence of the known EBNA coding regions from the defective genome.

DNA sequence and expression of the B95-8 Epstein-Barr virus genome

The complete (172,282 base pairs) nucleotide sequence of the B95-8 strain of Epstein-Barr virus has been established using the dideoxynucleotide/M13 sequencing procedure. Many RNA polymerase II promoters have been mapped and the mRNAs from these promoters have been assigned to the latent or early/late productive virus cycles. Likely protein-coding regions have been identified and three of these have been shown to encode a ribonucleotide reductase, a DNA polymerase and two surface glycoproteins.

Structural organization of human herpesvirus DNA molecules

The herpesviruses are among the largest and most complex of all DNA viruses, and their genomes display an astonishing diversity in size, structure, and organization. In 1974, the features of large inverted repeats and structural isomerization were first discovered, and these proved to be characteristic properties of many herpesvirus genomes. Since then, research using the powerful techniques of modern molecular biology has revealed a great deal of comparative structural information about the arrangement of repetitive sequences and the location, structure, and primary nucleotide sequences of the genes for several easily assayed or abundantly expressed gene products. Extensive restriction enzyme cleavage maps and complete sets of cloned DNA fragments have been constructed for each of the five human herpesviruses, HSV-1, HSV-2, CMV, EBV, and VZV, and the entire 175,000-bp nucleotide sequence of EBV DNA has been determined. Based on these maps and reagents, the procedures of "DNA fingerprinting" and "dot hybridization" are proving useful at a clinical level for characterization of isolates and studying herpesvirus epidemiology. Strain differences, localized heterogeneity, tandem-repeat-defective genomes, and sites of cell-virus DNA homology have been described in some detail. The attention of basic researchers is now turning to equating structure with function, and rapid progress is expected in studies aimed at a better understanding of the mechanisms of viral DNA replication, maintenance of the latent state, reactivation, transformation, packaging, and regulation of the lytic cycle, etc using cloned functionally active DNA fragments, isolated intact genes and promoters, and DNA transfection and in vitro expression systems.

Structure of defective DNA molecules in Epstein-Barr virus preparations from P3HR-1 cells

Epstein-Barr virus (EBV), isolated from P3HR-1 cells, induces early antigen and viral capsid antigen upon infection of human B-lymphoblasts. The strong early antigen- and viral capsid antigen-inducing activity is only observed in P3HR-1 virus preparations harboring particles with defective genomes, suggesting that this biological activity is directly associated with the defective DNA population. After infection of EBV genome-carrying Raji or EBV genome-negative BJAB cells, defective genomes of P3HR-1 EBV DNA are replicated in excess, depending on the multiplicity of infecting EBV particles. Hybridization of the DNA from such infected cells with 32P-labeled EBV DNA after HindIII cleavage reveals six hypermolar fragments. Mapping of these fragments shows that they form one defective genome unit containing four nonadjacent regions (alpha, beta, gamma, and delta) of the nondefective P3HR-1 EBV DNA. Two of the segments (alpha and beta) contain ca. 17 and 13 megadaltons, respectively, from the terminal regions of the P3HR-1 genome, whereas the two smaller segments (gamma and delta) contain ca. 3.7 and 3.0 megadaltons, respectively, originating from the central portion of the genome. In the defective molecule, the regions gamma and delta are present in the opposite orientation compared with nondefective P3HR-1 EBV DNA. Tandem concatemers are formed by fusion of the alpha and beta regions. Our model suggests that tandem concatemers of three defective genome units can be packaged into virions in P3HR-1 cells.

Epstein-Barr virus with heterogeneous DNA disrupts latency

By cloning the HR-1 Burkitt lymphoma line, we previously uncovered two distinct biological variants of nontransforming Epstein-Barr virus (EBV). The most commonly cloned variant has a low rate of spontaneous viral synthesis and is unable to induce early antigen in Raji cells (EAI-). A rare variant spontaneously releases virus which is capable of inducing early antigen in Raji cells (EAI+). Since EAI- virus lacks heterogeneous DNA (het-) and EAI+ virus contains heterogeneous DNA (het+), we suggested that spontaneous viral synthesis and induction of early antigen are biological properties which correlate with the presence of het sequences. The present experiments provide three new lines of experimental evidence in favor of this hypothesis. (i) Revertant subclones of the EAI+ het+ variant which have lost the het DNA concomitantly lost EAI ability. Thus, het DNA is not stably associated with the cells as are the episomes. (ii) het DNA was acquired by two het- subclones of the HR-1 line after superinfection with EAI+ virus. After superinfection, these clones synthesized EAI+ het+ virus. Thus, het DNA may be maintained in the HR-1 line by cell-to-cell spread. (iii) Virus with het DNA activated full expression of endogenous latent EBV of the transforming phenotype in a line of immortalized neonatal lymphocytes designated X50-7. By use of restriction endonuclease polymorphisms unique to both the superinfecting and endogenous genomes, we show that the genome of the activated virus resembles that of the virus which was endogenous to X50-7 cells. This result suggests that het sequences result in transactivation of the latent EBV. het DNA had homology with EBV sequences which are not normally contiguous on the physical map of the genome. het DNA was always accompanied by the presence of DNA of nonheterogenous HR-1. Thus, het DNA is a form of "defective" EBV DNA. However, the biological effect of this defective DNA is to enhance rather than to interfere with EBV replication. This is a novel property of defective virus.

Two deletions in the Epstein-Barr virus genome of the Burkitt lymphoma nonproducer line Raji

The Epstein-Barr virus genome carried in the Burkitt lymphoma nonproducer cell line Raji was characterized by partial denaturation mapping and by hybridization of cloned viral fragments to filters containing separated Raji DNA fragments. Partial denaturation mapping revealed that the EBV DNA population of Raji cells is homogeneous and that two deletions are observed in distant parts of the genome compared to linear DNA isolated from virus particles of different strains. These deletions were characterized by blot analysis. One deletion of 3.15 kb lies within HindIII-E; the second is 2.4 kb and is located close to the right terminus of linear viral DNA. The two deletions were observed in several cell lines derived from the Raji line. These deletions might contribute to the inability of Raji cells to produce EBV either spontaneously or upon induction.

Organization of the Epstein-Barr virus DNA molecule. III. Location of the P3HR-1 deletion junction and characterization of the NotI repeat units that form part of the template for an abundant 12-O-tetradecanoylphorbol-13-acetate-induced mRNA transcript

A 1,400-base-pair (bp) region within the BamHI H fragment of Epstein-Barr virus (EBV) (B95-8) DNA consists of a cluster of tandemly duplicated direct repetitions characterized by single sites for the NotI restriction endonuclease. Nucleotide sequencing revealed a 125-bp repeat unit of 84% guanine-plus-cytosine content which is theoretically capable of extensive secondary structure formation. The flanking sequences adjacent to the NotI repeat cluster contained an additional 38-bp portion of repeat unit DNA, thus establishing that EBV(B95-8) contains a nonintegral number of NotI repeats totalling 11.3 copies. Restriction site mapping of the homologous cloned BamHI "H" fragment from the nontransforming EBV (P3HR-1) isolate revealed that a contiguous 6,650-bp region including the entire NotI repeat cluster has been deleted from the BamHI-H, -Y, and -W regions of the P3HR-1 genome. By nucleotide sequencing across the novel junction, we have precisely identified the P3HR-1 deletion boundaries in BamHI-H and the internal repeat and suggest that a complex pattern of direct and inverted partial DNA homologies may have been involved in the original recombination event. The cloned BamHI H fragment and isolated NotI repeat unit have also been used as probes to detect homologous mRNA transcripts in the B95-8 and Raji cell lines of EBV-transformed lymphoblasts. These experiments showed that the NotI repeats form part of the template for a polyadenylated 2.5-kilobase mRNA transcript which becomes much more abundant after 12-O-tetradecanoyl-phorbol-13-acetate treatment of the cultures. The direction of transcription of this mRNA and the nucleotide sequence of most of its template and 5' flanking regions have been determined. The probable promoter for the 2.5-kilobase mRNA initiates transcription efficiently in an in vitro assay and contains several TAATGA-like elements that may be indicative of herpesvirus immediate-early class promoters. The need to repress expression of this gene during latency suggests a possible novel regulatory role for tandem repeat structures inside a eucaryotic virus transcription unit. The deletion in EBV(P3HR-1), which has been associated with the loss of lymphocyte "immortalizing" capacity in this isolate, eliminates part of the coding region as well as the NotI repeats from the 2.5-kilobase mRNA transcript, but the promoter and proximal 340-bp portions of the template remain.

Multiplicity-dependent induction of viral capsid antigen in Raji cells superinfected with Epstein-Barr virus

A quantitative analysis of Epstein-Barr virus (EBV)-induced early antigen (EA) and viral capsid antigen (VCA) syntheses was carried out in Raji cells superinfected with purified, concentrated P3HR-1 EBV. When the cells were exposed to the virus and assessed by immunofluorescence and immunoprecipitation, EA induction occurred significantly (17%) but not VCA (less than 1%), at a low-input multiplicity of infection (MOI) of 10 EBV DNA copies/cell. In contrast, at a high MOI of 500 EBV DNA copies/cell, the majority of cells were positive for both EA (82%) and VCA (61%). The latter VCA synthesis was accompanied by the replication of EBV DNA. Kinetic studies showed that EA induction was directly proportional to the dilution of the infecting virus, while VCA was made following three-hit kinetics. The implications of these results are discussed in relation to the heterogeneous nature of P3HR-1 EBV and a possible role of EA in VCA synthesis.

Identification of a rare Epstein-Barr virus variant that enhances early antigen expression in Raji cells

Early antigens (EAs) are made when the P3J-HR-1 strain of Epstein-Barr virus (EBV) infects cells that already harbor latent EB viral genomes. We wished to identify EBV genes that might participate in induction of EAs. We have recently isolated from the HR-1 line EB viral variants that are unable to induce EAs. We have now isolated a clone of HR-1 cells that releases virus with the capacity to induce EA. We compared the genome of the EB variant that possesses the capacity to induce EA with that of a variant that is unable to induce EA and with parental stock that was the source of both different biotypes of EBV. The variant that is able to induce EA contains, in molar or greater quantities, additional fragments of EBV DNA not found in the variant that lacks that capacity. These same DNA fragments are present in submolar quantities in the parental DNA, indicating that they represent a subpopulation in the parental viral DNA mixture. We thus provide evidence that EA induction is brought about by unusual forms of EBV DNA that are likely to act by regulating expression of the genome.

Non-immortalizing P3J-HR-1 Epstein-Barr virus: a deletion mutant of its transforming parent, Jijoye

The P3J-HR-1 strain of Epstein-Barr virus (EBV) fails to immortalize human lymphocytes. We wished to understand the nature of the genomic alterations which correlated with the loss of this ability. As a first step, the heterogeneity of DNA molecules in the P3J-HR-1 line was eliminated by cell cloning. Then a physical map was prepared of virion DNA from one cell clone, designated FF452-3. By comparison with the genomes of two EBVs, B95-8 and FF41, which are competent to immortalize lymphocytes, we identified a total of eight modifications of BamHI and EcoRI restriction endonuclease fragments of EBV (FF452-3) DNA consisting of insertions, deletions, or loss of a restriction endonuclease recognition site. To determine which of these alterations might be responsible for the loss of transforming phenotype, we examined homologous DNA fragments of the Jijoye strain of EBV, the progenitor of the HR-1 strain which still retains the ability to immortalize lymphocytes. We also studied viral DNA in lymphocytes transformed in vitro by Jijoye virus. Six of the eight alterations were found both in Jijoye and in clonal HR-1 DNA and were presumably genomic traits characteristic of this lineage of EBV. A small deletion in the BamHI-K fragment of HR-1 DNA was not found in Jijoye virion DNA, but this deletion was present in intracellular Jijoye DNA. Thus only one major genomic lesion in HR-1 DNA, a deletion of at least 2.4 x 10(6) molecular weight of DNA from a fused BamHI-H-Y fragment, consistently distinguished Jijoye DNA from its non-immortalizing P3J-HR-1 derivative. This deletion is likely to affect EBV genes which are directly or indirectly involved in immortalizing lymphocytes.

The B95-8 isolate of Epstein-Barr virus arose from an isolate with a standard genome

Blot hybridization studies revealed that the deletion which characterizes the DNA from the B95-8 strain of Epstein-Barr virus was not present in the virus from which the B95-8 strain was derived (883L). The deletion event must have occurred during establishment of the B95-8 cell line or very soon afterward, since the deletion was present in Epstein-Barr virus DNA from a cell line established with B95-8 virus soon after it became available. The presence of the deletion correlates with decreased expression of the gp220 viral envelope glycoprotein.

Deletion of the nontransforming Epstein-Barr virus strain P3HR-1 causes fusion of the large internal repeat to the DSL region

The nontransforming Epstein-Barr virus (EBV) strain P3HR-1 is known to have a deletion of sequences of the long unique region adjacent to the large internal repeats. The deleted region is believed to be required for initiation of transformation. To establish a more detailed map of the deletion in P3HR-1 virus, SalI-A of the transforming strain M-ABA and of P3HR-1 virus was cloned into the cosmid vector pHC79 and multiplied in Escherichia coli. The cleavage sites for BamHI, BglII, EcoRI, PstI, SacI, SacII, and XhoI were determined in the recombinant plasmid clones. Analysis of the boundary between large internal repeats and the long unique region showed that in M-ABA (EBV) the transition is different from that in B95-8 virus. The map established for SalI-A of P3HR-1 virus revealed that, in contrast to previous reports, the deletion has a size of 6.5 kilobase pairs. It involves the junction between large internal repeats and the long unique region and includes more than half of the rightmost large internal repeat. The site of the deletion in the long unique region is located between a SacI and a SacII site, about 200 base pairs apart from each other. The sequences neighboring the deletion in the long unique region showed homology to the nonrepeated sequences of the DS(R) (duplicated sequence, right) region. Sequences of the large internal repeat are thus fused to sequences of the DS(L) (duplicated sequence, left) region in P3HR-1 virus DNA under elimination of the DS(L) repeats. Jijoye, the parental Burkitt lymphoma cell line from which the P3HR-1 line is derived by single-cell cloning, is known to produce a transforming virus. Analysis of the Jijoye (EBV) genome with cloned M-ABA (EBV) probes specific for the sequences missing in P3HR-1 virus revealed that the sequences of M-ABA (EBV) BamHI-H2 are not represented in Jijoye (EBV). In Jijoye (EBV) the complete DS(L) region including the DS(L) repeats is, however, conserved. Further analysis of Jijoye (EBV) and of Jijoye virustransformed cell lines will be helpful to narrow down the region required for transformation.

Organization of the Epstein-Barr virus DNA molecule. II. Fine mapping of the boundaries of the internal repeat cluster of B95-8 and identification of additional small tandem repeats adjacent to the HR-1 deletion

We used cloned BamHI fragments from Epstein-Barr virus strain B95-8 [EBV(B95-8)]DNA to obtain detailed restriction maps of the region of the genome adjacent to the large internal repeat cluster. These maps together with the results of hybridization experiments using a 3.1-kilobase repeat probe defined more precisely the location of the injection between the internal repeat cluster and the flanking unique-sequence DNA. On one side (UL), the repeat sequences extended 600 +/- 80 base pairs (bp) into BamHI-Y; on the other side (US), they extended 1,300 +/- 200 bp into BamHI-C. Therefore, EBV(B95-8) DNA contained a nonintegral number of 3.1-kilobase repeat units, namely, 12.6 copies. The mapping studies also revealed a second series of internal tandem repetitions in EBV(B95-8) DNA located within the BamHI-H fragment. This cluster comprised 11 copies of a 135-bp repeat unit which contained a single site for the NotI restriction endonuclease. Hybridization to these cloned EBV(B95-8) fragments using total EBV(HR-1) DNA as probe indicated that the deletion in EBV(HR-1) removed all 3,000 bp of unique-sequence DNA which lay between the large 3.1-kilobase and the small 135-bp repeat clusters. Thus, the deletion which destroyed the transforming ability in the EBV(HR-1) virus was bounded on either side by tandem repetitions.

Herpesvirus sylvilagus I. Polypeptides of virions and nucleocapsids

Herpesvirus sylvilagus was propagated in juvenile cotton tail rabbit kidney cells and purified from the cytoplasmic fraction of the infected cells. The purification procedure included zonal centrifugation through a 5 to 30% dextran t-10 gradient, followed by equilibrium centrifugation in a 5 to 50% potassium tartrate gradient. H. sylvilagus formed one band after centrifugation through the tartrate gradient at a density of 1.22 g/cm3. Contamination of the purified virus preparation by cellular proteins was less than 0.2% as determined by the removal of radioactivity from an artificially mixed sample containing [35S]methionine-labeled control cells and nonlabeled infected cells. H. sylvilagus nucleocapsids were isolated from infected cell nuclei and purified by sedimentation through a 36% sucrose cushion, followed by equilibrium centrifugation in 5 to 50% tartrate gradient. Forty-four polypeptides ranging in molecular weight from 18,000 to 230,00 were resolved when [35S]methionine-labeled enveloped H. sylvilagus was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Seventeen polypeptides found within the enveloped virus were also identified with the nucleocapsid. Six additional nucleocapsid polypeptides han no counterparts within the enveloped virus. The major polypeptide within both the virus and the nucleocapsid had a molecular weight of 150,000.

Characterization of the major Epstein-Barr virus-specific RNA in Burkitt lymphoma-derived cells

Cytoplasmic RNA prepared from five lymphoid cell lines and a Burkitt lymphoma biopsy was radioactively labeled in vitro and hybridized to cloned EcoRI restriction endonuclease fragments of B95-8 Epstein-Barr virus DNA. The results confirmed that the most abundant cytoplasmic RNA species in such cells is specified by a small region of the genome defined by the EcoRI J fragment. Detailed mapping experiments precisely localized these transcripts within the sequence of the rightmost one-third of the EcoRI J fragment. DNA sequencing suggested that this region of the Epstein-Barr virus genome is unable to code for protein. The major early transcripts consisted of two non-polyadenylated RNA species, each about 170 nucleotides in length. They were both transcribed off the same strand of the DNA and showed significant sequence homology with each other. The coding sequences of the two small RNAs contained potential intragenic control regions for RNA polymerase III.

Identification of Epstein-Barr virus strain differences with monoclonal antibody to a membrane glycoprotein

Two monoclonal antibodies directed against Epstein--Barr virus (EBV)-induced membrane antigens (MA) were isolated in this study. On of the monoclonal antibodies, designated 2F5.6, was an IgG2 which, as detected by membrane and fixed cell immunofluorescence, reacted with MA-positive lymphoblastoid cell lines that produced transforming EBV but not with the MA-positive P3HR-1 cell line that produced the lytic, nontransforming strain of this virus. This antibody precipitated the Mr 320,000/350,000 glycoprotein from B-95 virus infected cultures and the Mr 300,000 and 220,000/250,000 glycoproteins from Raji cells superinfected with P3HR-1 virus but did not precipitate any of these EBV-specific glycoproteins from the P3HR-1 cell line. In contrast, the second monoclonal antibody, IgM designated B10.3, reacted with all virus-producing cell lines including the P3HR-1 cell line. The identity of the glycoprotein that serves as the target for this antibody is still unknown. Neither antibody had neutralizing activity against the B-95 or P3HR-1 strain of EBV. These results indicated that the 2F5.6 monoclonal antibody was directed against an antigenic determinant on the major membrane glycoprotein which is common to transforming strains of EBV but absent from the lytic P3HR-1 stain whereas the B10.3 monoclonal antibody was directed against a group-specific EBV-induced membrane determinant.

Epstein-Barr virus DNA. X. Direct repeat within the internal direct repeat of Epstein-Barr virus DNA

The 3,360-base-pair internal direct repeat (IR) in Epstein-Barr virus DNA separates the short and long unique DNA domains. IR has a single BamHI site. The juncture between the short unique domain and IR has been mapped by restriction endonucleases and is less than 2,600 nucleotides before the BamHI site in IR. The junction between IR and the long unique domain has been sequenced and is approximately 650 nucleotides after the BamHI site in IR. Thus, relative to the start of IR at the juncture with the short unique domain, the last repeat is at least 90 base pairs short of being complete. There is homology between the 250-nucleotide fragments to the left and the right of the unique BamHI site in IR. A 35-base-pair sequence of the left fragment is directly repeated within the right fragment, once fully and once partially. The implications of these findings are discussed.

Analysis of the transformation of human lymphocytes by Epstein-Barr virus III. Induction of early events by P3HR-1 strain without subsequent immortalization

T-cell depleted human cord blood lymphocytes were exposed to P3HR-1 strain of Epstein-Barr virus (EBV) and simultaneous observations of immunofluorescence, cellular morphology, and autoradiography were carried out in individual cells. Soon after infection, nuclear antigen (EBNA) synthesis, blastogenesis, and DNA synthesis occurred, as was previously observed B95-8 strain EBV infection. Although mitosis followed with characteristic cell aggregate formation, the cell proliferation was temporary and death followed in about 2 weeks. The synthesis of the early antigens (EA) and the viral capsid antigen (VCA) were not significant. These findings seem to indicate that the strain P3HR-1 EBV is capable of inducing early events of transformation in primary human B-lymphocytes, but the cells infected in this way have a short life span.