Epstein-Barr virus RNA. VIII. Viral RNA in permissively infected B95-8 cells

The BHLF1 Locus of Epstein-Barr Virus Contributes to Viral Latency and B-Cell Immortalization

The Epstein-Barr virus (EBV) BHLF1 gene encodes an abundant linear and several circular RNAs believed to perform noncoding functions during virus replication, although an open reading frame (ORF) is retained among an unknown percentage of EBV isolates. Evidence suggests that BHLF1 is also transcribed during latent infection, which prompted us to investigate the contribution of this locus to latency. Analysis of transcripts transiting BHLF1 revealed that its transcription is widespread among B-cell lines supporting the latency I or III program of EBV protein expression and is more complex than originally presumed. EBV-negative Burkitt lymphoma cell lines infected with either wild-type or two different BHLF1 mutant EBVs were initially indistinguishable in supporting latency III. However, cells infected with BHLF1 ^- virus ultimately transitioned to the more restrictive latency I program, whereas cells infected with wild-type virus either sustained latency III or transitioned more slowly to latency I. Upon infection of primary B cells, which require latency III for growth in vitro, both BHLF1 ^- viruses exhibited variably reduced immortalization potential relative to the wild-type virus. Finally, in transfection experiments, efficient protein expression from an intact BHLF1 ORF required the EBV posttranscriptional regulator protein SM, whose expression is limited to the replicative cycle. Thus, one way in which BHLF1 may contribute to latency is through a mechanism, possibly mediated or regulated by a long noncoding RNA, that supports latency III critical for the establishment of EBV latency and lifelong persistence within its host, whereas any retained protein-dependent function of BHLF1 may be restricted to the replication cycle.IMPORTANCE Epstein-Barr virus (EBV) has significant oncogenic potential that is linked to its latent infection of B lymphocytes, during which virus replication is not supported. The establishment of latent infection, which is lifelong and can precede tumor development by years, requires the concerted actions of nearly a dozen EBV proteins and numerous small non-protein-coding RNAs. Elucidating how these EBV products contribute to latency is crucial for understanding EBV's role in specific malignancies and, ultimately, for clinical intervention. Historically, EBV genes that contribute to virus replication have been excluded from consideration of a role in latency, primarily because of the general incompatibility between virus production and cell survival. However, here, we provide evidence that the genetic locus containing one such gene, BHLF1, indeed contributes to key aspects of EBV latency, including its ability to promote the continuous growth of B lymphocytes, thus providing significant new insight into EBV biology and oncogenic potential.

Translational profiling of B cells infected with the Epstein-Barr virus reveals 5' leader ribosome recruitment through upstream open reading frames

The Epstein-Barr virus (EBV) genome encodes several hundred transcripts. We have used ribosome profiling to characterize viral translation in infected cells and map new translation initiation sites. We show here that EBV transcripts are translated with highly variable efficiency, owing to variable transcription and translation rates, variable ribosome recruitment to the leader region and coverage by monosomes versus polysomes. Some transcripts were hardly translated, others mainly carried monosomes, showed ribosome accumulation in leader regions and most likely represent non-coding RNAs. A similar process was visible for a subset of lytic genes including the key transactivators BZLF1 and BRLF1 in cells infected with weakly replicating EBV strains. This suggests that ribosome trapping, particularly in the leader region, represents a new checkpoint for the repression of lytic replication. We could identify 25 upstream open reading frames (uORFs) located upstream of coding transcripts that displayed 5′ leader ribosome trapping, six of which were located in the leader region shared by many latent transcripts. These uORFs repressed viral translation and are likely to play an important role in the regulation of EBV translation.

From Conventional to Next Generation Sequencing of Epstein-Barr Virus Genomes

Genomic sequences of Epstein–Barr virus (EBV) have been of interest because the virus is associated with cancers, such as nasopharyngeal carcinoma, and conditions such as infectious mononucleosis. The progress of whole-genome EBV sequencing has been limited by the inefficiency and cost of the first-generation sequencing technology. With the advancement of next-generation sequencing (NGS) and target enrichment strategies, increasing number of EBV genomes has been published. These genomes were sequenced using different approaches, either with or without EBV DNA enrichment. This review provides an overview of the EBV genomes published to date, and a description of the sequencing technology and bioinformatic analyses employed in generating these sequences. We further explored ways through which the quality of sequencing data can be improved, such as using DNA oligos for capture hybridization, and longer insert size and read length in the sequencing runs. These advances will enable large-scale genomic sequencing of EBV which will facilitate a better understanding of the genetic variations of EBV in different geographic regions and discovery of potentially pathogenic variants in specific diseases.

Genomic diversity of Epstein-Barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples

Undifferentiated nasopharyngeal carcinoma (NPC) has a 100% association with Epstein-Barr virus (EBV). However, only three EBV genomes isolated from NPC patients have been sequenced to date, and the role of EBV genomic variations in the pathogenesis of NPC is unclear. We sought to obtain the sequences of EBV genomes in multiple NPC biopsy specimens in the same geographic location in order to reveal their sequence diversity. Three published EBV (B95-8, C666-1, and HKNPC1) genomes were first resequenced using the sequencing workflow of target enrichment of EBV DNA by hybridization, followed by next-generation sequencing, de novo assembly, and joining of contigs by Sanger sequencing. The sequences of eight NPC biopsy specimen-derived EBV (NPC-EBV) genomes, designated HKNPC2 to HKNPC9, were then determined. They harbored 1,736 variations in total, including 1,601 substitutions, 64 insertions, and 71 deletions, compared to the reference EBV. Furthermore, genes encoding latent, early lytic, and tegument proteins and glycoproteins were found to contain nonsynonymous mutations of potential biological significance. Phylogenetic analysis showed that the HKNPC6 and -7 genomes, which were isolated from tumor biopsy specimens of advanced metastatic NPC cases, were distinct from the other six NPC-EBV genomes, suggesting the presence of at least two parental lineages of EBV among the NPC-EBV genomes. In conclusion, much greater sequence diversity among EBV isolates derived from NPC biopsy specimens is demonstrated on a whole-genome level through a complete sequencing workflow. Large-scale sequencing and comparison of EBV genomes isolated from NPC and normal subjects should be performed to assess whether EBV genomic variations contribute to NPC pathogenesis.

IMPORTANCE

This study established a sequencing workflow from EBV DNA capture and sequencing to de novo assembly and contig joining. We reported eight newly sequenced EBV genomes isolated from primary NPC biopsy specimens and revealed the sequence diversity on a whole-genome level among these EBV isolates. At least two lineages of EBV strains are observed, and recombination among these lineages is inferred. Our study has demonstrated the value of, and provided a platform for, genome sequencing of EBV.

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.

Virus and cell RNAs expressed during Epstein-Barr virus replication

Changes in Epstein-Barr virus (EBV) and cell RNA levels were assayed following immunoglobulin G (IgG) cross-linking-induced replication in latency 1-infected Akata Burkitt B lymphoblasts. EBV replication as assayed by membrane gp350 expression was approximately 5% before IgG cross-linking and increased to more than 50% 48 h after induction. Seventy-two hours after IgG cross-linking, gp350-positive cells excluded propidium iodide as well as gp350-negative cells. EBV RNA levels changed temporally in parallel with previously defined sensitivity to inhibitors of protein or viral DNA synthesis. BZLF1 immediate-early RNA levels doubled by 2 h and reached a peak at 4 h, whereas BMLF1 doubled by 4 h with a peak at 8 h, and BRLF1 doubled by 8 h with peak at 12 h. Early RNAs peaked at 8 to 12 h, and late RNAs peaked at 24 h. Hybridization to intergenic sequences resulted in evidence for new EBV RNAs. Surprisingly, latency III (LTIII) RNAs for LMP1, LMP2, EBNALP, EBNA2, EBNA3A, EBNA3C, and BARTs were detected at 8 to 12 h and reached maxima at 24 to 48 h. EBNA2 and LMP1 were at full LTIII levels by 48 h and localized to gp350-positive cells. Thus, LTIII expression is a characteristic of late EBV replication in both B lymphoblasts and epithelial cells in immune-comprised people (J. Webster-Cyriaque, J. Middeldorp, and N. Raab-Traub, J. Virol. 74:7610-7618, 2000). EBV replication significantly altered levels of 401 Akata cell RNAs, of which 122 RNAs changed twofold or more relative to uninfected Akata cells. Mitogen-activated protein kinase levels were significantly affected. Late expression of LTIII was associated with induction of NF-kappaB responsive genes including IkappaBalpha and A20. The exclusion of propidium, expression of EBV LTIII RNAs and proteins, and up-regulation of specific cell RNAs are indicative of vital cell function late in EBV replication.

Epstein-Barr virus-encoded BILF1 is a constitutively active G protein-coupled receptor

Both beta- and gammaherpesviruses encode G protein-coupled receptors (GPCRs) with unique pharmacological phenotypes and important biological functions. An example is ORF74, the gamma2-herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded GPCR, which is highly constitutively active and considered the key oncogene in Kaposi's sarcoma pathogenesis. In contrast, the current annotation of the Epstein-Barr virus (EBV) genome does not reveal any GPCR homolog encoded by this human oncogenic gamma1-herpesvirus. However, by employing bioinformatics, we recognized that the previously established EBV open reading frame BILF1 indeed encodes a GPCR. Additionally, BILF1 is a member of a new family of related GPCRs exclusively encoded by gamma1-herpesviruses. Expression of hemagglutinin-tagged BILF1 in the HEK293 epithelial cell line revealed that BILF1 is expressed as an approximately 50-kDa glycosylated protein. Immunocytochemistry and confocal microscopy revealed that BILF1 localizes predominantly to the plasma membrane, similar to the localization of KSHV ORF74. Using chimeric G proteins, we found that human and rhesus EBV-encoded BILF1 are highly potent constitutively active receptors, activating Galphai. Furthermore, BILF1 is able to inhibit forskolin-triggered CREB activation via stimulation of endogenous G proteins in a pertussis toxin-sensitive manner, verifying that BILF1 signals constitutively through Galphai. We suggest that EBV may use BILF1 to regulate Galphai-activated pathways during viral lytic replication, thereby affecting disease progression.

Transcription of Epstein-Barr virus latent cycle genes in oral hairy leukoplakia

The hairy leukoplakia lesion (HLP) is a unique example of a permissive infection with Epstein-Barr virus (EBV) in the tongue epithelium. HLP contains abundant replicating viral DNA and may be coinfected with multiple EBV strains. In this study, characterization of viral gene transcription within HLP biopsy specimens revealed that several genes, usually expressed in latently infected lymphocytes, are also transcribed in the HLP lesion. The BamHI W and C promoters, (Wp and Cp) are consistently active in the HLP lesion, resulting in transcription and processing of mRNAs that encode the Epstein-Barr nuclear antigens (EBNAs) EBNA-LP, EBNA1, EBNA2, EBNA3B, and EBNA3C. The EBNA2 protein has been shown to activate expression of the EBV receptor, CD21. In HLP, CD21 transcription is also detected, usually in samples that contain transcripts for EBNA2. Transcripts encoding the LMP1 gene, the LMP2 gene, and rightward transcripts from the BamHI A fragment of the EBV genome are also detected in HLP. These gene products are invariably expressed in latently infected lymphocytes. This pattern of transcription suggests that genes characteristic of latent infection are also expressed in HLP. The activation of Wp and expression of EBNA2 and CD21 may contribute to the unique ability of the HLP lesion to permit superinfection and viral replication of multiple EBV strains.

Interferon-independent and -induced regulation of Epstein-Barr virus EBNA-1 gene transcription in Burkitt lymphoma

Replication of the Epstein-Barr virus (EBV) genome within latently infected cells is dependent on the EBV EBNA-1 protein. The objective of this study was to identify transcriptional regulatory proteins that mediate EBNA-1 expression via the viral promoter Qp, which is active in EBV-associated tumors such as Burkitt lymphoma and nasopharyngeal carcinoma. Results of a yeast one-hybrid screen suggested that a subset of the interferon regulatory factor (IRF) family may regulate EBNA-1 transcription by targeting an essential cis-regulatory element of Qp, QRE-2. Further investigation indicated that the transcriptional activator IRF-1 and the closely related IRF-2, a repressor of interferon-induced gene expression, are both capable of activating Qp. However, the major QRE-2-specific binding activity detected within extracts of Burkitt lymphoma cells was attributed to IRF-2, suggesting that interferon-independent activation of Qp is largely mediated by IRF-2 in these cells. We observed no effect of gamma interferon on Qp activity in transfection assays, whereas we observed a moderate but significant repression of Qp activity in response to alpha interferon, possibly mediated by either the interferon consensus sequence binding protein or IRF-7, a novel alpha interferon-inducible factor identified in this study. Since expression of IRF-1 and IRF-2 is increased in response to interferons, the Qp activity observed in the presence of interferon likely represented an equilibrium between IRF factors that activate and those that repress gene expression in response to interferon. Thus, by usurping both IRF-1 and its transcriptional antagonist IRF-2 to activate Qp, EBV has evolved not only a mechanism to constitutively express EBNA-1 but also one which may sustain EBNA-1 expression in the face of the antiviral effects of interferon.

Control of virus-induced lymphoproliferation: Epstein-Barr virus-induced lymphoproliferation and host immunity

Epstein-Barr virus (EBV) is a latent herpesvirus that is associated with a number of tumors. EBV-infected cells show three patterns of latency ranging from type 1, where only one EBV-encoded antigen is expressed, to type 3, where all nine latent cycle proteins encoded by EBV are expressed. Malignancies exhibiting the type 3 latency pattern are highly immunogenic and occur only in immunocompromised patients. It has recently been shown that adoptive immunotherapy with EBV-specific cytotoxic T lymphocytes is an effective therapy for such tumors. Immunotherapy strategies and approaches to increase tumor immunogenicity are now being evaluated in tumors expressing type 2 latency.

The Epstein-Barr virus gene BHRF1, a homologue of the cellular oncogene Bcl-2, inhibits apoptosis induced by gamma radiation and chemotherapeutic drugs

Analysis of apoptosis, active and controllable cell death, has demonstrated that the size of a cell population can be regulated by changes in the cell death rate as well as in the rates of proliferation and differentiation. Factors which alter the rate of cell death, such as expression of the proto-oncogene bcl-2, can therefore directly affect the number of cells within a population. Bcl-2 has been shown to suppress apoptosis in response to a variety of stimuli and to act as a complementary survival signal for the random acquisition of other oncogenic mutations, such as deregulated c-myc. The Epstein Barr virus (EBV) gene BHRF1 was the first of a family of bcl-2 homologues now being identified. BHRF1 and bcl-2 share 25% primary amino acid sequence homology. Here we show that gamma radiation and several cytotoxic anticancer agents induce apoptosis in Burkitt's lymphoma (BL) cell lines, as has been found in several other systems. Using gene transfection studies we have also shown that expression of either BHRF1 or bcl-2 in BL cell lines significantly suppresses apoptosis in response to a variety of anticancer treatment. This has confirmed that BHRF1 is functionally homologous to bcl-2 in B-cells and suggests that BHRF1 may act to prevent apoptosis during EBV infection, maximising virus particle production, as has been suggested for other human and insect viral genes. Suppression of chemotherapeutic drug induced cell death by bcl-2 and BHRF1 as demonstrated in this cell system, results in resistance to a variety of different agents and may represent an alternative mechanism by which multidrug resistance arises during chemotherapy.

5' Coding and regulatory region sequence divergence with conserved function of the Epstein-Barr virus LMP2A homolog in herpesvirus papio

B-lymphotropic herpesviruses naturally infecting Old World primates share biologic, epidemiologic, pathogenic, and molecular features with the human pathogen Epstein-Barr virus (EBV). These related gammaherpesviruses have colinear genomes with considerable nucleotide homology. The replicative cycle genes share a high degree of homology across species, whereas the transformation-associated EBV latent genes appear to be much more divergent. For example, the EBV BamHI Nhet fragment, which encodes all or part of the EBV latent infection membrane proteins, cross-hybridizes poorly to DNA from nonhuman primate B-lymphotropic herpesviruses. A viral DNA fragment corresponding to this region of the EBV genome was isolated from the baboon B-lymphotropic herpesvirus, herpesvirus papio, and used to clone a herpesvirus papio cDNA corresponding to EBV LMP2A. At least three tyrosine kinase interaction motifs are conserved despite significant amino acid divergence of the herpesvirus papio LMP2A first exon from the EBV homolog. Functionally, the herpesvirus papio LMP2A is tyrosine phosphorylated and induces tyrosine phosphorylation of cell proteins similar to EBV LMP2A. The 12 hydrophobic LMP2 transmembrane domains are well conserved. Two CBP (Jk) binding sites important for EBNA-2-induced transactivation of the LMP2A promoter are also present in the herpesvirus papio LMP2A promoter, and the simian LMP2A promoter is also responsive to EBV EBNA-2-induced transactivation in human B cells. Thus, transcriptional regulation, splicing, kinase interaction sites, and tyrosine phosphorylation of the LMP2A homologs have been conserved despite significant sequences heterogeneity in the preterminal repeat regions of these human and nonhuman primate EBVs. The conservation of the LMP2 gene, despite its apparent nonessential role for in vitro EBV infection, suggests an important role for LMP2A in vivo. The similarities between these human and simian B-lymphotropic herpesviruses, and the LMP2 genes in particular, suggest that the function of LMP2 in vivo could be addressed by using recombinant LMP2A-mutant simian viruses and experimental infection of Old World primates.

Characterization of the Epstein-Barr virus Fp promoter

Expression of the Epstein-Barr virus nuclear antigen-1 (EBNA-1) protein is mediated by the virus Fp promoter in Burkitt lymphoma and nasopharyngeal carcinoma. This promoter is silent in latently infected B lymphoblastoid and most Burkitt lymphoma-derived cell lines in vitro, which utilize separate promoters approximately 50 kb upstream of Fp to express EBNA proteins. Fp-mediated activation of EBNA-1 expression is also activated upon induction of the virus replication cycle. We previously demonstrated that activation of Fp in Burkitt cells requires cis-regulatory elements downstream of the site of transcription initiation. We have now mapped two positive regulatory elements within the Fp promoter. One element contains two potential binding sites for the cellular transcription factor LBP-1 between +138 and +150. A second regulatory element was mapped between +177 and +192 and can be specifically bound in vitro by protein from nuclear extracts of Burkitt cells. Although this element overlaps two partial E2F binding sites and Fp reporter plasmids could be activated in trans by the adenovirus E1A protein in cotransfection experiments, mutational analysis and DNA binding studies suggest that these are unlikely to be functional E2F response elements within Fp. We also demonstrate that Fp-directed transcription initiates at multiple sites within both the genome and the Fp reporter plasmids. However, the principal site of transcription initiation within the genome is not utilized within reporter plasmids, in which the majority of transcripts initiate at multiple sites between +150 and +200. This finding suggests that additional elements may be necessary for Fp to function normally in these assays or that the context of Fp within the viral genome is critical to its regulation.

The lytic origin of herpesvirus papio is highly homologous to Epstein-Barr virus ori-Lyt: evolutionary conservation of transcriptional activation and replication signals

Herpesvirus papio (HVP) is a B-lymphotropic baboon virus with an estimated 40% homology to Epstein-Barr virus (EBV). We have cloned and sequenced ori-Lyt of herpesvirus papio and found a striking degree of nucleotide homology (89%) with ori-Lyt of EBV. Transcriptional elements form an integral part of EBV ori-Lyt. The promoter and enhancer domains of EBV ori-Lyt are conserved in herpesvirus papio. The EBV ori-Lyt promoter contains four binding sites for the EBV lytic cycle transactivator Zta, and the enhancer includes one Zta and two Rta response elements. All five of the Zta response elements and one of the Rta motifs are conserved in HVP ori-Lyt, and the HVP DS-L leftward promoter and the enhancer were activated in transient transfection assays by the EBV Zta and Rta transactivators. The EBV ori-Lyt enhancer contains a palindromic sequence, GGTCAGCTGACC, centered on a PvuII restriction site. This sequence, with a single base change, is also present in the HVP ori-Lyt enhancer. DNase I footprinting demonstrated that the PvuII sequence was bound by a protein present in a Raji nuclear extract. Mobility shift and competition assays using oligonucleotide probes identified this sequence as a binding site for the cellular transcription factor MLTF. Mutagenesis of the binding site indicated that MLTF contributes significantly to the constitutive activity of the ori-Lyt enhancer. The high degree of conservation of cis-acting signal sequences in HVP ori-Lyt was further emphasized by the finding that an HVP ori-Lyt-containing plasmid was replicated in Vero cells by a set of cotransfected EBV replication genes. The central domain of EBV ori-Lyt contains two related AT-rich palindromes, one of which is partially duplicated in the HVP sequence. The AT-rich palindromes are functionally important cis-acting motifs. Deletion of these palindromes severely diminished replication of an ori-Lyt target plasmid.

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.

Expression of the Epstein-Barr virus BamHI A fragment in nasopharyngeal carcinoma: evidence for a viral protein expressed in vivo

A family of mRNAs that are transcribed rightward through the BamHI A fragment have been detected in C15, a nasopharyngeal carcinoma (NPC) which has been passaged in nude mice. Northern (RNA) blot hybridizations indicate that these RNAs are also expressed in three other NPCs which have been established in nude mice and in an NPC obtained at biopsy. Moreover, hybridization in situ detected transcription from BamHI A in 12 NPCs and 1 Epstein-Barr virus (EBV)-containing carcinoma of the parotid gland. In each case, transcription was detected in all of the malignant epithelial cells. Transcription was not detected in two cases of EBV-positive lymphoma biopsies by in situ hybridization nor in latently infected EBV-positive lymphoblastoid cell lines by Northern blot hybridization. The consistent transcription of these sequences in latently infected epithelial malignancy but not in lymphoid cells suggests that this viral function is associated with latent EBV infection of epithelial cells. Sequence analysis of a cDNA synthesized from the C15 tumor, representing the 3' end of BamHI A messenger RNA, revealed an open reading frame (ORF). Translation of this ORF in vitro produced several peptides that were immunoprecipitated with antisera from patients with NPC. The detection of antibodies to the protein encoded by the ORF present in the BamHI A cDNA indicates that BamHI A encodes a protein which is expressed in vivo and is antigenic.

BHRF1, the Epstein-Barr virus gene with homology to Bc12, is dispensable for B-lymphocyte transformation and virus replication

The Epstein-Barr virus (EBV) BHRF1 open reading frame is abundantly expressed early in the lytic replication cycle. BHRF1 is also transiently expressed in some latently infected cell lines in the absence of expression of other lytic cycle proteins. BHRF1 shares distant, but significant, colinear primary amino acid sequence homology to Bc12, a cellular gene strongly implicated in the evolution of follicular lymphoma. The experiments reported here used a molecular genetic approach to examine the role of BHRF1 in EBV infection. Isogenic EBV recombinants having either wild-type BHRF1 or a null mutation due to a translational stop signal in place of the 24th BHRF1 codon were used to infect primary B lymphocytes. The BHRF1 mutant recombinants did not differ from the wild type in their ability to infect and transform the growth of primary B lymphocytes, to replicate in the resultant lymphoblastoid cell lines, or to initiate a second round of primary cell transformation. Deletion of the entire BHRF1 open reading frame did not destroy the ability of the mutant virus to maintain cell growth transformation. The significance of these findings with regard to the role of BHRF1 in EBV infection is discussed.

Analysis of the HSV-1 strain 17 DNA polymerase gene reveals the expression of four different classes of pol transcripts

We have investigated the structure and the expression of transcripts of the HSV-1 strain 17 DNA polymerase gene (pol) by various mapping methods including cDNA cloning. The majority of mature pol transcripts is strictly colinear with the pol gene. But additionally, pol cDNAs show a defined heterogeneity in respect to their 5'-terminal regions and can be divided into four classes with characteristic differences; (i) class 1 represents the major transcript (pol-R1) with initiation at HSV-1 positions 62,605-62,610, (ii) class 2 initiates about 70 bp downstream, (iii) class 3 is generated by splicing the short open reading frame (SORF) to a 5'-truncated part of the long open reading frame (LORF) which results in a partially different coding potential, and (iv) class 4 starts 120 bp upstream of the major initiation site in the central part of the origin of replication (oriL). S1 and Exo VII nuclease and RNase protection assays as well as primer extension analyses confirm the classification regarding the genuine structure of pol mRNAs and the differential usage of transcriptional start sites. Furthermore, the transcript classes can be distinguished from each other by their kinetics of appearance/disappearance in the cytoplasm: The first transcription of the pol gene is indicated by the predominant presence of class 2 and class 4 mRNAs at 2 hr postinfection (h.p.i.), followed by an increase of class 1 transcripts up to 4 h.p.i. and a parallel decrease of class 2 mRNAs. These data suggest that expression of the pol gene is finely regulated already at the transcriptional and/or posttranscriptional level prior to the translation of pol mRNAs.

Restricted Epstein-Barr virus protein expression in Burkitt lymphoma is due to a different Epstein-Barr nuclear antigen 1 transcriptional initiation site

Epstein-Barr virus (EBV) expresses six nuclear antigens (EBNAs) and three integral latent membrane proteins (LMPs) in latently infected growth-transformed B lymphoblastoid cell lines (LCLs). In contrast, EBV protein expression in Burkitt lymphoma tissue or in newly established Burkitt lymphoma cell lines is frequently restricted to the EBV genome maintenance protein, EBNA-1. EBNA-1 expression in the absence of other EBNAs and LMP-1 has been an enigma since, in LCLs, all EBNA mRNAs are processed from a single transcript. We now show that the basis for restricted EBV expression in Burkitt lymphoma cells is selective EBNA-1 mRNA transcription from a hitherto unrecognized promoter that is 50 kb closer to the EBNA-1-encoding exon than previously described EBNA-1 promoters. Infected cells with EBNA-1-restricted expression could preferentially persist in vivo in the face of EBV-immune T-cell responses, which are frequently directed against other EBNAs and are also dependent on LMP-1 expression.

Epstein-Barr virus small nuclear RNAs are not expressed in permissively infected cells in AIDS-associated leukoplakia

Epstein-Barr virus (EBV) DNA structure and gene expression were analyzed in tissue specimens from oral hairy leukoplakia (HLP), a mucocutaneous lesion that develops in patients infected with human immunodeficiency virus (HIV). The structure of the terminal restriction enzyme fragments of EBV revealed that HLP is a permissive infection without a predominant, detectable population of EBV episomal DNA. In RNA preparations from this uniquely permissive infection, EBV replicative mRNAs could be identified by Northern analysis; however, the virally encoded small nuclear RNAs, the EBERs, were not detected in most HLP RNA preparations. In situ hybridization detected EBER expression in very rare cells. These data indicate that unlike other viral small nuclear RNAs, the EBERs are not expressed during viral replication and must participate in the complex maintenance of latent EBV infection.

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.

A second Epstein-Barr virus membrane protein (LMP2) is expressed in latent infection and colocalizes with LMP1

Recent cDNA cloning and sequencing of two Epstein-Barr virus (EBV)-specific mRNAs from latently infected cultures revealed that these RNAs are encoded across the fused terminal repeats of the viral genome and that they are likely to encode two nearly identical proteins with the same transmembrane domains. The smaller predicted protein (LMP2B) lacks 119 amino-terminal amino acids found in the larger one (LMP2A). To test whether these proteins are expressed in latently infected lymphocytes, antibodies to the LMP2 proteins were derived by immunizing rabbits with TrpE-LMP2A fusion proteins. Affinity-purified LMP2-specific antibodies recognized 54- and 40-kilodalton proteins, corresponding to LMP2A and LMP2B, in immunoblots of rodent fibroblasts stably transfected with eucaryotic expression plasmids containing either the LMP2A or LMP2B cDNA. Similar-size proteins were also identified in immunoblots of latently infected lymphocytes. LMP2A localized to membranes in cellular fractionation studies. In immunofluorescent studies, LMP2 localized in the plasma membrane of EBV-infected lymphocytes, with the majority of reactivity confined to the region of the LMP1 patch. This reactivity was detected in almost all lymphoblastoid cells latently infected with EBV.

Transcription of the Epstein-Barr virus genome during latency in growth-transformed lymphocytes

Nuclear run-on assays revealed extensive transcription of the Epstein-Barr virus genome during latent infection in in vitro-infected human fetal lymphoblastoid cells (IB-4). The EBER genes were the most heavily transcribed viral genes in these cells. Their transcription was partially inhibited in the presence of 1 microgram of alpha-amanitin per ml and fully inhibited at 100 micrograms/ml, consistent with RNA polymerase III transcription. All other transcription was inhibited at 1 microgram of alpha-amanitin per ml, consistent with RNA polymerase II sensitivity to alpha-amanitin. Other than EBER transcription, almost no transcription occurred from the U1 region. Specifically, no transcription was detected from the U1 latent promoter. RNA polymerase II transcription was highest in IR1, extending rightward through U2 and IR2 into the U3 domain and gradually decreased, but was measurable throughout the rest of the genome. This is consistent with EBNA gene transcription initiation within IR1. The higher level of transcription of the IR1 and U2 domains, which encode EBNA-LP and EBNA-2, as opposed to the domains which encode EBNA-3A, EBNA-3B, or EBNA-3C or EBNA-1, correlated with a higher level of EBNA-LP/EBNA-2 mRNA. Transcription extended through U4 into U5, even though no known latent-gene mRNAs are expressed from U4 downstream of the EBNA-1 open reading frame. This may result from inefficient termination of EBNA gene transcription. Leftward transcription from the latent membrane protein promoter was lower than EBNA transcription, although the latent membrane protein mRNA was the most abundant of the latent-gene mRNAs, indicating that this mRNA is more efficiently processed or has a longer half-life. Although transcription was detected from the DL strong early promoters and to a lesser extent from other early promoters, early mRNAs were less abundant than EBNA mRNAs or undetectable, suggesting that there may be posttranscriptional as well as transcriptional control over early mRNA expression in these latently infected cells.

Levels of Epstein-Barr virus DNA in lymphoblastoid cell lines are correlated with frequencies of spontaneous lytic growth but not with levels of expression of EBNA-1, EBNA-2, or latent membrane protein

The process of Epstein-Barr virus (EBV)-induced transformation of human B lymphocytes results in a cell line that is a mixture of latently and lytically infected cells, with the lytic cells composing roughly 5% to less than 0.0001% of the overall population. A set of nine normal lymphoblastoid cell lines that span a 100- to 200-fold range in average EBV DNA content were studied, and the frequency with which these cells entered a lytic phase of viral growth correlated with their EBV DNA copy number (as a population average). However, neither factor correlated with the levels of expression of transcript for the viral genes EBNA-1, EBNA-2, and latent membrane protein, nor did they correlate with the levels of EBNA-2 protein and latent membrane protein. The rate at which a cell line enters into lytic growth spontaneously is therefore not dependent on the overall steady-state levels of expression of these latent-phase genes.

Detection of Epstein-Barr virus by in situ hybridization. Progress toward development of a nonisotopic diagnostic test

This work presents some initial quantitation of an in situ hybridization method for detection of Epstein-Barr (EB) virus nucleic acids. The purpose is to develop evaluative criteria for diagnosis of viral presence in clinical tissue specimens. In this work simultaneous denaturation of probe and target DNA and an alkaline phosphatase conjugate to detect biotinated probe were used as described by Unger et al. For evaluation of the hybridization, a variety of cell lines, both productively and latently infected, that were hybridized in situ using nick translated 32P-labeled viral probe sequences and counted by scintillation after the method of Lawrence and Singer were used. Producer cells (B95-8) showed intense foci of staining in approximately 5% of cells, with most of the other cells showing varying staining intensity. Raji cells showed varying amounts of signal from cell to cell. Namalwa cells exhibited one spot in most cells that was decreased after cells were treated with Actinomycin D (dactinomycin, Merck Sharp & Dohme, West Point, PA). Signal was identified in only a third of these same cells after sectioning. EB virus-negative Ramos cells showed no signal. The nuclear punctate nature of the signal generated is diagnostic of infected cells, and may be a useful test for cultured cells or pathologic specimens.

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.

Two families of sequences in the small RNA-encoding region of Epstein-Barr virus (EBV) correlate with EBV types A and B

DNA sequence analysis was carried out on the 1-kilobase SacI-EcoRI region of the EcoRI J fragment of four strains of Epstein-Barr virus (EBV) (MABA, P3HR-1, FF41, and NPC-5), and the sequences were compared with the prototype sequence from strain B95-8. Ten single-base changes which grouped the strains into two families (1 and 2) were found. Restriction endonuclease polymorphisms predicted from the sequences were used to classify the EBV DNA from a further 26 EBV-positive cell lines into these two families. The EBNA-2 types (A or B) of the strains were found to correlate with the J region type; EBNA-2 type A DNA regularly contained J region sequence type 1, while EBNA-2 type B DNA generally carried J region sequence type 2. These data are consistent with the notion of there being two distinct families of EBV with discrete, conserved differences in DNA sequence.

Two related Epstein-Barr virus membrane proteins are encoded by separate genes

The structures of the 2.3- and 2.0-kilobase Epstein-Barr virus (EBV) mRNAs, partially encoded within the EcoRI J fragment DNA of the viral genome, were determined by analysis of their cDNAs. Both mRNAs are transcribed across the fused terminal repeats of the EBV episome and consist of nine exons. The mRNAs are transcribed from different promoters and have a unique 5' exon from the U5 region of the genome but eight common exons from the U1 region. One principal open reading frame is present in each mRNA and is predicted to encode 54,000- and 40,000-dalton integral membrane proteins. This result was confirmed by in vitro translation of RNAs in the presence of canine pancreatic microsomes. The 2.3-kilobase mRNA is not expressed in Raji cells, owing to the deletion of the 5' regulatory and coding region of this gene, whereas neither mRNA is expressed in Namalwa cells, owing to inactivation as a result of integration of the EBV genome via the terminal repeats. Since these mRNAs are readily detected in largely latently infected cells and do not increase in abundance with EBV replication, these putative latent-infection membrane proteins are tentatively designated LMP-2A and LMP-2B, respectively.

Synchronous and sequential activation of latently infected Epstein-Barr virus genomes

A lymphoid cell system was established that can induce the prompt and synchronous activation of latent Epstein-Barr virus (EBV) genomes and thus allows the identification of viral genes that are activated sequentially depending on their functions. With this system, we proved that disruption of EBV latency is initiated by activation of four EBV genes and that protein synthesis is not required prior to activation of latent EBV. The system should be an in vitro model for studying the mechanism of herpesvirus latency.

Genome rearrangements activate the Epstein-Barr virus gene whose product disrupts latency

A defective Epstein-Barr virus (EBV) containing a deleted and rearranged genome (het DNA) causes latent EBV to replicate. This activity maps to the 2.7-kilobase-pair WZhet fragment. The BZLF1 open reading frame, present within WZhet as well as in the standard viral BamHI Z fragment, encodes the protein ZEBRA, which induces viral replication. Using gene transfers into Burkitt lymphoma cells, we now demonstrate that rearranged sequences juxtaposed to BZLF1 in het DNA facilitate expression of ZEBRA protein. Two stretches of EBV sequences within a palindromic region of het DNA contain positive regulatory elements. One set, derived from the viral large internal repeat, is newly positioned upstream of BZLF1; the second set is downstream of BZLF1 in het DNA. The capacity of defective HR-1 viruses to disrupt latency of the standard EBV genome is due to abnormal regulation of the BZLF1 gene as a result of genomic rearrangements.

A new Epstein-Barr virus transactivator, R, induces expression of a cytoplasmic early antigen

Several Epstein-Barr virus (EBV) early promoters respond to a new EBV transactivator encoded by BRLF1, designated R. Transactivation was measured in chloramphenicol acetyltransferase assays on Raji, BHK, and Vero cells that were cotransfected with the transactivator and target promoters linked to the cat gene. The divergent promoter of BamHI-H was particularly responsive to R transactivation. This large promoter region consists of a leftward TATA box for the NotI repeat gene (BHLF1) and a probable rightward TATA box for the EA-R gene (BHRF1) separated by 940 base pairs of unusual sequence complexity. Sequences within this divergent promoter region appear to confer inducibility by EBV transactivators R and Z (BZLF1). The Z transactivator stimulated expression in both the leftward and rightward directions, and R stimulated expression primarily in the rightward direction, but the MS transactivator (BMLF1) had no activity in either direction. The adenovirus E3 promoter also responded to the R transactivator, but several other herpesvirus and human promoters were nonresponsive. When the divergent promoter was linked to the EA-R gene as it is in the EBV genome, the R and Z transactivators also induced the expression of EA-R in cotransfected cells. This cytoplasmic early antigen is encoded by BHRF1 and may be anchored in intracellular membranes by a carboxy-terminal transmembrane region.

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.

Identification of the Epstein-Barr virus gp85 gene

The Epstein-Barr virus glycoprotein gp85 has been mapped to the Epstein-Barr virus DNA open reading frame BXLF2 (R. Baer, A. Bankier, M. Biggin, P. Deininger, P. Farrell, T. Gibson, G. Hatfull, G. Hudson, S. Stachwell, C. Sequin, P. Tufnell, and B. Barrell, Nature [London] 310:207-211, 1984). A gp85-specific monoclonal antibody reacts with the BXLF2 in vitro transcription-translation product. The monoclonal antibody also precipitates an 85-kilodalton protein from rodent cells transfected with the BXLF2 open reading frame DNA. In these cells, gp85 localizes to the cytoplasm and nuclear rim rather than to the plasma membrane as in lymphocytes. Northern (RNA) blot hybridization and analysis of a cDNA clone containing BXLF2 indicate that gp85 is translated from an unspliced, late, 2.5-kilobase transcript. Similarities between the predicted amino acid sequences of gp85 and herpes simplex virus gH (D. McGeoch and A. Davison, Nucleic Acids Res. 14:4281-4292, 1986) are noted.

Epstein-Barr virus gene expression in P3HR1-superinfected Raji cells

The pattern of Epstein-Barr virus (EBV) RNAs expressed in Raji cells superinfected with P3HR1 EBV was examined. RNAs whose expression was of an immediate-early type (resistant to treatment of the cells with anisomycin) were identified. These RNAs, encoding the EBV reading frames BZLF1 and BRLF1, were probably expressed from defective virus within the P3HR1 preparation, and some of them were responsible for the induction of the EBV productive cycle in the Raji cells. The structures of the B95-8 RNAs equivalent to the anisomycin-resistant RNAs were determined. The RNA encoding the BZLF1 reading frame contained two splices which extended and modified the reading frame from that previously described.

Identification of an Epstein-Barr virus early gene encoding a second component of the restricted early antigen complex

When the latent Epstein-Barr virus (EBV) genome in B95-8 cells is induced into a replicative phase, two abundant early RNAs are transcribed rightward from the EBV BamHI H DNA fragment into BamHI F. Analysis of cDNA clones prepared from the RNA of cells replicating EBV revealed that both RNAs contain the BHRF1 open reading frame. Part of BHRF1, cloned into a prokaryotic fusion protein expression vector, expressed a fusion protein in Escherichia coli and the purified fusion protein was used to generate a monoclonal antibody against BHRF1. This antibody was then employed to characterize the protein encoded by BHRF1 in cells replicating EBV. The monoclonal antibody reacted with a 17-kDa protein component of the restricted early antigen (EA) complex. The distribution of the protein in cells was similar to that noted when sera from patients with African Burkitt's lymphoma were used to stain these cells. The protein was synthesized before the major 47-56 kDa protein associated with the diffuse component of EA in superinfected Raji cells. All human sera containing antibodies to EA as determined by immunofluorescence (IF) reacted with the protein as did some sera determined to be anti-VCA positive and anti-EA negative by IF. The predicted amino acid sequence of the protein has characteristics which suggest that it is a membrane protein. It also has significant homology with both the anchor region of polyoma middle T antigen and with the predicted protein product of the bcl-2 mRNA activated by the 14/18 chromosome translocation characteristic of follicular lymphomas. This latter homology is extensive and colinear, suggesting common evolution and function. However, neither a mRNA which could efficiently translate the BHRF1 protein nor the BHRF1 protein could be detected in latently infected cells. Thus, the bcl-2 predicted protein is similar to an EBV protein synthesized in the early phase of virus infection.

Isolation and characterization of cDNA clones corresponding to transcripts from the BamHI H and F regions of the Epstein-Barr virus genome

The Epstein-Barr virus (EBV) mutant P3HR1 is incapable of immortalizing B lymphocytes because of a 6.8-kilobase deletion in the BamHI W, Y, and H regions of the viral genome (M. Rabson, L. Gradoville, L. Heston, and G. Miller, J. Virol. 44:834-844, 1982). To characterize transcripts that are encoded in this region, poly(A)+ RNA from the EBV-transformed lymphoblastoid cell line JY was isolated, and this RNA was used to generate a cDNA library in lambda gt10. By screening 500,000 recombinant bacteriophages with the BamHI H fragment, we isolated 10 cDNA clones and characterized them in detail. One group of six cDNA clones was derived from a 2.9-kilobase early transcript encoded by the IR2 repeat element and showed restriction site polymorphism for the enzyme SmaI. The second group consisted of four cDNA clones, all of which contained the BamHI-H right reading frame (BHRF1), and used the polyadenylation signal at base pair 662 in the BamHI F fragment. Computer analysis of the hydrophobicity of the BHRF1 protein revealed that it is likely to be a membrane protein. Northern blotting experiments with RNA from an EBV producer line, B95-8, and a tightly latent lymphoblastoid B-cell line, IB4, revealed that BHRF1 is contained in at least two different mRNA species which can be detected during the latent cycle of EBV. These data and the recent characterization of a spliced transcript (containing five exons in common with other known latent messages [M. Bodescot and M. Perricaudet, Nucleic Acids Res. 14:7103-7113, 1986]) suggest that alternative splicing is used to generate transcripts containing BHRF1, as for the EBV nuclear antigen 1 transcripts. Furthermore, the observation that a potential oncogene activated in human follicular lymphomas is homologous to the BHRF1-encoded polypeptide (M. L. Cleary, S.D. Smith, and J. Sklar, Cell 47:19-28, 1986) suggests a possible role for this putative viral protein in EBV-induced growth transformation of B lymphocytes.

Human neonatal lymphocytes immortalized after microinjection of Epstein-Barr virus DNA

Epstein-Barr virus (EBV) is a highly efficient acute transforming agent in human cells, provided that the intact virus is used. To investigate the ability of viral DNA alone to transform cells, we introduced the EBV genome into human lymphocytes. After microinjection of EBV DNA into neonatal B lymphocytes, we established a cell line that in early passages contained multiple viral fragments. This cell line retained sequences from the short, unique (Us) region of the EBV genome and sequences from EcoRI-E. The viral sequences were not expressed; however, the cells expressed a 2.3-kilobase polyadenylated message homologous to the c-fgr oncogene, a cellular locus believed to be activated by EBV infection [M. S. C. Cheah, T. J. Ley, S. R. Tronick, and K. C. Robbins, Nature (London) 319:238-240.]. The cell line was monoclonal with rearrangement at the immunoglobulin locus and had a reciprocal translocation t(1;7)(p34;q34) and a deletion of sequences within the locus for the beta chain of the T-cell receptor. The close proximity of the translocation to the chromosomal loci for c-fgr on chromosome 1 and the T-cell receptor beta chain on chromosome 7 suggests that structural alteration of these genes was critical to this transformation event.

Expression and secretion in yeast of a 400-kDa envelope glycoprotein derived from Epstein-Barr virus

The major envelope glycoprotein (gp350) of Epstein-Barr virus has been expressed and secreted in the yeast Saccharomyces cerevisiae as a 400-kDa glycoprotein. This is the first example of the secretion of such a large, heavily glycosylated heterologous protein in yeast. Since gp350 proved highly toxic to S. cerevisiae, initial cellular growth required repression of the expression of gp350. Using temperature- or galactose-inducible promoters, cells could be grown and the expression of gp350 then induced. After induction, the glycoprotein accumulated both intracellularly as well as in the culture medium. Only the most heavily glycosylated form was secreted, suggesting a role for N-linked glycans in directing secretion. The extent of O-linked glycosylation of the yeast-derived protein was similar to that of the mature viral gp350. N-linked glycosylation varied slightly depending upon culture conditions and host strain used and was more extensive than that associated with the mature viral gp350. Although there is no evidence that more than a single mRNA for the glycoprotein was expressed from the recombinant plasmid, variously sized glycoproteins accumulated in yeast at early stages after induction, probably reflecting intermediates in glycosylation. The yeast-derived glycoproteins reacted with animal and human polyclonal antibodies to gp350 as well as with a neutralizing murine monoclonal antibody to gp350, suggesting that this glycoprotein retains several epitopes of the native glycoprotein.

The structure of the termini of the Epstein-Barr virus as a marker of clonal cellular proliferation

The linear virion form of Epstein-Barr virus (EBV) DNA has variable numbers of direct tandem 500 bp repeats at each terminus. The terminal restriction endonuclease fragments and the fused terminal fragments in the intracellular episomal form are heterogeneous in size, and vary by increments of 500 bp. The structure of the termini of EBV in carcinomas of the nasopharynx and the parotid gland was compared with the EBV termini in monoclonal and polyclonal tissues or cell lines. A single band representing the EBV joined termini was detected in each of the carcinomas and in the monoclonal lymphoid proliferations. Polyclonal cell lines contained multiple forms of the joined termini. The detection of a homogeneous episomal population suggests that EBV-associated epithelial malignancies are clonal expansions of a single EBV-infected progenitor cell.

Definitive identification of a member of the Epstein-Barr virus nuclear protein 3 family

Some Epstein-Barr virus (EBV) immune human antisera are known to react with a 142-kDa protein, EBV-encoded nuclear antigen 3 (EBNA3), which, like EBNA1 and EBNA2, is likely to be involved in the establishment of latent infection or growth transformation. We have now constructed gene fusions between Escherichia coli lacZ and an EBV DNA open reading frame (BERF1; BamHI E fragment rightward open reading frame 1), which is transcribed into an mRNA in latently infected cells. Purified hybrid protein from one of these constructs, chosen because of its reactivity with EBNA3-positive human antisera, was used to affinity purify the specific antibody from human antiserum. This specific antibody was used to prove that EBNA3 is encoded, at least in part, by BERF1, and that EBNA3 is in the nucleus of each latently infected cell. In rodent cells, BERF1 encodes a 120- to 130-kDa protein, which translocates to the nucleus and is recognized by EBNA3-positive human antisera. Two other proteins similar in size to EBNA3 are detected in latently infected cells by EBV immune human antisera. Two EBV open reading frames related to BERF1 may encode these proteins.

Coding content and expression of the EBV B95-8 genome in the region from base 62,248 to base 82,920

The DNA sequence of a 20,672-base region of the EBV B95-8 genome from the BamHI site separating fragments BamHI-F and BamHI-Q to the EcoRI site separating fragments EcoRI-G2 and EcoR1-F has been determined. S1 mapping and northern blotting with probes from M13 recombinants have been used to search for RNAs from this region. Five mRNAs have been identified and correlated with five open reading frames in the DNA sequence. Two of these open reading frames encode ribonucleotide reductase subunits. A further two open reading frames are present including one for a predicted protein of 340 kDa for which no transcript has yet been detected.

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.

The short unique region of the B95-8 Epstein-Barr virus genome

The 12-kbp short unique region of the B95-8 Epstein-Barr virus (EBV) genome has been sequenced and analysed for latent and lytic cycle transcripts. Two latent and three late mRNAs have been detected, the largest of the late transcripts potentially encoding a 143-kDa protein. The region containing oriP, the putative origin of replication of the genome as a plasmid in latently infected B lymphocytes, is shown to contain 21 direct repeats of a 30-bp A+T-rich sequence and a related large inverted repeat.

The BamHI F region of the B95-8 Epstein-Barr virus genome

The BamHI F region of the B95-8 Epstein-Barr virus (EBV) genome has been sequenced and analysed for transcription signals and open reading frames. S1 mapping and northern blotting with probes from M13 recombinants have been used to search for mRNAs. Four rightward-reading frames encoding basic proteins appear to be expressed by 3'-coterminal early mRNAs. Two leftward-reading frames appear to be expressed by 3'-coterminal early mRNAs.

Transformation by Epstein-Barr virus requires DNA sequences in the region of BamHI fragments Y and H

Eight independent recombinant Epstein-Barr virus genomes, each of which was a transforming strain, were made by superinfecting cell lines containing Epstein-Barr virus DNA (Raji or B95-8 strain) with a nontransforming virus (P3HR1 strain). A knowledge of the constitution of each transforming recombinant allowed the localization of the defect in the genome of the nontransforming parent to a 12-megadalton sequence within the EcoRI A fragment. Within this region, the nontransforming virus has a deletion of the BamHI Y fragment and about half of the sequences in the adjacent BamHI H fragment. The present data suggest that this deletion is responsible for the nontransforming phenotype. Furthermore, mapping a deletion in one of the recombinant genomes allowed the conclusion that a sequence (comprising about 20% of the Epstein-Barr virus genome) from the center of BamHI-D to BamHI-I' is not necessary for the maintenance of transformation by Epstein-Barr virus.

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.

Construction and use of cDNA clones for the mapping and identification of Epstein-Barr virus early P3HR-1 mRNAs

cDNA clones, specific for early Epstein-Barr virus (EBV) RNAs, were constructed from total cytoplasmic RNA of P3HR-1 TK- cells. From 10,000 cDNA clones screened, 22 virus-specific cDNA clones were selected by hybridization with a total EBV DNA. These clones were then precisely mapped on the EBV genome and the corresponding mRNAs were identified by Northern blot hybridizations. Most of them are clearly related to some of the open reading frames described by Baer et al. (Nature [London] 310:207-211, 1984). They represent at least 18 different genes active during the early viral cycle. The transcriptional activity of the virus during the early stage was also studied by dot blot hybridization of total early cDNA probe to EBV genomic fragments. Three main regions showed very strong hybridization with the cDNA probe: BamHI a, M, and L fragments, BamHI K, B, and G fragments, and BamHI B1 fragment (deleted in strain B95-8) and the adjacent right end of the DNA molecule. Seventeen of the cDNA clones were localized in these highly transcribed regions. The five others were dispersed all along the EBV genome.

Latent and viral replicative transcription in vivo from the BamHI K fragment of Epstein-Barr virus DNA

We mapped one latent and two replicative messages transcribed in vivo from the BamHI K fragment of the Epstein-Barr virus genome. The exon encoding Epstein-Barr nuclear antigen (EBNA), a major latent product, is 2,028 bases; the 3' end of this exon occurs 30 bases after the polyadenylation signal AATAAA, and the 5' end occurs within a splice acceptor site. The open reading frame which encodes the EBNA peptide is completely contained within this coding exon. The exon was faithfully transcribed after transfection of cloned BamHI-K into either COS-1 or TK- mouse L cells. In lymphocytes the abundance of the EBNA message is increased after cycloheximide treatment. The two viral replicative genes completely contained in BamHI-K were not transcribed in line X50-7, in which the genome is tightly latent. In contrast to the EBNA message, these mRNAs of 1.3 and 2.1 kilobases are inducible with phorbol ester and are unspliced. Their promoter regions are similar to those of each other and to replicative promoters mapped in other regions of the Epstein-Barr virus genome (P. J. Farrell, A. Bankier, C. Seguin, P. Deininger, and B. G. Barrell, EMBO J. 2:1331-1338, 1983). An unusual feature of these replicative genes is that the smaller mRNA begins within a long open reading frame of the larger mRNA. The identification of the structure of latent and replicative genes within one DNA fragment will facilitate analysis of regulation of expression for the two life cycles of the virus.