Recombination resulting in unusual features in the polyomavirus genome isolated from a murine tumor cell line

Polyomavirus-induced tumor formation in the adult natural mouse host has been investigated. Tumors were produced in nude mice with the transformation-defective mutant strain NG18 after a long latency period by apparent activation of a cryptic endogenous transforming viral function. A tumor cell line, designated ScB, was established and characterized. Cells from this morphologically distinct line were unusual in that they grew in soft agar but did not form foci. They were highly tumorigenic. They had a 3.1-kilobase major viral transcript that hybridized to probes derived from regions encoding both the T antigens and the structural proteins. ScB cells expressed polyomavirus small T antigen, a slightly altered middle T antigen, and a truncated large T antigen but no capsid proteins. Middle T antigen preserved its interactions with host proteins of 60 and 37 kilodaltons and with c-src. Analysis of cDNA and genomic clones indicated that the stable viral insert in the ScB genome contained multiple copies of the viral B-enhancer. The genome contained two intragenic inversions which created novel early- to late-strand switches. A simple model for the generation of one inversion is proposed that involves the juxtaposition of two stem-loop structures at an illegitimate recombination site; the location of the inverted segment within the integrated sequence permits use of the viral late polyadenylation signal in early-region transcripts, as confirmed by DNA sequence. A repetitive sequence may facilitate recombination at the other inversion site. Both the biological consequences of the observed rearrangements and the structure of the integrated viral DNA suggest that the recombination events are nonrandom.

Immortalization and transformation of human fibroblasts by regulated expression of polyoma virus T antigens

We have established conditions for the immortalization of human fibroblasts by the large T antigen of the rodent virus polyoma. This allows the mechanism of immortalization to be studied, without interference by transformation events, in cells with relatively stable chromosomes. Large T antigen could immortalize human fibroblasts if expression was driven by a heterologous promoter like the immediate early promoter/enhancer of cytomegalovirus or the inducible mouse mammary tumour virus (MMTV) promoter. Using the latter promoter and dexamethasone, three clones were obtained, the immortalized phenotype of which was strictly dependent on the induction of T-antigen expression. At least one of these clones became mortal after removal of the inducing agent. The expression of large T antigen was paralleled by PCNA gene expression, as shown by nuclear run-off transcription, whereas none of a number of other known proto-oncogenes was influenced in its activity. Immortalized fibroblasts were readily transformed by polyoma virus middle T antigen expressed from the MMTV promoter or by the activated c-Ha-ras oncogene. The reversibility of immortalization and transformation is considered.

CpG methylation of viral DNA in EBV-associated tumours

In EBV-immortalized lymphoblastoid cell lines (LCLs) a small number of "latent" proteins are expressed. These are the EBV nuclear antigens, EBNAs 1-6, and a latent membrane protein, LMP. We have investigated the expression of these proteins in a variety of EBV-associated tumours and cell lines. Whereas transplant and B-cell lymphomas from cotton-top tamarins appear to express the full range of antigens found in LCLs, we and others have found that in Burkitt's lymphomas (BL) and a nasopharyngeal carcinoma (NPC) isolate, EBNA expression is restricted to EBNA-I. (In NPC, but not in BL, LMP may also be expressed). In order to ask what restricts the expression of EBNA 2-6 in NPC and BL cells it seemed reasonable to consider the possibility that the DNA sequences normally regulating expression of these antigens could be chemically modified. In this analysis, a tight inverse correlation between methylation of CpG dinucleotides in the 5' flanking region of the EBNA-2 gene and the expression of EBNAs 2-6 has been revealed. In the NPC tumour, CpG methylation within the gene is also observed, as is specific methylation over the EBNA-I region I and II binding sites (in oriP). The significance of these observations is considered.

Establishment of immortalized primate epithelial cells with sub-genomic EBV DNA

The genetic information in a sub-fragment of EBV DNA, designated p31 (containing less than a quarter of the viral genome and derived from a recombinant DNA cosmid library) allows epithelial cells from primary monkey and human kidney cultures to escape senescence under standard tissue culture conditions. A number of epithelial cell lines, designated M1/31, 483/31, 199/31 and HK/31, have been established and characterized following transfection of primary cells with p31 DNA. They share many properties, although morphologically they are not all identical. The cultures are immortalized but not fully transformed or tumorigenic. They appear to be phenotypically stable, although DNA hybridization studies indicate that genotypic alterations, including amplification, occur subsequent to transfection with p31 DNA and the establishment of a continuously proliferating epithelium. All cell lines consistently express high levels of cytokeratin 18 and varying amounts of cytokeratin 7, demonstrating their epithelial origin. From a single marmoset kidney (designated 199) a series of related immortalized cells, with subtle phenotypic differences, have been generated by p31 or sub-fragments of it. Although hallmarks of a "hit-and-run" mechanism are apparent in all of our studies, 2 different techniques (in situ hybridization or selection for cell survival in semi-solid media, followed by nucleic acid hybridization) show that, in late-passaged cultures, a small proportion of the cells still contain some viral DNA. The studies focus on genetic information within the BamHI A and I regions as being relevant to immortalization. The role of the EBV DNA fragment in the genesis of epithelial cell lines is considered.

Visualization of single copies of the Epstein-Barr virus genome by in situ hybridization

Conditions have been established for demonstrating small numbers of genes of the Epstein-Barr virus (EBV) in B-lymphoid cells by in situ hybridization using biotinylated EBV-specific DNA from cloned BamHI fragments of the viral genome. Single copies of EBV genomes were successfully visualized with minimal background when the probe concentration was 0.2 micrograms/ml, the DNA denaturation step was performed at 100 degrees C, and the immunochemical detection system employed a three-layer peroxidase protocol with gold-silver amplification of the diaminobenzidine substrate. The minimal target DNA detectable was about 10 kilobase pairs. In the case of sectioned cells fixed overnight with formalin, simulating conditions used in routine tissue fixation, this approach failed to demonstrate EBV DNA present at less than 100 copies per cell, that is, at the level found in Raji cells. However, when denaturation was performed using microwave irradiation with the other optimized conditions maintained, EBV DNA could be visualized in 10-20% of such cells, although not in cells known to contain fewer than 10 copies per cell. Thus, microwave irradiation partially overcomes the limit of DNA target detection imposed by formalin.

EBV gene expression in an NPC-related tumour

A nasopharyngeal carcinoma tumour (designated C15) propagated in nude mice has been used to generate a large cDNA library that we have analysed for Epstein-Barr virus (EBV) gene expression. No gross alterations exist in viral DNA from C15 relative to other human isolates and the large deletion present in the B95-8 'prototype' viral strain established in marmoset cells is not found; C15 contains no linear virion DNA. In the cDNA library, of the six EBV nuclear antigens (EBNAs) expressed in latently infected B-lymphocytes, only clones for EBNA-1 are found. These data are confirmed by immunoblotting. Sequence analysis shows the EBNA-1 mRNA splicing pattern in the carcinoma to differ from that observed in B-lymphocytes. Further, contrary to observations with B-cell lines, most viral transcription in the tumour is localized onto the 'rightmost' region of the conventional EBV physical map. Transcripts identified corresponding to known genes include those for the latent membrane protein (LMP), the alkaline DNA exonuclease and probably the terminal protein; major transcripts are also derived from the BamHI D fragment and the region deleted in B95-8 EBV DNA. Novel transcripts have also been identified that proceed in an anti-sense direction to genes encoding functions associated with replication, such as the viral DNA polymerase. They contain a large, hitherto unidentified, open reading frame in the viral genome that is complementary to the putative function known as BALF3 and a smaller open reading frame complementary to BALF5 (the DNA polymerase gene). From the present studies we can conclude that: (i) EBV transcription patterns in the epithelial cells vary markedly from those identified previously in B-cells, reflecting differential use of promoters or splicing patterns. (ii) Transcription is tightly regulated and restricted in the C15 tumour with many latent genes, notably EBNAs 2-6, being 'switched off.' (iii) A family of cytoplasmic RNAs are transcribed in an antisense direction to a number of existing open reading frames in the EBV genome. (iv) There are a number of mutations in C15 transcripts relative to the B95-8 genome, some of which could result in amino acid alterations in proteins.

Epstein-Barr virus latent gene expression during the initiation of B cell immortalization

Epstein-Barr virus (EBV) has the capacity to immortalize a subpopulation of resting B lymphocytes. Lymphoblastoid cell lines (LCL) established in this way carry the latent EBV genome as multiple copies of an extrachromosomal episome. Viral gene expression in LCLs is highly restricted; products identified correspond to a membrane protein (latent membrane protein; LMP), a nuclear antigen complex (Epstein-Barr nuclear antigens; EBNAs 1 to 6), two small RNA species (EBERs 1 and 2) and RNA species thought to encode a second membrane-associated polypeptide designated terminal protein (TP). Here we have investigated the temporal sequence of expression of the characterized 'latent' proteins during the initiation of immortalization when resting B cells are stimulated to enter and traverse the cell cycle. The analysis has been carried out on prolymphocytic leukaemia cells infected in vitro with either the immortalizing B95-8 strain of virus or the non-immortalizing P3HR1 strain. The results reveal that following B95-8 infection, a sequence of EBV expression is initiated within approximately 8 h with the synthesis of detectable levels of EBNA 2 shortly followed by EBNAs 1, 3, 4, 5 and 6. There is then a delay of approximately 40 h until the expression of LMP completes the latent pattern of proteins found in LCLs. P3HR1 infection, however, produces only transient expression of some EBNA species in a small percentage of cells after approximately 48 h. These observations suggest the failure of P3HR1 virus to immortalize may not be due solely to the absence of EBNA 2 expression and that cellular and/or virus-mediated events occur after EBNA synthesis which then facilitate efficient LMP expression and immortalization.

Persistence of Epstein-Barr virus in salivary gland biopsies from healthy individuals and patients with Sjögren's syndrome

Salivary gland biopsies from 12 patients with primary Sjögren's syndrome and 10 controls were examined for Epstein-Barr virus (EBV) DNA by in-situ hybridization and for EBV proteins by immunofluorescence and peroxidase techniques. Viral DNA was found in biopsies from two out of 12 patients with primary Sjögren's syndrome and six out of the 10 controls. The DNA and early antigen were in epithelial cells lining the ducts and acini, early antigen expression being limited to the luminal side of the epithelium. In eight biopsies studied with other antibodies, membrane antigen was identified in both acini and ducts but viral capsid antigen and Epstein-Barr nuclear antigen were not detected. EBV was found in biopsies from five of the controls without inflammation or Class II expression. This suggests that, in health, persistence and replication occur without inducing an immune response, possibly due to the restricted expression of early antigen on the luminal of the epithelium, away from immune surveillance. The inflammation in Sjögren's syndrome could be due to a breakdown of this unusual mechanism for viral persistence leading to a vigorous immune response to the virus. However our study provides no evidence to suggest that EBV infection load is increased in this disease.

Expression of biologically active middle T antigen of polyoma virus from recombinant baculoviruses

Two different recombinant baculoviruses have been generated for expressing the middle T antigen (MT) of polyoma virus in insect (Sf9) cells. One (pAcI-PyMT) produces moderate levels of MT and the other (pVL-PyMT) high levels. Indirect immunofluorescence and cellular fractionation studies with pAcI-PyMT infected Sf9 cells give results similar to those observed with wild type polyoma virus infected mouse cells, and show MT to be mainly associated with cytoplasmic membranes in the insect cell. In the latter, a sub-population of MT is phosphorylated in in vitro protein kinase assays. The yields of MT from pVL-PyMT infected cells are high enough to suggest that this protein can now be produced by this method in sufficient amounts for definitive biochemical and crystallographic analyses.

Prediction and demonstration of a novel Epstein-Barr virus nuclear antigen

The protein sequence predicted by the Epstein Barr virus (EBV) BERF4 open reading frame includes a tetrapeptide, Lys-Arg-Pro-Arg (KRPR), shown for other proteins to be a component of a signal for rapid nuclear localization. A subgenomic fragment of EBV DNA containing BERF4 has been incorporated into an expression vector, transfected onto primate cells and the nuclear distribution of the resulting protein established by immunofluorescence using EBV positive human sera. These sera contained high titres of antibodies to a fusion protein, produced in E. coli, consisting of beta-galactosidase and the C-terminal 167 amino acids of BERF4. Immunoaffinity purified antibodies reactive with the EBV component of the fusion show the molecular weight of this antigen in EBV immortalized B-cell lines to be about 160 kD. The demonstration that BERF4 contains an exon encoding a nuclear protein identifies a new EBNA gene (EBNA-6) and suggests that KRPR is a signal sequence common to a number of viral and cellular nuclear polypeptides which bind to nucleic acids and may therefore be of predictive value in identifying karyophilic proteins.

Size heterogeneity of EBV and mitochondrial DNAs in Burkitt's lymphoma lines

A simple, reproducible affinity chromatography method has been adapted for separation of high molecular weight supercoiled circular molecules from mammalian cells. Electron microscopic analysis of EB viral DNA obtained by this method, from the non-producer Burkitt's lymphoma line Raji, revealed monomer-sized viral molecules only. In contrast, the EB viral episomes from recently established human producer lines BL-8 and LY91 were very heterogeneous in size, some being considerably smaller and others much larger than the monomeric DNA. The former are probably related to defective viral species in the B-cell population, but the origin of the latter are as yet unclear. All cell lines contained both monomers and concatemers of mitochondrial DNA; among the latter, molecules apparently greater than 100 kb were observed in the population.

Immunological variation in the 'common region' of the T antigens of polyoma virus

Characterization of a series of mouse monoclonal antibodies (designated alpha Py C21 to 26) against the region common to the large, middle and small T antigens of polyoma virus has revealed immunological diversities among the N termini of these antigens. Four of the antibodies (alpha Py C21 to 24) appeared to recognize all the T antigens present in lytically infected cells, but two of them (alpha Py C25, 26) failed to immunoprecipitate small T antigen either from 35S- or 32P-labelled cells and recognized only a subset of middle and large T antigens. None of the antibodies recognized the protein kinase activity normally associated with middle T antigen or the 60K mol. wt. antigen-related protein observed in polyoma virus lytically infected or transformed cells. The possible immunodominance of the N termini of the early gene products (as well as VP1) in the natural host of polyoma virus and the observed antigenic heterogeneity are considered.

Epstein-Barr virus genomes in lymphoid cells: activation in mitosis and chromosomal location

Biotin-labeled Epstein-Barr virus (EBV)-specific DNA probes have been used to detect viral genomes by in situ hybridization. Immunocytochemically amplified signals produced by the hybridized probe allow visualization of viral DNA even in cells previously reported to contain only one or two EBV genomes. In EBV producer lymphoid cell lines, such as B95-8, P3HR-1, or Daudi, activation of latent EBV DNA could be observed in mitotic cells; in non-virus-producing cells of these same lines, EBV was found to be present in low copy numbers. Noninducible cell lines such as IB4, AW-Ramos, and Namalwa exhibited low but clearly positive hybridization. Unexpectedly, significant variations in the amounts of EBV DNA per cell were observed between individual cells of these lines. The EBV DNA in the cloned IB4 cell line was localized to chromosome 4 in metaphase cells, but in the noncloned converted line AW-Ramos, the location of integrated viral DNA was essentially random.

Myristic acid is coupled to a structural protein of polyoma virus and SV40

In the lytic cycle of papova viruses, both uncoating of the viral genome after infection and assembly of functional virions take place in the cell nucleus. The mechanisms by which newly internalized virions are targeted to the nucleus and viral DNA encapsidated into particles are poorly understood. Although the major capsid protein VP1 is involved in endocytosis, and largely defines virion structure, the functions of the minor proteins VP2 and VP3 have remained obscure. Here we show that VP2 from both polyoma virus and simian virus 40 (SV40) is covalently linked to myristic acid; this is the first report of a myristylated protein in the nucleus and of a fatty acid being important in the structure of a nonenveloped virus. We consider the implications of this unusual modification on encapsidation and suggest that VP2 may be a scaffolding protein for virion assembly.

Subcellular localisation of the middle and large T-antigens of polyoma virus

The distribution of two of the polyoma virus early proteins (the large and middle T-antigens) in lytically infected mouse cells and transformed rat cells has been investigated by indirect immunofluorescence and immuno-electron microscopy using well-characterised monoclonal antibodies. By these techniques, the viral large T-antigen was found almost exclusively in the nucleus, sometimes in association with nuclear pores, but never in the nucleolus. In lytically infected, but not transformed cells, fluorescence was detected in discrete areas ('hot spots') within the nucleus and, in a minor population of lytically infected cells, cytoplasmic immunoreactive material was observed. The viral middle T-antigen was found in association with most cytoplasmic membranes and in the majority of cells mainly in the endoplasmic reticulum. Only a fraction of the staining was observed in the plasma membrane and no staining in the nucleoplasm was observed. The data suggest that the site of action of the major transforming activity of polyoma virus need not be at the plasma membrane. Functions associated with the viral antigens are discussed in terms of their subcellular distributions within cells.

Efficient oligodeoxyribonucleotide-directed deletion mutagenesis using pEMBL vectors: removal of early region introns from polyoma virus mutants

We have used oligodeoxyribonucleotide-directed deletion mutagenesis to remove early region introns from polyoma virus mutants. To this end we compared single priming, double priming, and gapped duplex approaches using either priming at 37 degrees C or at the critical temperature. The gapped duplex approach, coupled with priming at the critical temperature, resulted in up to 70% yield of the desired product. In conjunction with the use of the pEMBL vector system this method was simplified to yield specific deletions from cloned large DNA fragments with high efficiency. The resulting mutant plasmids could be used directly for biological assays without retransformation or recloning. RNA and protein analyses showed that removal of the large T- or middle T-antigen introns from polyoma early region mutants dl23 and dl8 was specific and resulted in DNA competent for the synthesis of only one T antigen.

Immortalization of monkey epithelial cells by specific fragments of Epstein-Barr virus DNA

Epstein-Barr virus (EBV) is unique among the DNA tumour viruses by virtue of its association with two human malignancies, Burkitt's lymphoma and nasopharyngeal carcinoma (NPC), the former a tumour of B lymphocytes and the latter encompassing low-differentiated epithelial cells of the nasopharynx. A viral gene product has not been definitively linked to these malignant diseases, although an EBV nuclear antigen(s) (EBNA) seems to be ubiquitous in EBV-infected cells; indeed, the detection of EBNA by immunofluorescence is often taken as an indication of the presence of the viral genome. As part of a study to investigate which part of the EBV genome is responsible for transformation and whether the same mechanism of cellular transformation is involved in the case of B lymphocytes and epithelial cells, we have tried to establish whether a detectable cellular alteration(s) can be induced in primate epithelial cells by the presence of a specific region of the EBV genome. We report here that it can--the result is immortalization of the cells.

Molecular characterization of the Epstein-Barr virus DNA in three new Burkitt's lymphoma-derived cell lines

Three new Epstein-Barr virus DNA populations have been isolated from the recently established Burkitt's lymphoma-derived cell lines, LY47, LY91 and BL8. Each of these lines carries one of the specific chromosome translocations associated with Burkitt's lymphoma but few if any other chromosomal abnormalities. An outline of their molecular organization, as determined by restriction enzyme analysis, is presented. Two of the isolates, LY47 and BL8, give patterns broadly similar to Epstein-Barr virus DNA molecules studied to date. The third, LY91, shows a highly unusual molecular organization, in particular within BamHI subfragments of the EcoRI A fragment, indicative of the presence of a major defective molecular species within this line. All three cell lines produce virions that are capable of transforming immature B-lymphocytes.

The EB virus genome in Daudi Burkitt's lymphoma cells has a deletion similar to that observed in a non-transforming strain (P3HR-1) of the virus

Epstein-Barr virus (EBV) DNA isolated from the frequently studied and unusual Burkitt's lymphoma cell line, Daudi, contains a 7.4-kb deletion, similar to (but larger than) that found in a non-transforming isolate of the virus, P3HR-1. A comparison of EBV sequence in Daudi cells with that from a comparable region in a wild-type, transforming strain of the virus (B95-8) indicates that at least two of the previously identified RNAs, a highly repetitive sequence, and other interesting coding or structural features should be absent in Daudi EBV DNA as a consequence of the deletion. The information removed by the deletion, as well as that which might be generated by juxtaposition of two regions of the genome that are not adjacent in most strains of the virus are discussed.

DNA binding activity of polyoma virus large tumor antigen

Polyoma virus large tumor antigen from productively infected mouse cells has been purified to greater than 50% homogeneity by a simple immunoaffinity procedure using monoclonal antibodies. A radioimmunoreaction was devised for assaying purity. The purified large tumor antigen retained its antigenicity and its ability to bind DNA specifically. The regions on the polyoma virus genome recognized by the protein were characterized. Three binding regions were localized within the portion of the genome between the viral origin of DNA replication and the protein coding sequence, overlapping the early promoter and the sites of initiation of mRNAs that specify the viral tumor antigens. The binding regions each contain direct repeats of the pentanucleotide sequence G-R-G-G-C.

Clustered repeat sequences in the genome of Epstein Barr virus

The genome of Epstein-Barr virus is composed of unique DNA interspersed with repetitive sequences. This organization suggests that Epstein-Barr virus provides a useful model for studying the function(s) of repetitive sequences in eukaryotic chromosomes. The primary structure of two of the repeat sequences, the 3072 bp large internal repeat, or BamHI-W repeat, and a smaller 125 bp, G, C-rich NotI repeat, are presented here. Their structures and possible functions are discussed.