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

Complexities associated with expression of Epstein-Barr virus (EBV) lytic origins of DNA replication

EBV has two lytic origins (oriLyt) of DNA replication lying at divergent sites on the viral genome within a duplicated sequence (DS). The latter contains potential hairpin loops, ‘hinge’ elements and the promoters for transcripts from viral genes BHLF1 and LF3. These genes themselves consist largely of 125 and 102 bp repetitive sequences, respectively, and encode basic proteins. We have examined these genomic regions in detail in attempts to understand why lytic replication—necessary for virus survival—is so inefficient, and to identify controlling elements. Our studies uncovered a diverse family of promoters (P) for BHLF1 and LF3, only one pair of which (P1) proved sensitive to chemical inducing agents. The others (P2–P3/4), abutting the replication ‘core’ origin elements in DS and extending into 5′-unique sequences, may play roles in the maintenance of viral latency. We further identified a family of overlapping small complementary-strand RNAs that transverse the replication ‘core’ origin elements in a manner suggesting a role for them as ‘antisense’ species and/or DNA replication primers. Our data are discussed in terms of alternative lytic replication models. We suggest our findings might prove useful in seeking better control over viral lytic replication and devising strategies for therapy.

The use of lymphocytes to screen for oxidative phosphorylation disorders

Biochemical analysis of oxidative phosphorylation (OXPHOS) disorders is traditionally carried out on muscle biopsies, cultured fibroblasts, and transformed lymphocytes. Here we present a new screening technique using lymphocytes to identify OXPHOS dysfunction and initially avoid an invasive diagnostic procedure. Lymphocytes represent an easily obtainable source of tissue that presents advantages over the use of fibroblasts or lymphoblast cell lines. The time delay in culturing skin fibroblasts and the interactions between cell transformation and mitochondrial activity are avoided in this methodology. The method requires a small amount of blood (<5 mL); can be completed in a few hours, and allows for repeated measurements. Our assay has been adapted from published methods utilizing cultured fibroblasts and transformed lymphocytes, and our data suggest that measurement of ATP synthesis in lymphocytes is an effective screening tool for diagnosing OXPHOS disorders. This method may also provide an objective tool for monitoring response to treatment and evaluating progression of disease.

Expression of two related viral early genes in Epstein-Barr virus-associated tumors

The transcription of two early "leftwardly" expressed genes carrying repetitive sequences, IR2 and IR4, has been studied for Epstein-Barr virus-associated tumors, and for established B-cell lines, using sequence-specific probes generated for this purpose. Whereas the IR4 transcript was identified in every tumor and cell line assessed (except B95-8, with a deletion that removes the gene), expression of the IR2 gene was restricted to B lymphocytes. Though the promoters for both transcripts lie within homologous regions (D(L) and D(R)) in the viral genome, the IR2 promoter appears more tightly regulated. Detailed characterization of the IR4 transcript from a nasopharyngeal carcinoma tumor, C15, identifies a sequence variant of this gene that differs from those reported for B cells; in situ hybridization methods show transcription to be restricted to a subset of cells, with the strongest signals seen adjacent to host stroma. As with B cells in culture (Y. Gao, P. R. Smith, L. Karran, Q. L. Lu, and B. E. Griffin, J. Virol. 71:84-94, 1997), chemical induction enhanced transcriptional expression of the IR4 gene in the C15 tumor, although staining for both the IR4 antigen and that of the virus lytic switch, Zta, gave negative results. In a Burkitt's lymphoma biopsy specimen, however, both proteins were found expressed, notably in the same subset of cells. The data here and elsewhere (Gao et al., J. Virol., 1997) are consistent with a block to intracellular transport of the transcript(s) and suggest nuclear roles for it in tumors, possibly in RNA processing and viral lytic replication. Both roles could be fulfilled in the absence of translation.

A shuttle system for transfer of YACs between yeast and mammalian cells

The development of a system for shuttling DNA cloned as yeast artificial chromosomes (YACs) between yeast and mammalian cells requires that the DNA is maintained as extrachromosomal elements in both cell types. We have recently shown that circular YACs carrying the Epstein-Barr virus origin of plasmid replication (oriP) are maintained as stable, episomal elements in a human kidney cell line constitutively expressing the viral transactivator protein EBNA-1. Here, we demonstrate that a 90-kb episomal YAC can be isolated intact from human cells by a simple alkaline lysis procedure and shuttled back into Saccharomyces cerevisiae by spheroplast transformation. In addition, we demonstrate that the 90-kb YAC can be isolated intact from yeast cells. The ability to shuttle large, intact fragments of DNA between yeast and human cells should provide a powerful tool in the manipulation and analysis of functional regions of mammalian DNA.

Marked variation in the size of genomic plasmids among members of a family of related Epstein-Barr viruses

Epstein-Barr virus (EBV) genomes in the P3J-HR-1 (HR-1) Burkitt lymphoma cell line rearrange at a high rate. Previously described deletions and rearrangements in HR-1 cells have been found at sites of EBV replication in vivo, suggesting that DNA rearrangement may be an integral aspect of EBV biology and pathogenesis. We examined the structure of linear EBV genomes in subcultures of HR-1 cells using contour-clamped homogenous electric field gel electrophoresis. We developed a second pulsed electrophoretic technique to separate intracellular circular EBV plasmids. The standard, linear HR-1 EBV genome was approximately 155 kilobases in length. Linear molecules of less than unit length, presumably defective genomes, were seen in numerous subcultures. Linear intracellular genomes greater than 155 kilobases were also detected, but only linear genomes of 155 kilobases or less were packaged into virions. The size of circular EBV plasmids also varied greatly among HR-1 subcultures, some of which contained two plasmids of different size. The progeny of the unusual circular plasmids could be either standard or nonstandard linear genomes. No aberrant linear or circular form was detected in a subculture carrying the previously described het fragments. Pulsed-gel electrophoresis has provided two additional characteristics of mutant EBVs: abnormal linear and circular genome configurations.