Origin of replication in episomal bovine papilloma virus type 1 DNA isolated from transformed cells

Nucleosome Positioning on Episomal Human Papillomavirus DNA in Cultured Cells

Several human papillomaviruses (HPV) are associated with the development of cervical carcinoma. HPV DNA synthesis is increased during the differentiation of infected host keratinocytes as they migrate from the basal layer of the epithelium to the spinous layer, but the molecular mechanism is unclear. Nucleosome positioning affects various cellular processes such as DNA replication and repair by permitting the access of transcription factors to promoters to initiate transcription. In this study, nucleosome positioning on virus chromatin was investigated in normal immortalized keratinocytes (NIKS) stably transfected with HPV16 or HPV18 genomes to determine if there is an association with the viral life cycle. Micrococcal nuclease-treated DNA analyzed by Southern blotting using probes against HPV16 and HPV18 and quantified by nucleosome scanning analysis using real-time PCR revealed mononucleosomal-sized fragments of 140-200 base pairs that varied in their location within the viral genome according to whether the cells were undergoing proliferation or differentiation. Notably, changes in the regions around nucleotide 110 in proliferating and differentiating host cells were common to HPV16 and HPV18. Our findings suggest that changes in nucleosome positions on viral DNA during host cell differentiation is an important regulatory event in the viral life cycle.

Plasmid Partitioning by Human Tumor Viruses

The human tumor viruses that replicate as plasmids (we use the term plasmid to avoid any confusion in the term episome, which was coined to mean DNA elements that occur both extrachromosomally and as integrated forms during their life cycles, as does phage lambda) share many features in their DNA synthesis. We know less about their mechanisms of maintenance in proliferating cells, but these mechanisms must underlie their partitioning to daughter cells. One amazing implication of how these viruses are thought to maintain themselves is that while host chromosomes commit themselves to partitioning in mitosis, these tumor viruses would commit themselves to partitioning before mitosis and probably in S phase shortly after their synthesis.

Plasmid DNA replication and topology as visualized by two-dimensional agarose gel electrophoresis

During the last 20 years, two-dimensional agarose gel electrophoresis combined with other techniques such as Polymerase Chain Reaction, helicase assay and electron microscopy, helped to characterize plasmid DNA replication and topology. Here we describe some of the most important findings that were made using this method including the characterization of uni-directional replication, replication origin interference, DNA breakage at the forks, replication fork blockage, replication knotting, replication fork reversal, the interplay of supercoiling and catenation and other changes in DNA topology that take place as replication progresses.

The bovine papillomavirus replicon

The bovine papillomavirus genome contains two cis-acting sequences which can serve as signals for replication. At least three virally encoded genes seem to be involved in plasmid replication: E6, E6/7 and E1. Mutations in either the E6 or the E7 open reading frame create plasmids that are maintained at a low copy number per cell. Mutations in the E1 open reading frame are absolutely lethal to replication. Complementation experiments show that these mutations define separate genes. Experiments are described which show that cells harbouring plasmids with mutations in either the E6 or the E7 open reading frame acquire an immunity to high copy-number plasmids. We suggest that either the cell or the virus encodes a repressor. The positive action of E6 and E6/7 modulates the activity of this repressor to allow for the high copy-number state. Though the viral oncogenes are capable of transforming cells separately when they are expressed as part of certain recombinant DNA expression systems, it is clear that, in the context of the entire viral replicon, interactions between the transforming functions and replication functions must exist.

Organization and expression of the genome of bovine papillomavirus type 1

The viral mRNAs present in C127 cells transformed by bovine papillomavirus type 1 (BPV-1) have been mapped by a variety of techniques, including S1 nuclease analysis, Northern blot analysis, primer extension and electron microscopic heteroduplex analysis. The results reveal a very complex mRNA pattern, comprising at least five types of spliced cytoplasmic mRNAs. Both unspliced and partially processed nuclear RNA species have also been identified. The transforming region of BPV-1 contains several promoter regions. A major cap site is located at coordinate 1 and another putative cap site at coordinate 31. A third candidate cap site maps around coordinate 39.

The chromatin structure of the long control region of human papillomavirus type 16 represses viral oncoprotein expression

The long control region (LCR) of human papillomavirus type 16 (HPV-16) has a size of 850 bp (about 12% of the viral genome) and regulates transcription and replication of the viral DNA. The 5' segment of the LCR contains transcription termination signals and a nuclear matrix attachment region, the central segment contains an epithelial cell-specific enhancer, and the 3' segment contains the replication origin and the E6 promoter. Here we report observations on the chromatin organization of this part of the HPV-16 genome. Treatment of the nuclei of CaSki cells, a cell line with 500 intrachromosomal copies of HPV-16, with methidiumpropyl-EDTA-Fe(II) reveals nucleosomes in specific positions on the LCR and the E6 and E7 genes. One of these nucleosomes, which we termed Ne, overlaps with the center of the viral enhancer, while a second nucleosome, Np16, overlaps with the replication origin and the E6 promoter. The two nucleosomes become positioned on exactly the same segments after in vitro assembly of chromatin on the cloned HPV-16 LCR. Primer extension mapping of DNase I-cleaved chromatin revealed Np16 to be positioned centrally over E6 promoter elements, extending into the replication origin. Ne covers the center of the enhancer but leaves an AP-1 site, one of the strongest cis-responsive elements of the enhancer, unprotected. Np16, or a combination of Np16 and Ne, represses the activity of the E6 promoter during in vitro transcription of HPV-16 chromatin. Repression is relieved by addition of Sp1 and AP-1 transcription factors. Sp1 alters the structure of Np16 in vitro, while no changes can be observed during the binding of AP-1. HPV-18, which has a similar arrangement of cis-responsive elements despite its evolutionary divergence from HPV-16, shows specific assembly in vitro of a nucleosome, Np18, over the E1 binding site and E6 promoter elements but positioned about 90 bp 5' of the position of Np16 on the homologous HPV-16 sequences. The chromatin organization of the HPV-16 and HPV-18 genomes suggests important regulatory roles of nucleosomes during the viral life cycle.

The ColE1 unidirectional origin acts as a polar replication fork pausing site

Co-orientation of replication origins is the most common organization found in nature for multimeric plasmids. Streptococcus pyogenes broad-host-range plasmid pSM19035 and Escherichia coli pPI21 are among the exceptions. pPI21, which is a derivative of pSM19035 and pBR322, has two long inverted repeats, each one containing a potentially active ColE1 unidirectional origin. Analysis of pPI21 replication intermediates (RIs) by two-dimensional agarose gel electrophoresis and electron microscopy revealed the accumulation of a specific RI containing a single internal bubble. The data obtained demonstrated that initiation of DNA replication occurred at a single origin in pPI21. Progression of the replicating fork initiated at either of the two potential origins was transiently stalled at the other inversely oriented silent ColE1 origin of the plasmid. The accumulated RIs, containing an internal bubble, occurred as a series of stereoisomers with different numbers of knots in their replicated portion. These observations provide one of the first functional explanations for the disadvantage of head-to-head plasmid multimers with respect to head-to-tail ones.

Rolling-circle replication of a high-copy BPV-1 plasmid

We investigated the replicating form of a bovine papillomavirus type 1 (BPV-1) deletion mutant by direct electron-microscopic analysis of low molecular weight cellular DNA fractions. The detection of viral plasmid DNA replication intermediates was facilitated by the isolation of a spontaneously transformed mouse cell subclone containing an unusually high viral genome copy number (approx. 1000 per cell), and by employing a slight modification of the Hirt fractionation procedure to reduce the level of contaminating linear chromosomal DNA fragments. We observed exclusively rolling-circle-type viral DNA replication intermediates, at a frequency of detection of approximately one replication intermediate per 200 monomeric circular viral DNA molecules. The demonstration of rolling-circles with longer-than-genome-length tails indicated that this high-copy viral plasmid was not subject to a strict once-per-cell-cycle mode of DNA replication. Our observations provide further evidence in favour of an alternative replication mode of the BPV-1 genome, and may help to explain earlier conflicting findings concerning the mechanism of stable BPV-1 plasmid copy-number-control.

Plasmids bearing mammalian DNA-replication origin-enriched (ors) fragments initiate semiconservative replication in a cell-free system

Four plasmids containing monkey (CV-1) origin-enriched sequences (ors), which we have previously shown to replicate autonomously in CV-1, COS-7 and HeLa cells (Frappier and Zannis-Hadjopoulos (1987) Proc. Natl. Acad. Sci. USA 84, 6668-6672), were found to replicate in an in vitro replication system using HeLa cell extracts. De novo site-specific initiation of replication on plasmids required the presence of an ors sequence, soluble low-salt cytosolic extract, poly(ethylene glycol), a solution containing the four standard deoxyribonucleoside triphosphates and an ATP regenerating system. The major reaction products migrated as relaxed circular and linear plasmid DNAs, both in the presence and absence of high-salt nuclear extracts. Inclusion of high-salt nuclear extract was required to obtain closed circular supercoiled molecules. Replicative intermediates migrating slower than form II and topoisomers migrating between forms II and I were also included among the replication products. Replication of the ors plasmids was not inhibited by ddTTP, an inhibitor of DNA polymerase beta and gamma, and was sensitive to aphidicolin indicating that DNA polymerase alpha and/or delta was responsible for DNA synthesis. Origin mapping experiments showed that early in the in vitro replication reaction, incorporation of nucleotides occurs preferentially at ors-containing fragments, indicating ors specific initiation of replication. In contrast, the limited incorporation of nucleotides into pBR322, was not site specific. The observed synthesis was semiconservative and appeared to be bidirectional.

Unidirectional replication as visualized by two-dimensional agarose gel electrophoresis

Two-dimensional (2D) agarose gel electrophoresis is progressively replacing electron microscopy as the technique of choice to map the initiation and termination sites for DNA replication. Two different versions were originally developed to analyze the replication of the yeast 2 microns plasmid. Neutral/Neutral (N/N) 2D agarose gel electrophoresis has subsequently been used to study the replication of other eukaryotic plasmids, viruses and chromosomal DNAs. In some cases, however, the results do not conform to the expected 2D gel patterns. In order to better understand this technique, we employed it to study the replication of the colE1-like plasmid, pBR322. This was the first time replicative intermediates from a unidirectionally replicated plasmid have been analyzed by means of N/N 2D agarose gel electrophoresis. The patterns obtained were significantly different from those obtained in the case of bidirectional replication. We showed that identification of a complete are corresponding to molecules containing an internal bubble is not sufficient to distinguish a symmetrically located bidirectional origin from an asymmetrically located unidirectional origin. We also showed that unidirectionally replicated fragments containing a stalled fork can produce a pattern with an inflection point. Finally, replication appeared to initiate at only some of the potential origins in each multimer of pBR322 DNA.

A key DNA-protein interaction determines the function of the 5'URR enhancer in human papillomavirus type 11

The 5' end of the upstream regulatory region (URR) of human papillomavirus type 11 (HPV-11) has enhancer function and binds cellular proteins. We have determined that one particular motif, a CCNGTNAC pair, is both necessary and sufficient for enhancer activity. This enhancement of expression can be competed in vivo by concatenated double-stranded oligonucleotides, indicating that protein-DNA binding is a requisite for enhancer activity. A 41-kDa protein, present in all epithelial cells assayed, binds to this enhancer motif. The 5'URR fragment functions as an enhancer both in primary keratinocytes from a variety of body sites and in fibroblasts. We conclude that tissue specificity is not a feature of this enhancer, and that the 41-kDa binding protein is ubiquitous. These data provide evidence that the 5'URR enhancer activity is dependent on only a few sequences and perhaps only one protein.

Classes of autonomously replicating sequences are found among early-replicating monkey DNA

Thirteen new independent clones of origin-enriched sequences (ors) that are capable of autonomous replication have been identified from a library of 100 ors i clones that had been previously isolated from early replicating monkey (CV-1) DNA. Autonomous replication was assayed by transient episomal replication in transfected HeLa cells; ors-plasmid DNA was isolated at various times after transfection and screened by the DpnI resistance assay and the bromodeoxyuridine (BrdUrd) substitution assay to differentiate between input and newly replicated DNA. Four of the autonomously replicating clones were identified by screening the ors-library with probes of ors 3, 8, 9 and 12, previously shown to be capable of autonomous replication (Frappier and Zannis-Hadjopoulos, Proc. Natl. Acad. Sci. USA (1987) 84, 6668-6672). The other nine functional ors clones were identified among 18 randomly chosen ones, which were similarly screened for autonomous replication. Nucleotide sequence analyses of 11 of the newly identified functional ors plasmids revealed, in most of them, features similar to those present in other viral or eukaryotic replication origins, notably the presence of AT-rich regions and inverted repeats. Pairwise comparisons between the newly identified ors showed no extensive sequence homologies, other than the presence of the alpha-satellite repetitive sequence family in three ors and of the repetitive Alu sequence family in one ors. The results suggest that there exist different classes of mammalian replication origin, highly or moderately repetitive and unique, and that their activation is most probably dependent on the presence of structural determinants rather than on a particular sequence.

Targeting the E1 replication protein to the papillomavirus origin of replication by complex formation with the E2 transactivator

The mechanism by which transcription factors stimulate DNA replication in eukaryotes is unknown. Bovine papillomavirus DNA synthesis requires the products of the viral E1 gene and the transcriptional activator protein encoded by the E2 gene. Experimental data showed that the 68-kilodalton (kD) E1 protein formed a complex with the 48-kD E2 transcription factor. This complex bound specifically to the viral origin of replication, which contains multiple binding sites for E2. Repressor proteins encoded by the E2 open reading frame failed to complex with E1 suggesting that the 162-amino acid region of E2 that participates in transactivation contained critical determinants for interaction with E1. The physical association between a replication protein and a transcription factor suggests that transcriptional activator proteins may function in targeting replication initiator proteins to their respective origins of replication.

Replication of bovine papillomavirus type 1 DNA initiates within an E2-responsive enhancer element

When bovine papillomavirus transforms cells in vitro, it maintains its genome as a multicopy nuclear plasmid. Plasmid DNA extracted from such transformed cells was analyzed by the two-dimensional gel electrophoresis technique of Brewer and Fangman (B. Brewer and W. Fangman, Cell 51:463-471, 1987). The replication intermediates detected in these assays were found to be the sums of the oligomeric and monomeric forms of the replicating plasmids. The multimeric DNAs were shown by field inversion gel electrophoresis and partial restriction digestion to be head-to-tail concatemers of the monomeric forms. Furthermore, the multimers progressed in size by steps of one monomer, indicating that they did not arise by replication segregation mistakes of the unit length, which would predict a ladder spaced by integrals of two monomers. To map the plasmid DNA replication origin, the replication intermediates of the monomers were isolated by successive sucrose gradient centrifugation and then examined by the two-dimensional gel electrophoresis method. The patterns detected show that bovine papillomavirus type 1 replicates in these cells bidirectionally and that one replication origin site in the viral genome is utilized. By employing several restriction enzymes and specific viral DNA probes to dissect the replication intermediates, we were able to map the origin of initiation site with some precision. The initiation site, which maps to bovine papillomavirus type 1 DNA position 7730 +/- 100 bp, places the origin within that region of the viral upstream regulatory region which contains the major cluster of transcription factor E2-binding sites, E2RE1. Thus, the actual viral plasmid origin of replication maps near, but outside, genetic elements previously shown to be important for plasmid maintenance.

Proteins encoded by the bovine papillomavirus E1 open reading frame: expression in heterologous systems and in virally transformed cells

The E1 open reading frame (ORF) of bovine papillomavirus type 1 is required for the persistence of viral genomes as multicopy plasmid molecules in transformed rodent fibroblasts. E1 has been reported to contain two separate complementation groups (M and R, corresponding to N- and C-terminal domains, respectively) which regulate viral replication. However, E1 behaves as a single gene with respect to cell transformation and viral transcription. We examined the proteins translated from the entire ORF by using three antisera raised against E1 peptide or bacterial fusion proteins. The capacity of the whole ORF to encode a 72-kDa protein was demonstrated by translation of synthetic RNA in a reticulocyte lysate system, by microinjection of RNA into Xenopus oocytes, and by expression in recombinant baculoviruses and vaccinia viruses. In eucaryotic cells, this protein was found to be phosphorylated and targeted to the cell nucleus. In vitro translation also produced shorter peptides, containing only the E1 C-terminal domain, because of internal translation starts on the third and fourth methionine codons within E1 ORF. On the other hand, mammalian cells infected by vaccinia E1 recombinant virus contained additional larger E1 phosphoproteins (transient 85-kDa and stable 88-kDa species), likely representing processed forms of the 72-kDa species. The E1 72-kDa nuclear phosphoprotein was detected in bovine papillomavirus type 1-transformed cells. We report the biochemical characteristics of full-sized and truncated E1 proteins: (i) the C-terminal half of E1 ORF contains a phosphorylation site(s); (ii) the full-sized E1, but not the C-terminal protein, binds DNA, without indication for recognition of defined sequences, and critical determinants for this activity are likely confined to an N-terminal domain of the protein; (iii) covalent affinity labeling experiments performed on vaccinia virus-encoded E1 proteins with an ATP analog confirmed our previous observation of sequence similarities between the E1 C-terminal domain and the ATPase domain of simian virus 40 large T antigen.

The E2 protein of human papillomavirus type 16. Over-expression and purification of an active transcriptional regulator

The E2 open reading frame of human papillomavirus type 16 was inserted into the Escherichia coli vector pKK223-3, and expressed to greater than 15% of total cellular protein when induced with isopropyl beta-D-thiogalactopyranoside. The highest expressing clone was grown in bulk and the E2 protein purified to homogeneity by the following procedure: (a) isolation of the insoluble protein fraction; (b) extraction with urea; (c) quaternary amino-ethyl-Sepharose ion-exchange chromatography and (d) renaturation and chromatography on dextran sulphate. That the purified protein was fully functionally active was confirmed by its specific DNA-binding properties and its ability to activate gene transcription by over two orders of magnitude in an in vivo assay.

The human papillomavirus type 18 (HPV18) E2 gene product is a repressor of the HPV18 regulatory region in human keratinocytes

The human papillomavirus type 18 (HPV18) long control region (LCR) harbors transcriptional promoter and enhancer elements. Recombinant plasmids bearing all or part of the HPV18 LCR cloned in enhancer or promoter configuration upstream of the chloramphenicol acetyltransferase (CAT) gene were transfected into human fibroblasts and keratinocytes. Although the HPV18 enhancer can function in the absence of E2 gene products in both fibroblasts and keratinocytes, the promoter activity of the HPV18 LCR is detectable in keratinocytes but not in fibroblasts, suggesting that it is tissue specific. This promoter activity was repressed in human keratinocytes not only by the bovine papillomavirus type 1 E2 gene product but also by the homologous HPV18 E2 gene product. The promoter involved in the HPV18 E2 repression is located within a 230-base-pair domain directly upstream of the E6 open reading frame of the HPV18 LCR and is probably the previously identified E6 promoter. Although one cannot rule out the possibility that this repressing effect is mediated by a truncated form of HPV18 E2 protein, as was previously demonstrated for bovine papillomavirus type 1, a more likely explanation would be that the full-length HPV18 E2 protein behaves as a repressor. Indeed, at the same doses at which it inhibits transcription from the homologous HPV18 LCR, the HPV18 E2 gene product activates transcription from constructs bearing E2-binding palindromes cloned in enhancer configuration upstream of a heterologous promoter. The fact that the homologous HPV18 E2 gene product acts as a transcriptional repressor of the HPV18 LCR suggests a possible explanation for the overexpression of E6 and E7 open reading frames in cervical carcinoma cells and in cell lines derived from them.

Loss of bovine papillomavirus DNA replication control in growth-arrested transformed cells

The bovine papillomavirus type 1 (BPV-1) genome replicates as a plasmid within the nuclei of BPV-1-transformed murine C127 cells at a constant multiple copy number, and spontaneous amplification of the viral DNA is rarely observed. We report here that a mutant BPV-1 plasmid within a contact-inhibited C127 cell line replicated as a stable multicopy plasmid in exponentially growing cells but amplified to a high level in confluent cell culture. In situ hybridization analysis revealed that most of the mutant viral DNA amplification occurred in a minor subpopulation of cells within the culture. These consisted of giant nondividing cells with greatly enlarged nuclei, a cell form which was specifically induced in stationary-phase cultures. These observations indicated that expression of a viral DNA replication factor was cell growth stage specific. Consistent with this hypothesis, considerable amplification of wild-type BPV-1 DNA associated with characteristic giant cell formation was observed in typical wild-type virus-transformed C127 cultures following a period of growth arrest achieved by serum deprivation. Further observations indicated that induction of the giant-cell phenotype was dependent on BPV-1 gene expression and implicated a viral E1 replication factor in this process. Moreover, heterogeneity in virus genome copy numbers within the giant-cell population suggested a complex regulation of induction of DNA synthesis in these cells. It appears that this process represents a mechanism employed by the virus to ensure maximal viral DNA synthesis within a growth-arrested cell. Fundamental questions concerning the integration of the virus-cell control circuitry in proliferating and resting cells are discussed.

Identification of DNA-protein interactions and enhancer activity at the 5' end of the upstream regulatory region in human papillomavirus type 11

We have examined the 5' end of the noncoding region of the genome of a human papillomavirus, HPV-11, for regulatory elements using permissive host cells. This region of unknown function in the upstream regulatory region (URR) is known to have unusual DNA structure and frequently contains rearrangements which are associated with some more virulent isolates. This 5' 269-bp fragment was found to exhibit both specific DNA-protein binding using laryngeal papilloma protein extracts and enhancer activity in normal and papillomatous primary laryngeal cells. The viral DNA flanks the L1 open reading frame and does not contain the viral E2 binding site. Three distinct protein binding sites are contained in a 50-bp region of the fragment. This fragment, as a whole, functions as an enhancer in primary laryngeal and papilloma cells when ligated to the SV40 promoter and SV40 T-antigen gene. We conclude that this part of the noncoding region of the papillomaviruses has elements characteristic of regulatory elements in cells permissive for infection by these viruses.

Evidence for multiple vegetative DNA replication origins and alternative replication mechanisms of bovine papillomavirus type 1

By following up the chance detection in the electron microscope of a DNA replication intermediate within a preparation of bovine papillomavirus (BPV-1) DNA isolated from purified virus particles, information was obtained about the mechanism of BPV-1 genome replication during the final stages of virus multiplication in naturally infected bovine wart tissue. The structure of viral replication intermediates was investigated by electron microscopic analysis of viral DNA linearized by digestion with restriction endonucleases which cleave the circular BPV-1 chromosome at defined sites. Both Cairns and rolling circle-type molecules were identified. Furthermore, replication eyes were widely distributed within the viral genome, indicating that vegetative BPV-1 DNA replication origins are largely uncoupled from previously described plasmid maintenance sequence elements.

Numerous nuclear proteins bind the long control region of human papillomavirus type 16: a subset of 6 of 23 DNase I-protected segments coincides with the location of the cell-type-specific enhancer

The long control region of the human papillomavirus type 16 genome is 856 base pairs (bp) long. It contains a cell-type-specific enhancer, a glucocorticoid response element, and sequences mediating the response to the viral gene products of open reading frame E2; all three regulate the promoter P97. We mapped binding sites of trans-acting proteins relevant for the cell-type-specific enhancer and other cis-acting elements by DNase I footprint experiments with nuclear extracts from HeLa cells. Throughout the human papillomavirus type 16 long control region 23 footprints protect 557 of 900 bp. Nine footprints fall into a 400-bp segment that was previously identified to contain the cell-type-specific enhancer. Variations of the protein concentration in the footprint reaction do not affect six of these nine footprints. At high protein concentrations, three footprints fuse to a 106-bp protected region, suggesting that this segment specifically binds several proteins of lower affinity or abundance. Unexpectedly, extracts from human MCF7 and mouse 3T3 cells, in which the enhancer is inactive, give footprints identical to those obtained with HeLa extracts. Seven footprints contain the sequence 5'-TTGGC-3'. Footprint competition experiments suggest that factor NFI binds to these seven motifs. Competition with cloned oligonucleotides in transfections suggests that these elements contribute to the enhancer function. Subcloning identifies a 232-bp fragment between positions 7524 and 7755 as sufficient for full enhancer activity. Several of the six footprinted elements on this segment may cooperate functionally, since subclones of this region show decreased or no cell-type-specific enhancer function.

Nucleic acid hybridization as a diagnostic tool for the detection of human papillomaviruses

At this time nucleic acid hybridization tests are the most sensitive and reproduceable methods for the detection and differentiation of HPV types in clinical samples. The hybridization method of choice depends on the information desired and the availability of the proper diagnostic nucleic acid probes. Assuming most of the HPV nucleic acid probes become readily available in the near future, then the most sensitive test for screening clinical specimens--albeit the most laborious--will be the Southern blot procedure. As more information covering the involvement of HPV infections with the progression of lesions from benign to malignant is compiled, the need to know the particular subtype or status of HPV integration may become more or less important in the screening of clinical samples. If this information becomes less important, or unnecessary for a simple screening procedure, then dot blot hybridization may prove to be a much easier method for obtaining the information desired. If the sensitivity of in-situ hybridization using non-radioactive probes increases, then this method would become the fastest, easiest, and cleanest technique for the screening of a large number of clinical samples where limited information is desired. The ideal test for the future would be automated. In order to automate a test for HPV infections, the test design must become much simpler, and in order to design a simpler test, more information will be needed concerning the biology of HPV infections, how they cause benign or malignant cellular proliferation, and how the host immune system responds to HPV infections.

Human papillomaviruses and carcinomas

The recognition of multiple types of human papillomaviruses has resulted in remarkable progress in the detection of persisting viral nucleic acid sequences in carcinomas. The consistent transcription in tumors of two early open reading frames, E6 and E7, with few exceptions (Lehn et al., 1985), indicates a role for the products of these genes in the induction and/or maintenance of the transformed state. A number of studies have shown that in vitro transformation can be achieved by transfection of E6/E7 DNA, and proteins encoded by these DNA sequences can be demonstrated in primary human keratinocytes immortalized by this DNA (Kaur et al., 1989). Mutagenesis experiments are needed to determine the absolute requirement for and function of these genes in transformation. A preferential association of some types with benign lesions while others may be frequently found in malignant tumors has been observed. HPV types 5 and 8 in epidermodysplasia verruciformis patients and types 16, 18, 31, 33, etc. in genital lesions are most frequently associated with progression to malignancy, whereas other types, such as HPV-6,-10, -11, and -20, are regularly identified in benign warts. Such distinctions are not absolute but provide the initial steps toward establishing a causal role for some human papillomaviruses in carcinomas. The need for well-designed epidemiological studies in concert with optimum molecular and serologic evaluations is evident (Armstrong et al., 1988). The data from human and animal studies indicate that papillomaviruses contribute significantly to the development of many, if not all, carcinomas, but we do not yet have a clear understanding of the importance of other interacting viral, chemical, or cellular factors. The application of gene cloning and non-stringent hybridization (Law et al., 1979) has provided us with an apparently ever-increasing catalog of human papillomaviruses. More effort is now required to establish their prevalence, the natural history of infection, and the mechanism of neoplastic transformation.

Viral and cellular oncogenes in papillomavirus-associated cancers

Papillomaviruses are one of several factors implicated in the aetiology of squamous cell carcinomas both in man and in animals. Their potential for malignant transformation is fully expressed when co-operation takes place between viral functions, cellular functions and chemical or physical co-carcinogens. This review presents a brief description of the viral transforming genes and of the cellular genes involved in transformation, and attempts to analyse how the co-operation between the two sets of genes is achieved.

A novel spontaneous mutation of the bovine papillomavirus-1 genome

A cell clone (cl.2) having an atypical transformed morphology was isolated from a murine C127 cell culture experimentally infected with a bovine papillomavirus type 1 (BPV-1) virion preparation. cl.2 cells exhibited minimal transformed characteristics and contained multiple copies of a BPV-1 plasmid with a molecular size slightly less than that of the wild type viral genome. A simple deletion of 277 bp was mapped to the distal portion of the viral 69% transforming fragment where the early gene region merges with the late gene region. None of the recognized early open reading frames were affected by the deletion but sequences including the common early gene mRNA polyadenylation (poly(A] signal and several base pairs of the "distal" enhancer element were deleted. Transfection of C127 cultures with low molecular weight (Hirt) DNA prepared from cl.2 cells led to the appearance of transformed cell foci, and Southern blotting analysis of a cl.2 Hirt DNA-transformed cell line confirmed that the deletion did not destroy the ability to replicate as a high copy plasmid. Removal of the natural early poly(A) signal did not obligate use of the alternative natural viral poly(A) signal located towards the end of the late region. Instead, a new major early mRNA polyadenylation site was mapped close to the unique BamHI recognition sequence at the distal end of the transforming region. Our results underline previous observations that there is a block to the production of stable mRNAs from the late gene region in BPV-1-transformed C127 cells, yet this is not necessarily explained by premature termination of transcription within this region.

The molecular biology of human papillomaviruses and the pathogenesis of genital papillomas and neoplasms

Numerous studies over the past several years have demonstrated that human papillomaviruses (HPV) may play a significant role in the development of several types of human neoplasia. Although it has been accepted for some time that HPVs are responsible for benign epithelial tumors, data accumulated in more recent years have implicated this group of animal viruses in a number of premalignant lesions, as well as a variety of epithelially derived malignancies. Genital, oral, and some rare types of cutaneous cancers have all been found to contain varying degrees of HPV DNA. In several instances secondary tumors resulting from metastases to lymph nodes and lungs have also been demonstrated to contain HPV DNA. Although there is a strong correlation between the presence of the virus and the malignant phenotype in several of these cancers, the precise role of the virus in the development of malignant tumors has not yet been elucidated. A major difficulty in elucidating the role of papillomaviruses in oncogenesis has been the lack of an appropriate in vitro culture system that would permit the growth of the virus and allow an analysis of its transforming properties. Nevertheless, recent advances in molecular biology have permitted the molecular cloning and amplification of HPV viral DNA, thereby facilitating its use as a probe for the detection of miniscule amounts of HPV DNA and HPV RNA in tumor biopsies. Moreover, DNA transfections of cells in culture have been extremely useful in the study of viral DNA replication and transformation properties, providing information on the maintenance and oncogenicity of HPV DNA. These advances have implications for the improved detection of HPV infections, which will aid in patient diagnosis and prognosis. In addition, future treatment and prevention programs may come as a direct result of these basic studies on the mechanism of HPV-induced oncogenesis.

A transcriptional repressor encoded by BPV-1 shares a common carboxy-terminal domain with the E2 transactivator

A negative-acting transcriptional regulatory factor encoded by bovine papillomavirus type 1 (BPV-1) was identified. This factor inhibits BPV-1-mediated transformation of mouse C127 cells; inhibition is BPV-1-specific and occurs only when the BPV-1 transforming genes are regulated by authentic transcriptional control elements. Plasmids expressing the inhibition function also repress E2 transactivation of the BPV-1 E2-dependent enhancer, and this repression is mediated by the same cis-acting element required for E2 transactivation. Inhibition of transformation may result from down-regulation of E2-dependent viral gene expression. Analysis of cDNA expressing the inhibition/repression activities mapped the function to the 3' domain of the E2 open reading frame. The E2 open reading frame thus encodes both positive and negative transcriptional regulatory factors, and these factors share a carboxy-terminal domain.

A model for the development of the tandem repeat units in the EBV ori-P region and a discussion of their possible function

This paper presents an analysis of the repeat units of the ori-P region of the Epstein-Barr virus (EBV) genome. These repeat units are well-conserved palindromes. The pattern of these repeats, their lengths, phases, and the distribution of the relatively few substitutions are explained by a scenario that gives a reasonable course for the evolutionary development of the pattern. The scenario suggests a model for the production of an initiating 3/2 palindrome from a moderately lengthy sequence. The palindromic units are then multiplied in judicious combinations by mechanisms of unequal crossing-over events associated with some point substitutions and a few instances of slippage replication. The potential secondary structures of the two separated tandem palindromic repeat regions in ori-P are contrasted. Possible modes of binding of Epstein-Barr nuclear antigen (EBNA) 1 protein to these hairpins are discussed. A number of possibilities for the origin and development of the ori-P region in relation to viral and cellular function are considered.

A promoter with an internal regulatory domain is part of the origin of replication in BPV-1

Extrachromosomal elements that are stably maintained at a constant copy number through cell doublings are a good model system for the study of the regulation of DNA replication in higher eukaryotes. Previous studies have defined both cis and trans functions required for the regulated plasmid replication of the bovine papilloma virus in stably transformed cells. Here, a sequence known to be a cis-dominant element of the replication origin of the plasmid is shown to contain a promoter for transcription. Both in vitro and in vivo assays have been used to define this promoter and show that a sequence located just 3' to the transcriptional start site is required for activity. This DNA sequence element, which has been defined through deletions, coincides with a binding site for a cellular factor and is also required for a functional origin of replication. Possible models for how a transcription factor may play a role in the regulation of DNA replication are discussed.

Structure, DNaseI hypersensitivity and expression of integrated papilloma virus in the genome of HeLa cells

Three integrated copies of human papilloma virus-18 (HPV-18) have been identified in HeLa DNA as HindIII bands. HPV-18 has no HindIII restriction site in its genome. The three segments: A, 8.4 kb; B, 7.9 kb and C, 5.8 kb, have an incomplete viral genome. All of them have most of the 1.1-kb BamH1 non-coding fragment of HPV-18, which seems to contain the viral origin of replication and regulatory elements. Two of the segments (A and B) have a common 5'-end break-point in the viral genome within the L2 open reading frame (ORF). In both segments the second early transcriptional unit of the virus (E6, E7 and E1) is structurally conserved in a new environment. The 3'-end break-point for segments A and B is within the E2 ORF. Segment C has the L2 and L1 ORF but none of the genes of the early region. Segments A and B have a specific DNaseI-hypersensitive site located in the E7/E1 region. The nucleotide sequence of this region has twelve papova virus enhancer-like consensus sequence (5'-TACCACANTA-3') and a double inverted repeat with fixed spacing capable of forming a hairpin loop. Two viral RNA transcripts of 4.8 kb and 1.7 kb have been detected in poly(A)-rich RNA. The larger transcripts hybridizes to E6, E7 and E1 ORFs as well and has 2.4 kb of host sequence in its 3' end. The smaller transcript hybridizes with E6 and E7 ORFs and the beginning of E1, the final 0.7 kb of E1 are not detectable. No transcripts have been detected carrying E2, E4, E5, L2 and L1 ORF sequences. The transcripts are derived from segments A or B. Segment C is not transcriptionally competent.

The noncoding region of HPV-6vc contains two distinct transcriptional enhancing elements

HPV-6vc subgenomic fragments were inserted into an enhancer-dependent expression vector for chloramphenicol acetyltransferase (CAT) and assayed for the presence of transcriptional enhancing elements. A transcriptional enhancing element was detected in the noncoding region (NCR) of the HPV-6vc viral genome when the CAT assays were performed in viral transformed human kidney cell lines (293 and 324K), in human cervical carcinoma cell lines (HeLa and Siha), and in bovine papillomavirus type 1 (BPV-1) transformed mouse cells (C127-53). The NCR region of the HPV-6b genome was only capable of enhancing transcription of the CAT gene in the HeLa cell line at a level one-third that of the HPV-6vc NCR. The HPV-6vc NCR enhancing activity in C127-53 cells was further stimulated by the addition of sodium butyrate to the growth medium. Localization of the DNA sequences in the HPV-6vc NCR responsible for enhancing transcription revealed two distinct enhancer elements. One element (HPV-6vc position 7218-7544) was active in the 293, HeLa, Siha, and C127-53 cells. The second enhancer element (HPV-6vc position 7544-7971) was only capable of stimulating transcription in HeLa, C127-53, and Siha cells. When the HPV NCR-CAT expression vectors were cotransfected with a competitor plasmid (pNCR75) into C127-53 or HeLa cells then transcriptional enhancement decreased, indicating competition of cellular factors which affect both segments of the HPV-6vc NCR.

Negative control of DNA replication in composite SV40-bovine papilloma virus plasmids

To identify DNA sequences that function in the control of DNA replication, we designed a hybrid replicon consisting of linked SV40 and BPV DNA sequences. In the composite SV40-BPV plasmid negative control encoded by BPV is dominant over the uncontrolled replication encoded by the positive factor, SV40 T antigen. Using a transient replication assay, we show that replication control requires three BPV elements. Two cis-acting sequences are closely linked to BPV replication origins. A third trans-acting element is encoded within the 5' part of the BPV E1 open reading frame (ORF) and is separable from the positive replication factor encoded within the 3' part of the same ORF. The controlled replication of SV-BPV composite replicons has enabled us to create permanent COS cell lines that stably maintain these plasmids as episomes.

Epidermodysplasia verruciformis-associated human papillomavirus 8: genomic sequence and comparative analysis

Human papillomavirus (HPV) 8 induces skin tumors which are at high risk for malignant conversion. The nucleotide sequence of HPV8 has been determined and compared to sequences of papillomaviruses with different oncogenic potential. The general organization of the HPV8 genome is similar to that of other types. Highly conserved, genus-specific sequences were found in open reading frames (ORFs) E1, E2, and L1. In ORFs E6, E7, and L2, HPV8 is more distantly related, but it was possible to differentiate subgenera in which HPV8 belonged to the HPV1-cottontail rabbit papillomavirus group. Sequences within ORF E4 and part of ORF L2 are rather type specific. HPV8 stands out by several unique features: the considerably reduced size of the noncoding region (397 base pairs), with a seemingly low potential for forming complex secondary structures; a cluster of putative promoter elements in the 3' half of ORF E1; an RNA polymerase III promoter-like sequence close to the C terminus of ORF E2; and of particular interest, the homology between the putative protein encoded by ORF E4 and the Epstein-Barr virus nuclear antigen 2 protein, which may reflect similar mechanisms in virus-mediated transformation.

Properties of intracellular bovine papillomavirus chromatin

Episomal nucleoprotein complexes of bovine papillomavirus type 1 (BPV-1) in transformed cells were exposed to DNase I treatment to localize hypersensitive regions. Such regions, which are indicative for gene expression, were found within the noncoding part of the genome, coinciding with the origin of replication and the 5' ends of most of the early mRNAs. However, there were also regions of hypersensitivity within the structural genes. These intragenic perturbations of the chromatin structure coincide with regulatory sequences at the DNA level. One of these regions maps in close proximity to a Z-DNA antibody-binding site which is located near the putative BPV-1 enhancer sequence.

The nucleotide sequence and genome organization of human papilloma virus type 11

The complete nucleotide sequence of human papilloma virus type 11 (HPV11) DNA (7931 bp) was determined. HPV11 DNA which has been isolated from laryngeal papillomas and from genital warts (condylomata acuminata) shows a high degree of sequence homology to HPV6b (82%). The arrangement of open reading frames is very similar to HPV6b, the homology of the deduced amino acid sequences varies between 58 and 92%. Characteristic features of the noncoding region between the L1 and E6 open reading frames is an AT-rich domain of about 200 bp with extended stretches of alternating thymine-purine bases and a 12-bp inverted repeat element ACCG NNNN CGGT arranged in tandem upstream of the putative early promoter TATA box.

Replication of the bovine papillomavirus type 1 genome; antisense transcripts prevent episomal replication

A subgenomic fragment, representing 69% of the bovine papillomavirus type 1 (BPV-1) genome, has the capacity to transform mouse C127 cells in vitro and to replicate episomally in these cells. In the present study we have cloned this BPV-1 fragment between two retrovirus-derived long terminal repeats (LTRs) in the two possible orientations. The constructs were designated pMR and pML. The pMR construct contained the BPV-1 genome in the same transcriptional orientation as that of the LTRs whereas the pML construct contained the BPV-1 fragment in the opposite orientation. Both types of construct were capable of transforming mouse C127 cells with approximately the same efficiency. Analysis of the intracellular DNA from cells transformed with pMR and pML revealed that both cell types contained a large number of viral DNA copies. However, whereas the pMR-transformed cell clones contained episomally replicating BPV-1 DNA, the pML-transformed cell clones all contained integrated viral genomes. Analysis of RNA from the transformed cells revealed that the pML-transformed cells, unlike the pMR-transformed cells, contained large amounts of antisense BPV-1 transcripts which presumably interfere with the mRNAs that are required for episomal BPV-1 replication. The results are of importance for the future design of BPV-1 vector constructs.