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

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.

Bovine papillomavirus E2 gene regulates expression of the viral E5 transforming gene

We have performed transient-expression experiments with CV1 monkey kidney cells to investigate the role of the bovine papillomavirus type 1 (BPV1) E2 gene in the regulation of the E5 transforming gene. Direct analysis of the 7-kilodalton open reading frame (ORF) E5 protein and measurements of the expression of an E5-chloramphenicol acetyltransferase fusion protein indicate that the efficient expression of ORF E5 requires the full-length E2 gene, which can be supplied in trans. The viral long control region is required in cis for this response to ORF E2, and it acts in a position- and orientation-independent fashion characteristic of a transcriptional enhancer. Deletion analysis suggests that the P2443 promoter is required for efficient expression of the E5 gene. The E2 repressor activity encoded in the 3' end of the E2 gene inhibits the expression of ORF E5. These effects define a major BPV1 regulatory circuit and appear to explain the transformation behavior of a variety of BPV1 mutants.

Use of simian virus 40 replication to amplify Epstein-Barr virus shuttle vectors in human cells

We have increased the copy number of Epstein-Barr virus vectors that also carry the origin of replication of simian virus 40 (SV40) by providing a transient dose of SV40 T antigen. T antigen was supplied in trans by transfection of a nonreplicating plasmid which expresses T antigen into cells carrying Epstein-Barr virus-SV40 vectors. A significant increase in vector copy number occurred over the next few days. We also observed a high frequency of intramolecular recombination when the vector carried a repeat segment in direct orientation, but not when the repeat was in inverted orientation or absent. Furthermore, by following the mutation frequency for a marker on the vector after induction of SV40 replication, it was determined that SV40 replication generates a detectable increase in the deletion frequency but no measurable increase in the frequency of point mutations.

An origin unwinding activity regulates initiation of DNA replication during mammalian cell cycle

An in vitro assay was developed to study the positive factors that regulate the onset of DNA replication during the mammalian cell cycle. Extracts prepared from cells at defined positions in the cell cycle were used to examine the replication of SV40 DNA in a cell free system. Extracts prepared from S phase cells were ten times more efficient at initiating replication at the SV40 origin than were extracts from G1 cells, whereas elongation rates were similar in G1 and S reactions. At a discrete point in the cell cycle, just before the cell's entry into S, an activity appeared that was required, in conjunction with SV40 T antigen, for site specific initiation at the SV40 origin. This factor had a role in unwinding DNA at the replication origin.

The product of the bovine papillomavirus type 1 modulator gene (M) is a phosphoprotein

The M gene of bovine papillomavirus type 1 has been genetically defined as encoding a trans-acting product which negatively regulates bovine papillomavirus type 1 replication and is important for establishment of stable plasmids in transformed cells. The gene for this regulatory protein has been mapped in part to the 5' portion of the largest open reading frame (E1) in the virus. We constructed a trpE-E1 fusion gene and expressed this gene in Escherichia coli. Rabbits were immunized with purified fusion protein, and antisera directed against the product were used to identify the M gene product in virus-transformed cells. In this way a polypeptide with an apparent molecular mass of 23 kilodaltons was detected. The virus-encoded product is phosphorylated and can be readily detected by immunoprecipitation assays from cells transformed by the virus. Cells that harbor viral DNA without M as integrated copies do not produce this protein, whereas cells that harbor integrated viral genomes which are defective for another E1 viral gene important for plasmid replication, R, do produce this protein. The protein has an anomalously low electrophoretic mobility. An in vitro translation product of an SP6 RNA product of a sequenced cDNA predicts a molecular mass of 16 kilodaltons for the protein, and this in vitro translation product has an electrophoretic mobility identical to that of the in vivo immunoprecipitated protein. The results of these studies confirm our previous genetic studies which indicated that part of the E1 open reading frame defined a discrete gene product distinct from other putative products which may be encoded by this open reading frame.

The adeno-associated virus rep gene inhibits replication of an adeno-associated virus/simian virus 40 hybrid genome in cos-7 cells

A hybrid adeno-associated virus (AAV)/simian virus 40 (SV40) genome is described. In this construct SV40 regulatory sequences, including the early promoter/enhancers and origin of DNA replication, were substituted for the AAV p5 promoter, which normally controls expression of the AAV rep gene. The hybrid genome was phenotypically indistinguishable from wild-type AAV in human cells in the presence or absence of helper virus. Upon transfection into cos-7 cells, which constitutively produced the SV40 tumor antigen, the genome replicated as a plasmid when the SV40 origin was used, although with a low efficiency compared with that of a non-AAV/SV40 replicon. The low level of replication was due to an inhibitory effect of an AAV rep gene product and was specific for replicons containing AAV sequences. Target AAV sequences required for inhibition by rep appeared to reside in the terminal repetitions since deletion of these sequences allowed efficient replication in the presence of the rep gene. The possible role for negative autoregulation of AAV DNA replication in latent infection and helper-dependent replication by AAV is discussed.

[Warts and viruses]

The discovery that papillomaviruses are correlated with various types of cancer in man has led to increased interest in this virus group. A more detailed study of these viruses has only become possible with the introduction of recombinant DNA techniques. The most thoroughly studied representative, the bovine papillomavirus type 1, has now itself become a tool in genetic engineering.

"Hit and run" transformation of mouse C127 cells by bovine papillomavirus type 4: the viral DNA is required for the initiation but not for maintenance of the transformed phenotype

Morphological transformation of C127 mouse fibroblasts by bovine papillomavirus type 4 (BPV-4) DNA depends on additional factors, including cell density, the presence of TPA, the concentration of fetal calf serum, and the physical state of the input DNA. Low cell density or the presence of TPA allows the achievement of full transformation, suggesting that disturbance of cell-to-cell contact may be necessary for the expression of the malignant phenotype. TPA also induces a burst of viral DNA synthesis and transcription. The frequency of focus formation is fivefold higher in the presence of high serum than in low serum, indicating that growth factors are required during the early stages of transformation. Although the same number of foci is obtained with either circular or linear DNA, the cells transfected with linear DNA are at a more advanced stage of transformation, being capable of anchorage-independent growth and tumorigenic in nude mice; only 5 out of 21 of these cell lines contain viral DNA in integrated and rearranged forms. In contrast cells transfected with circular DNA are anchorage-dependent but tumorigenic in mice, and do not contain any viral DNA. The linear DNA has an interrupted E1 ORF and fully transformed cells are obtained also with a subgenomic viral DNA fragment containing part of the L1 ORF, the complete E6, E7, and E8 ORFs, and the truncated E1 ORF under the control of the BPV-4 regulatory region; viral DNA is not maintained in any of these cell lines. In total, only 15% of the transformed cell lines contains viral DNA. These results are discussed in the light of the "hit and run" model of cell transformation.

A role for the nuclear envelope in controlling DNA replication within the cell cycle

In eukaryotes the entire genome is replicated precisely once in each cell cycle. No DNA is re-replicated until passage through mitosis into the next S-phase. We have used a cell-free DNA replication system from Xenopus eggs to determine which mitotic changes permit DNA to re-replicate. The system efficiently replicates sperm chromatin, but no DNA is re-replicated in a single incubation. This letter shows that nuclei replicated in vitro are unable to re-replicate in fresh replication extract until they have passed through mitosis. However, the only mitotic change which is required to permit re-replication is nuclear envelope permeabilization. This suggests a simple model for the control of DNA replication in the cell cycle, whereby an essential replication factor is unable to cross the nuclear envelope but can only gain access to DNA when the nuclear envelope breaks down at mitosis.

Identification of a UV-induced trans-acting protein that stimulates polyomavirus DNA replication

Previous studies provided indirect evidence that the ability of a variety of DNA-damaging agents to induce asynchronous polyomavirus DNA replication in the H3 rat fibroblast cell line is mediated by a trans-acting factor. Using an erythrocyte insertion technique to introduce protein fractions from UV-irradiated cells into unirradiated H3 cells, we have now obtained evidence that this factor is a 60-kilodalton protein. These findings provide evidence that DNA damage in mammalian cells induces a factor that can alter the replication of a viral DNA.

Cis-acting negative control of DNA replication in eukaryotic cells

We show that in stable monkey cell lines, the replication of a chimeric SV40-BPV episomal replicon occurs once and only once per cell cycle. The copy number of this episome is stably maintained even when an excess of the limiting initiation factor T antigen is provided. These experiments therefore uncover a cis-acting negative control mechanism whereby replication control is not focused on limiting the activity of positive factors; rather, replication is permitted in unreplicated replicons but is actively prevented, in cis, in replicons that have already been duplicated. We also find that the initiation factor SV40 T antigen remains associated with its SV-BPV episomal template in a kinetically stable and potentially heritable state.

Multiple cis-active elements in the long control region of bovine papillomavirus type 1 (BPV-1)

A 1.0 kb region of the BPV-1 genome (the long control region, LCR), contains controls for transcription and the origin of replication. Transcription directed by the LCR is activated by the viral encoded E2 protein. To define the essential cis acting elements that are required to control transcription we have constructed a series of deletions throughout the LCR. We have identified three important domains in the LCR, two of which respond to E2. We have analysed the ability of small subcloned regions of the E2 responsive domains to act as enhancers in a heterologous assay system. This has led to the identification of five independent E2 responsive elements. We have shown that a fragment of only 38 base pairs is sufficient to respond to activation by E2. We also present evidence to suggest two types of E2 responsiveness that result in strong or weak activation. Strong response is correlated with the presence of the sequence 5'-ACCG/TNNNC/TCGGTGC-3' whereas weak response is correlated with the presence of a related sequence 5'-ACC(N)6GGT-3'. The contribution of these multiple elements to viral transcription is discussed.

Chromosome replication in cell-free systems from Xenopus eggs

Cell-free systems from eggs of the frog Xenopus laevis are able to perform most of the acts of eukaryotic chromosome replication in vitro. This now includes the crucial regulatory step of initiation, which had only been achieved for viral systems previously. Purified DNA or nuclei are able to initiate and complete semi-conservation replication in egg extracts in vitro (Blow & Laskey, Cell 47, 557-587 (1986). Replication does not require specialized DNA sequences either in vitro or in microinjected eggs, but in both systems large templates replicate more efficiently than small templates. In some cases replication can re-initiate, excluding the possibility that replication is primed by preexisting primers in the template preparations. When nuclei are replicated in vitro, only one round of replication is observed in a single incubation resembling the single round of replication observed for purified DNA after micro-injection. The mechanism that prevents re-initiation of replication within a single cell cycle is discussed and certain models are eliminated. Nucleosome assembly from histones and DNA has also been studied in cell-free systems from Xenopus eggs. Fractionation has led to the identification of two acidic proteins called nucleoplasmin and N1, which bind histones and transfer them to DNA. The sequences of both proteins have been determined by cDNA cloning and sequencing. Both proteins are found as complexes with histones in eggs.

Amplification of a chorion gene cluster in Drosophila is subject to multiple cis-regulatory elements and to long-range position effects

We have used P-element transformation to study cis-acting elements involved in the control of amplification of the third chromosome chorion gene cluster (66D12-15) in Drosophila melanogaster. To reduce position effects large fragments (5.7 to 12 kb; kb = 10(3) bases) of chorion DNA and the 7.2 kb ry+ fragment were used to "buffer" these putative elements from sequences at the insertion site. Nevertheless, even the longest constructs were profoundly affected by the insertion sites and showed amplification levels ranging from undetectable to higher than in the endogenous locus. Any amplification was tissue and temporally correct and extended into the neighboring ry+ sequences. Analysis of amplification levels at various points along two constructs bearing the same 10 kb chorion insert in opposite orientations showed maximal levels occurring at one end of the chorion fragment, irrespective of whether that end was buffered at the middle of the transposon or exposed close to the insertion site. The maximally amplifying region encompasses the amplification control element (ACE), which has been shown to be necessary for amplification, in agreement with its putative role as a replication origin. We have additionally identified amplification-enhancing elements present elsewhere in the 10 kb chorion fragment, which are needed for attainment of high copy number. These elements, distinct from the ACE, have been only coarsely localized within two 2.25 to 2.3 kb regions. Some interesting sequence similarities between these two regions and the ACE element are pointed out.

Human papillomavirus types 6 and 11 mRNAs from genital condylomata acuminata

We have identified and mapped a number of RNA species of human papillomavirus types 6 and 11 from condylomata acuminata by the electron microscopic R-loop technique. Each of the early (E)- and late (L)-region open reading frames (ORFs) deduced from the DNA sequences was represented in one or more transcripts. In addition, RNA species that could encode the modulator of DNA replication and the repressor of transcription, functions recently identified in the genetically similar bovine papillomavirus type 1, were also detected. Some ORFs were 5' proximal in one or more transcripts, whereas others were not 5' proximal in any species, suggesting that internal initiation of translation might be required to gain access to these latter ORFs. Virtually all transcripts had their 5' ends located in the E region and were polyadenylated at one of two sites, i.e., at the end of the E region or at the end of the L region. The great majority of the RNAs were derived from the E region of the genome, with one species approximately 50 to 100 times more abundant than the others. For most of the RNAs, the 5' end mapped near nucleotide 700; minor populations had 5' ends near nucleotide 100 or 1200. By correlating our mapping data with the genomic DNA sequences as well as available RNA structures and cDNA sequences of several papillomaviruses, we predict a number of mRNA splice donor and acceptor sites and suggest that the papillomaviruses have sophisticated usage of ORFs through alternative promoters, mRNA splice sites, and polyadenylation sites.

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.

Differential promoter utilization by the bovine papillomavirus in transformed cells and productively infected wart tissues

Expression of the 'late' genes of bovine papillomavirus type 1 (BPV-1) occurs only in the differentiated keratinocytes of the productively infected fibropapilloma. A detailed analysis of viral transcription in the fibropapilloma was performed and compared to BPV-1 specific transcription in transformed C127 cells. A cDNA library was constructed from bovine fibropapilloma mRNA using the method of Okayama and Berg. Analysis of full length cDNAs showed that the majority of viral transcripts in the fibropapilloma have 5' termini near nt 7250 and utilize a common splice donor site at nt 7385. This mRNA start site was confirmed by the combination of primer extension and nuclease S1 analyses; it is not utilized in the BPV-1-transformed C127 cell, thus identifying it as a wart specific, 'late' promoter. Upstream of this mRNA start site is a tandemly repeated sequence element homologous to the SV40 late promoter sequence GGTACCTAACC, which has been shown to be important for the efficient utilization of the SV40 major late start site. Two additional mRNA start sites at nt 7185 and nt 7940 in the long control region (LCR) were identified and were found to be used in bovine warts as well as in BPV-1-transformed mouse cells. The promoter region upstream of the nt 7940 mRNA start site contains the E2 responsive enhancer mapping between nt 7611 and nt 7805 [Spalholz, B.A., Lambert, P.F., Yee, C. and Howley, P.M. (1987) J. Virol., in press].(ABSTRACT TRUNCATED AT 250 WORDS)

Trans-activation of an upstream early gene promoter of bovine papilloma virus-1 by a product of the viral E2 gene

The approximately 1000 nucleotide long upstream regulatory region (URR) of bovine papilloma virus-1 (BPV-1) contains a cis element which responds to trans-activation by a diffusible factor encoded in the viral E2 open reading frame (ORF). A series of URR DNA fragments have been linked to two heterologous genes, bacterial chloramphenicol acetyl transferase (cat) or herpes simplex virus-1 thymidine kinase (tk), and tested in transient transfection assays for transcription initiating at the authentic upstream early viral promoter, P89. Transcriptional activity of the P89 promoter was greatly elevated in the presence of the E2 trans-activator gene product. The E2-responsive cis element (E2R) of P89 has been mapped to sequences -277 to -131 nucleotides upstream from the transcription start site (BPV nucleotide 89). The E2R element functioned as a strong transcriptional enhancer in cis with the SV40 early or the tk promoter in the presence, but not in the absence, of the E2 gene product. However, several heterologous promoters which lack sequences related to the E2R element were also trans-activated in transient cotransfections by a function encoded in the E2 ORF of BPV-1, albeit to a much lesser extent. In addition to activation of early viral gene transcription, the E2 regulatory gene(s) may therefore have the potential to alter cellular gene expression.

A bovine papillomavirus type 1-encoded modulator function is dispensable for transient viral replication but is required for establishment of the stable plasmid state

A bovine papillomavirus (BPV) type 1-encoded function (M) which is a negative regulator of viral plasmid replication has been described elsewhere (Berg et al. Cell, in press; Roberts and Weintraub, Cell, in press). We report here that expression of M, which is a repressor of transient BPV replication and is not required as a positive factor in these assays, is required for the establishment of the viral genome as a stable nuclear plasmid. This function is encoded in part by the 5' portion of the BPV E1 open reading frame, whereas the 3' part of this open reading frame encodes a positive replication function (R). The R function is required for early replication events. We used transient replication assays to define the phenotypes of mutants in both the R and M genes and complementation tests to show that R and M define two separate genes. We showed that R- and M- mutants could also complement each other in stable assays. In cotransfection experiments, M- mutants had a lethal effect on the growth of G418-resistant colonies, and in addition their morphological transformation efficiencies were reduced. The rare colonies which did appear contained the mutant DNA integrated into the cellular genome. R- mutants transformed with wild-type efficiency, and the mutant DNA was also found integrated. When cotransfected, R- and M- mutants could each be established as unrearranged plasmids.