Characterization of K virus and its comparison with polyoma virus.

The antigenic relationship between the two murine papovaviruses, K virus and polyoma virus, was examined by serological techniques to determine whether they shared any antigenic components. No cross-reactivity was found associated with the viral (V) antigens by the indirect immunofluorescence, neutralization, or hemagglutination-inhibition tests. The tumor (T) antigens expressed in transformed cells or cells productively infected by either K or polyoma virus did not cross-react by indirect immunofluorescence. An antigenic relationship was detected, however, among the late proteins of K virus, polyoma virus, simian virus 40, and the human papovavirus BKV, when tested with either hyperimmune sera prepared against polyoma virus and simian virus 40 or sera prepared against disrupted virions. The nucleic acids of K and polyoma viruses were compared by agarose gel electrophoresis and restriction endonuclease analysis. No nucleotide sequence homology between the genomes of these two viruses was detectable by DNA-DNA hybridization techniques under stringent conditions. The genome of K virus was found to be slightly smaller than that of polyoma virus, and the cleavage patterns of the viral DNAs with six restriction endonucleases were different. These findings indicate that there is little relationship between these two murine papovaviruses.     

Lack of sequence homology between the nucleic acids of Rauscher leukaemia virus and polyoma virus Y8e produced simultaneously in a continuous mouse cell line.

In a continuous cell line (Y8e) from spleen and thymus cells of mice, infected with RLV, the presence of both RLV and polyoma virus Y8e in a single cell could be demonstrated by electron microscopy. A comparison of the nucleic acids of RLV and polyoma virus from Y8e cells by two molecular hybridization methods showed lack of sequence homology between the viral nucleic acids.     

Conserved polynucleotide sequences among the genomes of papillomaviruses.

The DNAs of different members of the Papillomavirus genus of papovaviruses were analyzed for nucleotide sequence homology. Under standard hybridization conditions (Tm - 28 degrees C), no homology was detectable among the genomes of human papillomavirus type 1 (HPV-1), bovine papillomavirus type 2 (BPV-2), or cottontail rabbit (Shope) papillomavirus (CRPV). However, under less stringent conditions (i.e., Tm - 43 degrees C), stable hybrids were formed between radiolabeled DNAs of CRPV, BPV-1, or BPV-2 and the HindIII-HpaI A, B, and C fragments of HPV-1. Under these same conditions, radiolabeled CRPV and HPV-1 DNAs formed stable hybrids with HincII B and C fragments of BPV-2 DNA. These results indicate that there are regions of homology with as much as 70% base match among all these papillomavirus genomes. Furthermore, unlabeled HPV-1 DNA competitively inhibited the specific hybridization of radiolabeled CRPV DNA to bpv-2 DNA fragments, indicating that the homologous DNA segments are common among these remotely related papillomavirus genomes. These conserved sequences are specific for the Papillomavirus genus of papovaviruses as evidenced by the lack of hybridization between HPV-1 DNA and either simian virus 40 or human papovavirus BK DNA under identical conditions. These results indicate a close evolutionary relationship among the papillomaviruses and further establish the papillomaviruses and polyoma viruses as distinct genera.     

An electron microscopic method for studying and mapping the region of weak sequence homology between simian virus 40 and polyoma DNAs.

A procedure for investigating the possibility of small amounts of partial DNA sequence homology between two defined DNA molecules has been developed and used to test for sequence homology between simian virus 40 and polyoma DNAs. This procedure, which does not necessitate the use of separated viral DNA strands, involves the construction of hybrid DNA molecules containing a simian virus 40 DNA molecule covalently joined to a polyoma DNA molecule, using the sequential action of EcoRI restriction endonuclease and Escherichia coli DNA ligase. Denaturation of such hybrid DNA molecules then makes it possible to examine intramolecularly rather than intermolecularly renatured molecules. Visualization of these intramolecularly renatured “snapback” molecules with duplex regions of homology by electron microscopy reveals a 15% region of weak sequence homology. This region is denatured at about 35 °C below the melting temperature of simian virus 40 DNA and therefore corresponds to about 75% homology. This region was mapped on both the simian virus 40 and polyoma genomes by the use of Hemophilus parainfluenzae II restriction endonuclease cleavage of the simian virus 40 DNA prior to EcoRI cleavage and construction of the hybrid molecule. The 15% region of weak homology maps immediately to the left of the EcoRI restriction endonuclease cleavage site in the simian virus 40 genome and halfway around from the EcoRI restriction endonuclease cleavage site in the polyoma genome.     

Vitamin A inhibition of polyoma virus replication

Vitamin A (retinoic acid) inhibited polyoma virus replication in confluent mouse embryo cells. A significant, dose dependent inhibition was observed when cell monolayers were pretreated with concentrations of vitamin A (10(-8) to 10(-6) M) thought to approximate those found in vivo. This inhibitory effect could be reduced by increasing the input multiplicity of infection. Growth curves of polyoma virus in the presence and absence of vitamin A suggested that vitamin A actually inhibited, and did not simply delay, virus replication. The cell density dependence of this inhibitory effect suggested its association with the prevailing level of cellular DNA synthesis. Vitamin A caused a significant decrease in overall (viral plus cellular) DNA synthesis. Other viruses which do not require induction of host cell DNA synthesis for their replication in confluent, non-dividing cells were not inhibited by vitamin A. These results are consistent with the known inhibitory effects of vitamin A on papovavirus infection in vivo and suggest a mechanism of vitamin A action at the level of the infected cell.     

Sequence repeats in a polyoma virus DNA region important for gene expression.

The sequenced prototype strains (A2 and A3) of polyoma virus lack sequence duplications characteristic of other papovaviruses. However, we found that five polyoma virus strains (P16, Toronto large plaque, MV, Ts 48, and NG59R) contain tandemly duplicated sequences in a region near the late RNA leader. Although the duplications vary in size (31 to 84 base pairs) and location (between nucleotide [nt] 5068 and nt 5185), the sequence between nt 5114 and nt 5137 is contained within all five duplicated segments. This region is known to be important in polyoma virus early gene expression, and it contains sequences capable of enhancing the expression of nonviral genes. Inspection of the sequences at and around the ends of the repeats indicated that the duplications do not arise by homologous recombination, and there was no indication that a sequence-specific mechanism results in their formation. However, the variation in the structure of the repeats among different polyoma virus strains suggests that these sequence duplications are a recent evolutionary occurrence. The potential biological significance of this variation is discussed.     

The high affinity binding site on polyoma virus DNA for the viral large-T protein.

In order to map the high affinity binding site for the viral large-T protein on polyoma virus DNA, we have developed an assay which does not require purified protein. It is based on the specific elution of the large-T ATPase activity from calf thymus DNA cellulose by recombinant DNA molecules including known sequences of the viral DNA. Using this assay, a high affinity binding site has been mapped on the early region side of the ori region. Binding requires the integrity of a sequence /AGAGGC/TTCC/AGAGGC/ (nucleotides 49 to 64 in the DNA sequence of the A2 strain). Similar repeats of a PuGPuGGC sequence within less than 20 bases are not found within the viral coding regions, but are strikingly common in the control regions of papovaviruses and other eukaryotic DNAs.     

Specific interaction of cellular factors with the B enhancer of polyoma virus.

Specific interactions between proteins from mouse 3T6 cells and the enhancer sequence of polyoma virus were detected using the method of band shifting on polyacrylamide gels. Proteins eluted from 3T6 nuclei using a buffer containing 0.55 M NaCl, formed a stable complex with the B enhancer of polyoma virus. At least two different factors are involved in this interaction. The contact sites which were mapped on the DNA sequence using DNase I footprinting correspond to a GC-rich palindrome surrounded by two sequences homologous respectively to the immunoglobulin and to the immunoglobulin and SV40 enhancers. Moreover Bal31 deletion analysis confirmed that similar sequences are required for the formation of the complex. In spite of a common function and partial sequence homology among some enhancers, neither the polyoma A enhancer, the mouse immunoglobulin heavy chain gene enhancer, nor the origin-promoter-enhancer region of SV40 efficiently competed with the polyoma B enhancer for the binding of these molecules.     

Cytoplasmic RNA from normal and malignant human cells shows homology to the DNAs of Epstein-Barr virus and human adenoviruses.

Cytoplasmic RNA prepared from several human cell lines and tissues was hybridised to DNA from Epstein-Barr virus, human adenovirus types 2, 3 and 12 and human papovaviruses BK and JC. RNA from all the cells, regardless of whether or not they were virally infected, hybridised to specific regions of the Epstein-Barr virus or adenovirus genomes but not to papovavirus DNA. The cellular cross-hybridising species appear to be repetitive sequences which are conserved in higher eukaryotes. Mismatch estimations indicate a high degree of homology between the viral and host sequences. Detailed analysis of selected regions of viral DNA failed to reveal any primary-structural peculiarities.     

Mutant din-21, a variant of polyoma virus containing a mouse DNA sequence in the viral genome.

An unusual non-defective mutant of polyoma virus with an anomalously large genome, designated din-21, has been isolated. The viral chromosome lacks 49 base pairs of the putative control region between the origin of replication and the initiation codon for the early proteins, the T-antigens. In their stead , 95 base pairs, with limited homology to the deleted sequence and apparently of mouse origin, have been inserted. The primary sequence of the insert DNA has been determined and some of the biological properties of the mutant examined. It transforms rat-1 cells slightly better than wild-type virus and grows slightly less well in lytically infected mouse cells. It does not interfere with the growth of wild-type polyoma virus. The properties of this mutant suggest that it is a natural isolate of mouse cells. The mutant was presumably generated by reciprocal recombination between polyoma DNA and mouse host DNA. This could be associated with the integration of a viral DNA sequence into the host chromosome during the viral replicative cycle.     

Nuclear location signals in polyoma virus large-T

We have found two mutually independent sequence elements that contribute to the nuclear location of polyoma virus large-T. The first sequence (pro lys lys282 ala arg glu asp) resembles the SV40 large-T nuclear signal (pro lys lys128 lys arg lys val) and occurs at a corresponding position within polyoma large-T. The second sequence (val ser arg lys192 arg pro arg) may be structurally related to the SV40 signal, although it has little sequence homology and falls in a region of the protein that has no counterpart in SV40 large-T. The data suggest that nuclear location signals with characteristics similar to the SV40 large-T prototype may be a more general feature of nuclear proteins, and that several such signals in a given protein can exert cooperative effects.     

Studies of polyoma virus DNA: cleavage map of the polyoma virus genome.

A small-plaque polyoma virus, MPC-1, was isolated from a mouse plasmacytoma. The DNA of this polyoma virus was cleaved with a restriction enzyme from Haemophilus influenzae (Hin d), and the molecular weights of the limit products were analyzed by electrophoresis and electron microscopy. The fragments produced by this enzyme have been ordered by analysis of partial digest products. A physical map of the polyoma virus genome was then constructed.     

Oncogenes: Growth regulation and the papovaviruses polyoma and SV40

Cellular oncogenes and their activated and retrovirus-coded counterparts play an important role in cellular regulation. Here the relationship between such oncogenes and the genes coding for the transforming proteins of the papovaviruses, polyoma viruses, and simian virus 40 (SV40) is discussed. It is concluded that polyoma virus may transform established cells by a mechanism involving activation of a cellular oncogene product, whereas SV40 may transform by a mechanism involving a previously little studied cytoplasmic form of the transforming protein.     

High affinity binding of the large T protein of polyoma virus to a genomic mouse DNA sequence

We purified a fragment of mouse DNA to which the large T protein of polyoma virus was bound in chromatin prepared from transformed mouse cells. This sequence, which is not repeated to a measurable extent within the mouse genome, does not show any significant homology to the viral ori region, except in a short region, which comprises a sequence related to the consensus for recognition by large T proteins ((A,T)GPuGGC). This region of pCG4 was confirmed by in vitro binding assays to be essential for T antigen binding.     

The hr-t gene of polyoma virus

Malignant transformation of cells by polyoma virus results from the continual expression of a viral gene (hr-t) the normal function of which is to facilitate productive viral infection. The series of investigations described here on the polyoma hr-t gene originated with attempts to understand polyoma virus-cell interactions along lines suggested by temperate bacteriophage. Nucleic acid hybridization experiments indicated clearly that viral DNA persists in transformed cells and continues to be expressed. Radiobiological and other experiments, however, suggested a function for the expressed gene(s) which was not expected of a prophage: the promotion, rather than repression, of lytic virus growth. The hr-t gene acts pleiotropically to alter the physiological state of the host in a manner which facilitates virus production and induces a transformed cellular phenotype. The cellular alterations are manifested transiently during productive infection or abortive transformation, but permanently when the viral genome is integrated in stably transformed cells. hr-t mutants are defective in their growth in mice and in most cultured mouse cell lines. They are also unable to induce tumors or any of the morphological, structural, or growth-related changes which accompany cells transformation by the wild-type virus.The 22 kDa and 56 kDa proteins encoded in the early region of the viral DNA constitute dual products of the hr-t gene. hr-t mutants are localized in a narrow segment of the early region that specifies an amino acid sequence shared by these two overlapping proteins. Current efforts to link structural (i.e., mutational) changes with functional changes in these proteins center around the 56 kDa middle T antigen and its associated protein kinase activity. Assayed in vitro, this activity leads to phosphorylation of the 56 kDa protein itself, predominantly at a specific tyrosine residue in the C-terminal portion of the molecule. The middle T protein is anchored in cellular membranes by a hydrophobic tail close to the C-terminus. Membrane association is essential for transformation, as well as for the kinase activity. The common region of the 22 kDa/56 kDa proteins where hr-t mutants map has local regions of homology with highly conserved sequences in the pituitary glycoprotein hormones. The integrity of this region is also essential for transformation and for kinase activity. In vivo, the 56 kDa protein is a substrate for cellular kinase(s) and undergoes multiple phosphorylations (serine and/or threonine) that may affect the tyrosine-specific activity. These kinase reactions, originating in cellular membrane but potentially affecting pathways into the cytoplasm and nucleus, currently provide the most plausible biochemical mechanism underlying the pleiotropic effects of the hr-t gene.     

Genomic structure of human polyoma virus JC: nucleotide sequence of the region containing replication origin and small-T-antigen gene

The nucleotide sequence of the region of human polyoma virus JC DNA between 0.5 and 0.7 map units from a unique EcoRI cleavage site was determined and compared with those of the corresponding regions of another human polyoma virus, BK, and simian virus 40 DNAs. Within this region consisting of 945 base pairs, we located the origin of DNA replication near 0.7 map units, the entire coding region for small T antigen, and the splice junctions for large-T-antigen mRNA. The deduced amino acid sequences for small T antigen and the part of large T antigen markedly resembled those of polyoma virus BK and simian virus 40. The results strongly suggest that polyoma virus JC has the same organization of early genome as polyoma virus BK and simian virus 40 on the physical map, with the EcoRI site as a reference point.     

Structural and biological analysis of integrated polyoma virus DNA and its adjacent host sequences cloned from transformed rat cells.

EcoRI fragments containing integrated viral and adjacent host sequences were cloned from two polyoma virus-transformed cell lines (7axT and 7axB) which each contain a single insert of polyoma virus DNA. Cloned DNA fragments which contained a complete coding capacity for the polyoma virus middle and small T-antigens were capable of transforming rat cells in vitro. Analysis of the flanking sequences indicated that rat DNA had been reorganized or deleted at the sites of polyoma virus integration, but none of the hallmarks of retroviral integration, such as the duplication of host DNA, were apparent. There was no obvious similarity of DNA sequences in the four virus-host joins. In one case the virus-host junction sequence predicted the virus-host fusion protein which was detected in the transformed cell line. DNA homologous to the flanking sequences of three out of four of the joins was present in single copy in untransformed cells. One copy of the flanking host sequences existed in an unaltered form in the two transformed cell lines, indicating that a haploid copy of the viral transforming sequences is sufficient to maintain transformation. The flanking sequences from one cell line were further used as a probe to isolate a target site (unoccupied site) for polyoma virus integration from uninfected cellular DNA. The restriction map of this DNA was in agreement with that of the flanking sequences, but the sequence of the unoccupied site indicated that viral integration did not involve a simple recombination event between viral and cellular sequences. Instead, sequence rearrangements or alterations occurred immediately adjacent to the viral insert, possibly as a consequence of the integration of viral DNA.     

Homologous recombination of polyoma virus DNA in mouse cells

Summary We have produced nonviable deletion mutants of polyoma virus in order to study homologous recombination after DNA transfection into mouse cells. The frequency of recombination was determined by the formation of infectious virus. It was dependent on the amount of DNA transfected and the size of the region of homology between the mutations. Recombination frequencies were highest when both mutated genomes were transfected in closed circular form rather than after linearization of one or both of the recombination partners. The system described may be useful for a more detailed analysis of physiological and genetic conditions influencing the frequency of homologous recombination in mouse cells as well as to study enzymes involved and intermediates produced in this process.