An excision event that may depend on patchy homology for site specificity

In mouse cells transformed by a mutant polyomavirus genome, recombination between integrated viral DNA and flanking cellular DNA resulted in the excision of two readily amplifiable chimeras, designated RmI and RmII. The crossing-over that generated RmII was unique in that it involved a simple cellular sequence in which the triplet 5'-CTG-3' was repeated many times. We show that the sequence across the junction resulting from excision was identical in several molecules of RmII, as if the cross-over generating this junction always involved exactly the same two sites on the viral and cellular DNA. We also show that the cellular site mapped where the replacement of a G by an A in one of many successive 5'-CTG-3' triplets generated a homology of five nucleotides (5'-CTACT-3') with the viral site. Oligonucleotides on both sides of these sites are probably involved in matching the two DNAs prior to recombination.

An amplified genome that may have resulted from recombination within bidirectionally replicating DNA

Temperature shift-down of permissive mouse cells transformed by a temperature-sensitive (ts) polyomavirus (Py) genome has been shown to induce the accumulation of free copies of the viral DNA. We report here on an unusual product from such induction. The structure of this product is that expected from the occurrence of recombination between growing points in a bidirectionally replicating Py-mouse DNA molecule. This observation may be relevant to the mechanism of gene amplification in mammalian cells.

Mouse cells surviving polyoma virus infection generally retain the whole viral genome

Permissive mouse 3T6 cells were exposed to polyoma virus--either wild-type or early mutant--at high multiplicities of infection. From colonies arising from surviving cells, so-called lines and clones were derived under conditions precluding superinfection. These lines and clones were examined for the presence of viral genetic information, using a variety of techniques. Two salient findings were made: most lines or clones analyzed had retained viral genetic material; generally, this material was nondefective, as evidenced by the production of virus and/or viral DNA molecules of genomic size. These findings indicate that mouse cells can survive for many generations while carrying a complete, infectious, and potentially cytocidal polyoma virus genome.

Alternative excision products originating from a single integration of polyomavirus DNA

The Cyp cell line consists of mouse cells transformed by a thermosensitive polyomavirus (Py) genome and routinely propagated at 39 degrees C. Cyp cells are readily induced to synthesize free Py DNA by being transferred to 33 degrees C. In one subclone (C12/a1/S48, or S48) of this line, such induction resulted in the intracellular accumulation of three discrete species of cyclic DNA, i.e., genomic Py DNA, RmI, and RmII. RmI and RmII are Py-mouse chimeras, each of which contains a distinct set of sequences originating from the site of integration. Conceivably, genomic Py DNA, RmI, and RmII could persist at 39 degrees C as free replicating plasmids or originate from distinct populations of cells in S48 cultures. The data indicated that all three species arise at 33 degrees C from a genetically homogeneous cell population in which neither RmI nor RmII replicates at 39 degrees C. Examination of the sequence at the viral-cellular junction unique to RmII indicated that this chimera is excised from the host chromosome through a recombination event involving a complex viral sequence and a simple cellular sequence. Therefore, RmII provides another example of precise recombination occurring between nonhomologous sequences in a mammalian cell, as already observed for RmI (B. S. Sylla, D. Huberdeau, D. Bourgaux-Ramoisy, and P. Bourgaux, Cell 37:661-667, 1984).

A mouse DNA sequence that mediates integration and excision of polyoma virus DNA

In mouse cells transformed by a temperature-sensitive polyoma virus (Py) genome, the integrated viral genome recombines with adjacent chromosomal DNA to yield a small cyclic molecule (RmI) with defined viral and cellular components. We have cloned the cellular component (Ins), determined its sequence, and examined its distribution in normal mouse DNA. The sequence of Ins displays several homologies with that surrounding the replication origin (ori) of Py or SV40 DNA.

The temperature-sensitive defect in polyoma virus P155 mutant

P155 is a temperature-sensitive mutant of polyoma virus that transforms normally, but replicates poorly, under restrictive conditions (Eckhart, 1969, 1975). We have observed that the temperature-sensitive character of P155 maps within the portion of the viral DNA coding exclusively for large T antigen, a viral gene product which is thermolabile in P155-infected cells. The phenotype of P155 may indicate that large T antigen fulfills different functions in virus replications and in cell transformation.

Site-specific excision of integrated polyoma DNA

Cyp cells are permissive murine cells carrying a thermosensitive polyoma virus genome that remains integrated at 39 degrees C, but is effectively excised and replicated after transfer to 33 degrees C. In rare subclones of the Cyp line, temperature shift-down yields predominantly homogeneous populations of chimeric molecules that appear to reflect the circularization of defined segments of DNA spanning one of the junctions between the integrated viral genome and the adjacent cellular DNA. Such accurate and frequent excision requires a specific recombination mechanism. We examined both the cellular and the viral sequences that cross-over to generate one of these chimeric molecules, Rm I. The homology at the cross-over site is one of 1 or 2 base pairs at most; patches of homology, amounting in total to 19 or 20 base pairs, are found in perfect register on both sides of this site; and the two stretches of DNA that are joined to form RM I contain similar 12-14 base pair sequences (5'- CTCCTTTACAGAGG -3' and 5'- CTCCTTTCAAGG -3') in opposite orientations.

Inducible permissive cells transformed by a temperature-sensitive polyoma virus: superinfection does not allow excision of the resident viral genome

After exposure of mouse embryo cells to the early temperature-sensitive mutant tsP155 of polyoma virus (Py), a transformed cell line (Cyp line) that can be readily induced to synthesize Py by transfer to 33 degrees C was isolated at 39 degrees C (7). Virus production and synthesis of free viral DNA occurring after temperature shiftdown or superinfection with wild-type Py or both were studied in several clonal isolates of the Cyp cell line. Measurements of virus yields indicated that, although some could be induced more effectively than others, all cell clones behaved as highly permissive when subjected to superinfection. We analyzed the origin of free viral DNA accumulating in the superinfected cultures, taking advantage of (i) the unique physical properties of the low-molecular-weight DNA which, in the case of one of the Cyp clones, accumulates during temperature shiftdown, and (ii) the differences between resident and superinfecting viral genomes in their susceptibilities towards restriction endonucleases. At 33 degrees C, both viral genomes were found to accumulate in all clones studied whereas in the case of the clones with lower inducibility, the replication of the resident genome appeared to be enhanced by superinfection. At 39 degrees C, however, accumulation of the superinfecting genome was not accompanied by that of the resident genome, unless it had already been initiated before superinfection. These findings demonstrate that, when routinely cultivated at 39 degrees C, Cyp cells contain few viral DNA molecules readily available for autonomous replication and that, upon transfer to 33 degrees C, therefore, excision must first take place before the resident genome can accumulate as free viral DNA. Our findings also suggest that, unlike the P155 gene product provided by the resident viral genome upon induction, the allelic gene product supplied by the superinfecting genome may be less effective in triggering excision than in promoting replication.

Integrated polyoma genomes in inducible permissive transformed cells

Using the approach described by Botchan, Topp, and Sambrook (Cell 9:269-287, 1976), we analyzed the organization of the integrated viral sequences in five clonal isolates from the same permissive, inducible cell line (Cyp line) transformed by the tsP155 mutant of polyoma virus. In all five clones, viral sequences were found that could be assigned to a common integration site, as they were joined to the cellular DNA in the same fashion in every instance. However, the sequences comprised between these points differed markedly from clone to clone, as if cell propagation had been accompanied by amplification or recombination or both within the viral insertion. When the clones were compared, no correlation could be found between the abundance, or the organization, of the integrated viral sequences and the amount, or the nature, of the free viral DNA molecules produced during induction. Altogether, our findings suggest that specific events, occurring during either the excision or the subsequent replication of the integrated viral sequences, are responsible for the predominant production of nondefective viral DNA molecules by permissive transformed cells, such as Cyp cells.

Two classes of replicating molecules of adenovirus type 2 DNA

Replicating DNA of human adenovirus type 2, identified as partly single-stranded viral DNA in which [3H]thymidine is readily incorporated, was found to be separated into two fractions by chromatography on hydroxyapatite. Whereas one of the these fractions was eluted with 180 mM phosphate, the other one was eluted at the same concentration, 240 mM, as fully double-stranded DNA. The physical properties of the 180 and 240 mM fractions, in particular their buoyant densities in solutions of CsCl and Cs2SO4, were compared both before and after treatment by various enzymes such as Neurospora crassa nuclease, pancreatic ribonuclease, ribonuclease H and the Klenow fragment of DNA polymerase I of Escherichia coli, used alone or in various combinations. Unlike the 240 mM fraction, the 180 mM fraction was found to include a substantial amount of single-stranded DNA, some of it being hydrogen-bonded to RNA. Both of these features confer to the 180 mM fraction the high buoyant density in cesium salt solution which was described, for several adenoviruses, as one of the characteristic properties of replicating DNA.

Biological properties of polyoma DNA fragments cloned in plasmid pBR322

The two HindIII fragments of polyoma virus DNA were cloned in the HindIII site of plasmid pBR322, and the biological activity of the recombinant plasmids was tested in tissue culture cells. A mixture of recombinant plasmids containing the HindIII-A and HindIII-B fragments was infectious, but only after cleavage with HindIII. Recombinant plasmids containing the HindIII-A fragment, but not those containing the HindIII-B fragment, induced the transformation of Fischer rat 3T3 cells. These findings indicate that about half of the early region of polyoma virus DNA is not essential for the initiation of the maintenance of transformation.

Induction of virus multiplication in permissive cells transformed by a temperature-sensitive polyoma virus. I. Isolation and partial characterization of survivors

A fibroblastic cell line transformed by ts-P155, an early temperature-sensitive mutant of polyoma virus, has been isolated after infection of secondary mouse embryo cells at the restrictive temperature of 39. These cells, designated Cyp, undergo a massive CPE accompanied by the production of infectious, temperature-sensitive virus when transferred to the nonrestrictive temperature of 33. Several independent clones were established from cells which survived the induction of virus multiplication occurring at 33. When routinely cultured at this temperature, these cells, termed R, displayed the growth properties of transformants and produced variable amounts of infectious, temperature-sensitive virus. This shedding of virus could not be "cured' by the addition to the culture medium of antipolyoma serum which had already been found to effectively suppress virus production in Cyp cell cultures transferred to 33. Moreover, R cells seemed to have developed a resistance to superinfection that the parent Cyp cell line did not exhibit. Therefore, virus production in R cell cultures probably reflects the occasional excision and replication of integrated viral genomes rather than a carrier state.

Further studies on the replication of adenovirus type 2 DNA

Monolayer cultures of KB cells infected with adenovirus type 2 (Ad2) were subjected to short pulses of tritiated thymidine, at the time of maximal viral DNA synthesis. Nascent viral DNA was selectively extracted from the cells, purified, and fractionated into partly single-stranded (or replicating) molecules and double-stranded (or completed) molecules. Completed molecules were cleaved by the restriction endonucleases from either Escherichia coli (EcoRI), Haemophilus influenzae (Hind III), Haemophilus parainfluenzae (Hpa I), or by the latter two enzymes in succession, and the resulting fragments were separated by electrophoresis through agarose–acrylamide slab gels. In the case of replicating molecules, the double-stranded fragments generated after treatment with the same enzymes were first separated from the partly single-stranded fragments by chromatography on benzoylated–naphthoylated DEAE (BND) cellulose before being subjected to electrophoresis. The relative yields of tritium of the various fragments resolved by the gels were then determined. As already described in several reports, the analysis of the completed molecules obtained after the shorter pulses revealed a strong preferential labeling of the fragments derived from the molecular ends, as expected if both of these ends contained termini for replication. The analysis of double-stranded fragments from replicating molecules revealed a predominant labeling of the central portion of the genome which could be reconciled with initiation occurring either centrally or at both molecular ends. In addition, two gradients of labeling, ascending toward each molecular end and encompassing the outer quarters of the molecule, were noted which slowly receded when the pulse length was increased. The latter finding, which is in agreement with our earlier results, could reflect an overrepresentation of molecules in the late stages of replication in the pool of nascent DNA, such as one would expect if replication slows down when it nears the termination site(s). This interpretation is consistent with the kinetics of labeling of the various portions of the genome observed in the pool of completed molecules. Because of this complication, however, the distribution of label in replicating molecules cannot be used to ascertain unambiguously the location of the origin(s) of replication on the Ad2 DNA molecule.

Structures of polyoma virus: on the histone component and virion core

We have observed that purified polyoma virus is able to take up an amount of calf thymus histone equivalent to 10 to 50% of its normal histone content under conditions allowing the binding of considerably lesser amounts of several other proteins. Some of the bound histone could not be released by procedures procedures routinely used for virus purification. We have also found that some of the histone present in purified polyoma virus could be selectively released without major breakdown of virus particles. Possible models for virus structure are discussed in the light of the present and other recent data.

Transformation of human cells by temperature-sensitive mutants of simian virus-40

Conditions necessary for the establishment and maintenance of transformation of human cells by wild type and temperature-sensitive mutants of SV40 were examined. For both early and late mutants, the frequency of transformation was found to be up to 5-fold higher, and virus yield 100-fold lower, at 39 degrees than at 33 degrees. No such effect was observed with the wild type virus under the same conditions. This observation is apparently at variance with previously published work, but may be explained by the semipermissive nature of the cells that we used. Increasing the temperature to 40.5 degrees caused cells transformed by the early mutant, tsA30, to lose T-antigen as detectable by staining, and also to lose the ability to grow to high density, while it produced no effect on cells transformed by wild type virus.