Specific association of simian virus 40 tumor antigen with simian virus 40 chromatin

Simian virus 40 and protein transfer

Protein transfer to solid supports after polyacrylamide gel electrophoresis, and subsequent probing with specific antibodies, is one of the most important tools in modern molecular and cellular biology. Since its development in 1979, the improvement of the technique has been impressive, from new apparatus to streamline the electrophoresis step to different modalities of the transfer step or solid supports for the transfer. Perhaps most impressive has been the explosion of the production and availability of antibodies. In this chapter, I describe the environment and conditions that led to the development of this technique in George Stark's laboratory.

T-antigen is not bound to the replication origin of the simian virus 40 late transcription complex

Simian virus 40 tumor antigen (T-antigen) plays a central role in determining which gene is transcribed from viral DNA late in infection. Results from several studies have led to a model in which the binding of T-antigen to the viral origin of replication results in repression of transcription from the stronger early gene promoter and stimulation of transcription from the late gene promoter. We have tested this model by determining directly the occupancy of the T-antigen binding site in the origin of replication of the late transcription complex. Thus, viral transcription complexes were digested with BglI, a restriction enzyme that cuts in the viral replication origin. The enzyme cleaved 78(+/- 12)% of the late transcription complexes. Control experiments demonstrated that cleavage is blocked when T-antigen is bound to the origin site, that exogenously added T-antigen can bind to the site in the transcription complex, and that T-antigen is not released during isolation of the complex. These results indicate that most of the late transcription complexes do not have T-antigen bound to the origin site, and are therefore inconsistent with models that require this site to be occupied by T-antigen to maintain proper regulation of gene transcription late in infection.

Specific interaction of simian virus 40 large T antigen with cellular chromatin and nuclear matrix during the course of infection

We analyzed the subnuclear distribution of the simian virus 40 (SV40) large tumor (large T) antigen during the course of viral infection. Three distinct nuclear subclasses were detected in SV40 lytically infected TC7 cells (large T antigen in the nucleoplasm, at the cellular chromatin, and at the nuclear matrix). During the course of infection the relative subnuclear distribution of large T antigen changed significantly at about the switch from the early to late phase of infection: at early times postinfection, large T antigen was present mainly in the nucleoplasm and at the cellular chromatin, and nuclear-matrix-associated large T antigen was barely detectable. Concomitant with the onset of viral DNA replication, the amount of nuclear-matrix-associated large T antigen increased drastically. During the further course of infection large T antigen accumulated at the cellular chromatin and nuclear matrix, paralleling the increase in viral DNA synthesis. The biological significance of this correlation was corroborated by analysis of cells infected with the SV40 mutant tsA58 at permissive (32 degrees C) and restrictive (39 degrees C) temperatures. tsA58 large T antigen failed to initiate viral DNA replication in infected cells kept at the restrictive temperature and also failed to associate with the cellular chromatin and nuclear matrix. By blocking viral DNA synthesis with aphidicolin, an inhibitor of DNA polymerase alpha, we were able to show that the accumulation of large T antigen at these structures does not result from the binding of large T antigen to viral chromatin but reflects an association with cellular components of the chromatin and nuclear matrix of infected cells.

Monoclonal antibodies as probes for a function of large T antigen during the elongation process of simian virus 40 DNA replication

Various monoclonal antibodies specific for simian virus 40 large tumor antigen (T antigen) inhibit the elongation process of viral DNA replication in an in vitro system. The results provide strong evidence for a function intrinsic to T antigen during ongoing replicative-chain elongation. The antibody inhibition studies were further used to establish a correlation between the known biochemical activities of T antigen and its function during the elongation phase. The data demonstrate that, in addition to DNA binding and ATPase, a third function of T antigen is required for replicative chain elongation. This function is most probably related to the recently described DNA helicase activity of T antigen. This conclusion is based on the following results: aphidicolin treatment of actively replicating simian virus 40 minichromosomes causes a partial uncoupling of parental DNA strand separation and DNA synthesis; the strand separation reaction is blocked by the same monoclonal antibodies which strongly inhibit the elongation process. DNA helicase activity of isolated T antigen is equally well inhibited by the same set of monoclonal antibodies that affect minichromosome replication in vitro.

Free and viral chromosome-bound simian virus 40 T antigen: changes in reactivity of specific antigenic determinants during lytic infection

Simian virus 40 (SV40) large T antigen (TAg), both free and bound to mature 70S and replicating 90S SV40 chromosomes, was prepared from lytically infected cells. The relative reactivity of the different TAg-containing fractions toward 10 monoclonal antibodies directed against three different regions in SV40 TAg and toward an antibody against the p53 protein was measured. The results for free TAg indicated that all of the determinants in both the amino-terminal (0.65 to 0.62 map units) and carboxy-terminal (0.28 to 0.17 map units) regions were highly reactive, whereas all five determinants located between 0.43 and 0.28 map units in the midregion of TAg were poorly reactive. For TAg bound to replicating chromosomes, all but one of the antibodies specific for TAg were highly reactive. Thus, antigenic sites in the middle of TAg, the region important for nucleotide binding and ATP hydrolysis (an activity required for viral DNA replication), were more accessible in TAg-replicating DNA complexes. As replicating molecules matured into 70S chromosomes, three or more determinants at different locations in TAg bound to chromatin became two- to fivefold less reactive, indicating other changes in TAg structure. Overall, at least nine different antigenic determinants in the TAg molecule were identified. Anti-p53 was reactive with about 10% of the free TAg and the same amount of SV40 chromosomes of all ages, suggesting that p53-TAg complexes are not preferentially associated with either replicating or mature viral chromosomes. When the reactivity of both mature and replicating labeled SV40 chromosomes with polyclonal tumor anti-T was measured as a function of time after purification, TAg bound to mature chromosomes appeared to dissociate about fourfold faster than that bound to replicating chromosomes. The relative amount of TAg in various subcellular fractions was measured by an enzyme-linked immunosorbent assay. Approximately 1.3% of the total TAg was estimated to be associated with SV40 chromosomes in infected cells. Based on the relative amounts of TAg and viral DNA in the 70S and 90S fractions, replicating chromosome-TAg complexes were estimated to bind 4.8 times more TAg per DNA molecule, on the average, than mature chromosome-TAg complexes. Together, these results are consistent with major differences in TAg structure when free and associated with replicating and nonreplicating SV40 chromosomes.

Kinetics of nuclear transport and oligomerization of simian virus 40 large T antigen

The kinetics of nuclear transport and of oligomerization of simian virus 40 (SV40) large T antigen in lytically infected cells were investigated by pulse-chase experiments, cell fractionation, and sedimentation analyses in sucrose gradients. After synthesis, large T was rapidly translocated to the nucleus. Within 10 min, half of the pulse-labeled molecules had entered the nucleus and after an additional 30 min, nuclear accumulation of large T reached a constant plateau of about 95%. Within that time, the majority of large T was in monomeric form suggesting that nuclear transport takes place in this state. In the nucleus, conversion to tetramers proceeded slowly and steadily. By 60 min half of the molecules had formed tetramers and by 6 hr a steady-state ratio between tetramers and monomers of 4:1 was observed. A small fraction of large T remaining in the cytoplasm oligomerized considerably faster than large T in the nuclear fraction. This phenomenon of accelerated oligomerization was also observed with a mutant of large T defective for nuclear transport. Perhaps, the nuclear envelope is a barrier for the complex forms of large T which prevents premature oligomers in the cytoplasm from entering the nucleus and oligomers in the nucleus from migrating back to the cytoplasm.

An immunoaffinity purification procedure for SV40 large T antigen

A rapid purification procedure for SV40 large T antigen has been developed which combines the use of an adenovirus-SV40 hybrid virus which overproduces large T antigen, and immunoaffinity chromatography on an anti-large T monoclonal antibody coupled to protein A Sepharose. The protein exhibits the p53-binding, ATPase, and sequence-specific DNA-binding activities of T antigen. The purification procedure can be completed in 1 day and allows the isolation of milligram amounts of large T in excellent yield. The pure protein is extremely antigenic and is tolerant of iodination to high specific activity, permitting the development of a competition radioimmunoassay for large T that reliably detects nanogram amounts of the protein.

A large-tumor-antigen-specific monoclonal antibody inhibits DNA replication of simian virus 40 minichromosomes in an in vitro elongation system

In productively infected cells, a fraction of large-tumor antigen (T antigen) is tightly bound to replicating simian virus 40 (SV40) minichromosomes and does not dissociate at salt concentrations of greater than 1 M NaCl. We present electronmicrograms demonstrating the presence of T antigen on the replicated sections of replicating SV40 minichromosomes. We also show that the fraction of tightly bound T antigen is recognized by antibodies from mouse tumor serum and, more specifically, by a particular T-antigen-specific monoclonal antibody, PAb 1630. A second T-antigen-specific monoclonal antibody, PAb 101, does not react with the T-antigen fraction remaining on replicating SV40 chromatin at high salt concentrations. We used an in vitro replication system which allows, via semiconservative DNA replication, the completion of in vivo-initiated replicative intermediate DNA molecules. We show that monoclonal antibody PAb 1630, but not monoclonal antibody PAb 101, inhibits viral DNA replication. We discuss the possibility that SV40 T antigen may play a role in chain elongation during SV40 chromatin replication.

DNA-binding activity of simian virus 40 large T antigen correlates with a distinct phosphorylation state

The state of phosphorylation and the relationship of various subclasses of simian virus 40 large T antigen (large T) differing in DNA-binding activity, degree of oligomerization, age, and subcellular distribution were investigated. Young large T (continuously labeled for 4 h late in infection) comprised about 20% of the total cellular large T. It was phosphorylated to a low degree and existed primarily in a monomeric form, sedimenting at 5S. More than 50% of this fraction bound to simian virus 40 DNA, preferentially to origin-containing sequences. Old large T (continuously labeled for 17 h, followed by a 4-h chase) represented the majority of the population. It was highly phosphorylated and predominantly in an oligomeric form, sedimenting at 15S to 23S. Only 10 to 20% of this fraction bound to simian virus 40 DNA. Another subclass of large T which was extracted from nuclei with 0.5 M salt resembled newly synthesized molecules in all properties tested; it was phosphorylated to a low degree, sedimented at 5S, and bound to viral DNA with high efficiency (greater than 70%). Two-dimensional phosphopeptide analysis of the individual subclasses revealed two distinct phosphorylation patterns, one characteristic for young, monomeric, and DNA-binding large T, the other for old, oligomeric, and non-DNA-binding large T. All sites previously identified in unfractionated large T (K.H. Scheidtmann et al., J. Virol. 44:116-133, 1982) were also phosphorylated in the various subclasses, but to different degrees. Peptide maps of the DNA-binding fraction, the 5S form, and the nuclear high-salt fraction showed two prominent phosphopeptides not previously characterized. Both peptides were derived from the amino-terminal region of large T, presumably involved in origin binding, and probably represent partially phosphorylated intermediates of known phosphopeptides. Our data show that the DNA-binding activity, age, and oligomerization of large T correlate with distinct states of phosphorylation. We propose that differential phosphorylation might play a role in the interaction of large T with DNA.

Polyomavirus minichromosomes: associated DNA topoisomerase II and DNA ligase activities

Polyomavirus minichromosomes were isolated and fractionated as described previously (B. B. Gourlie, M. R. Krauss, A. J. Buckler-White, R. M. Benbow, and V. Pigiet, J. Virol. 38:805-814, 1981). Specific assays for DNA topoisomerase II and DNA ligase activity were carried out on each fraction. The enzymatic activity in each fraction was determined by quantitative electron microscopy and compared with the number of replicative intermediate and total polyomavirus DNA molecules in each fraction. DNA topoisomerase II activity cosedimented with polyomavirus replicative intermediate minichromosomes. DNA ligase activity cosedimented with mature polyomavirus minichromosomes.

Analysis of simian virus 40 chromosome-T-antigen complexes: T-antigen is preferentially associated with early replicating DNA intermediates

The fraction and DNA composition of simian virus 40 chromosomes that were complexed with large T-antigens (T-Ag) were determined at the peak of viral DNA replication. Simian virus 40 chromatin containing radiolabeled DNA was extracted by the hypotonic method of Su and DePamphilis (Proc. Natl. Acad. Sci. U.S.A. 73:3466-3470, 1976) and then fractionated by sucrose gradient sedimentation into replicating (90S) and mature (70S) chromosomes. Viral chromosomes containing T-Ag were isolated by immunoprecipitation with saturating amounts of either an anti-T-Ag monoclonal antibody or an anti-T-Ag hamster serum under conditions that specifically precipitated T-Ag protein from cytosol extracts. An average of 10% of the uniformly labeled DNA in the 90S pool and 7.5% in the 70S pool was specifically precipitated, demonstrating that under these conditions immunologically reactive T-Ag was tightly bound to only 8% of the total viral chromosomes. In contrast, simian virus 40 replicating intermediates (RI) represented only 1.2% of the viral DNA, but most of these molecules were associated with T-Ag. At the shortest pulse-labeling periods, an average of 72 +/- 18% of the radiolabeled DNA in 90S chromosomes could be immunoprecipitated, and this value rapidly decreased as the labeling period was increased. Electron microscopic analysis of the DNA before and after precipitation revealed that about 55% of the 90S chromosomal RI and 72% of the total RI from both pools were specifically bound to T-Ag. Comparison of the extent of replication with the fraction of RI precipitated revealed a strong selection for early replicating DNA intermediates. Essentially all of the RI in the 70S chromosomes were less than 30% replicated and were precipitated with anti-T-Ag monoclonal antibody or hamster antiserum. An average of 88% of the 90S chromosomal RI which were from 5 to 75% replicated were immunoprecipitated, but the proportion of RI associated with T-Ag rapidly decreased as replication proceeded beyond 70% completion. By the time sibling chromosomes had separated, only 3% of the newly replicated catenated dimers in the 90S pool (<1% of the dimers in both pools) were associated with T-Ag. Measurements of the fraction of radiolabeled DNA in each quarter of the genome confirmed that T-Ag was preferentially associated with newly initiated molecules in which the nascent DNA was nearest the origin of replication. These results are consistent with a specific requirement for the binding of T-Ag to viral chromosomes to initiate DNA replication, and they also demonstrate that T-Ag does not immediately dissociate from chromosomes once replication begins. The biphasic relationship between the fraction of T-Ag-containing RI and the extent of DNA replication suggests either that 1 or 2 molecules of T-Ag remain stably bound until replication is about 70% completed or that 4 to 6 molecules of T-Ag are randomly released from each RI at a uniform rate throughout replication.

Binding of simian virus 40 large T antigen from virus-infected monkey cells to wild-type and mutant viral replication origins

The binding of purified simian virus 40 (SV40) large T antigen (T) from monkey cells infected with wild-type SV40 virus to viral replication origin-containing DNA fragments was studied by DNase footprinting and restriction endonuclease protection methods. A strong affinity binding site (site 1) of 30 base-pairs and a second, adjacent 40 base-pair lower affinity binding site (site 2), which includes the origin of replication, were detected in these assays. These sites appear identical to those previously noted in similar assays performed with the Ad2 + D2 (D2) T protein. Heating T prior to incubation with DNA significantly increased the binding to these two sites, and the order of binding did not change. Moreover, protection of sequences was observed on both strands in these two sites suggesting that both strands can participate in binding of T to these two sites. Studies with DNAs from two internal site 2 deletion mutants as well as with a DNA fragment lacking the distal 13 base-pairs of site 2 revealed that sequences in the "early" portion of site 2 are sufficient for T binding to the intact site. Furthermore, use of a new assay that measures protection of DNA sequences from specific restriction enzyme cleavage revealed that site 2 can be subdivided into two subsites, 2A and 2B, where 2A corresponds to the above-noted early segment of this locus. In titration experiments, the affinity of 2A for T was greater than that of 2B. Hence, binding to a major portion of the replication initiation sequence (i.e. site 2) is the product of at least two interactions. Finally, analyses performed with DNA from a site 1 deletion mutant, cs1085, revealed that prior binding of T to this locus did not facilitate its binding to site 2. The opposite effect was observed when D2T was employed in these assays. Thus, although similar in many respects, these proteins display a detectable difference in their DNA binding mechanisms.

Salt-resistant association of simian virus 40 T antigen with simian virus 40 DNA in nucleoprotein complexes

Treatment of nucleoprotein complexes (NPCs) from simian virus 40 (SV40)-infected TC7 cells with NaCl (1 or 2 M) or guanidine-hydrochloride (1 or 2 M) resulted in a significant fraction of T antigen still associated with SV40 (I) DNA. Immunoprecipitation of the salt-treated NPCs with SV40 anti-T serum indicated that T antigen is preferentially associated with SV40 (I) DNA rather than with SV40 (II) DNA. Treatment of the NPCs with 4 M guanidine-hydrochloride, however, resulted in a substantial decrease in the amount of SV40 (I) and (II) DNA associated with T antigen. As the temperature was increased to 37 degrees C during incubation of NPCs with NaCl or guanidine-hydrochloride, there was a decrease in the amount of SV40 (I) and (II) DNA immunoprecipitated with SV40 anti-T serum. In the absence of salt, temperature had no effect on the association of T antigen with the SV40 DNA in the NPCs. Treatment of NPCs from SV40 wildtype or tsA58-infected cells grown at the permissive temperature with 1 or 2 M NaCl indicated that tsA T antigen has the same sensitivities as wild-type T antigen to high salt treatment when bound to DNA in NPCs. Characterization of the proteins associated with SV40 (I) DNA after high salt treatment revealed that, in addition to T antigen, a certain amount of viral capsid proteins VP1 and VP3 remained associated with the DNA. Complexes containing SV40 (I) DNA had a sedimentation value of 53S after 1 M NaCl treatment and 43S after 2 M NaCl treatment.

The simian-virus-40 large-tumor antigen in replicating viral chromatin. A salt-resistant protein-DNA interaction

The large tumor antigen (T antigen) is a genome regulation protein, coded by simian virus 40, that binds with high affinity to specific binding sites on viral DNA. The specifically bound T antigen is released from these sites in 0.2-0.3 M NaCl. Immunoprecipitation techniques were used to show that T antigen also dissociates in 0.2-0.3 M NaCl from mature viral chromatin but not from replicating viral chromatin. In fact, a considerable fraction of T antigen remains associated with replicating chromatin at NaCl concentrations as high as 1.2 M NaCl when most chromatin proteins, including histones, dissociate. However, T antigen binding to both replicating DNA and mature DNA is sensitive to intercalating drugs such as caffeine and ethidium bromide. We consider the possibility that the unexpectedly tight binding of T antigen to replicating DNA is related to the function that T antigen performs during viral DNA replication.

Simian virus 40 large tumor antigen on replicating viral chromatin: tight binding and localization on the viral genome

Pulse-labeled simian virus 40 (SV40) chromatin as well as uniformly labeled viral chromatin are immunoprecipitable by an SV40-specific tumor antiserum and therefore contain bound tumor antigen (T antigen). Single-stranded calf thymus DNA, immobilized on cellulose, competes effectively for T antigen binding with uniformly labeled nonreplicating, but not with pulse-labeled replicating, chromatin. Furthermore, T antigen dissociates in 0.5 M NaCl from nonreplicating chromatin and from purified SV40 DNA, whereas most T antigen remains associated with replicating chromatin even in the presence of 1.2 to 1.5 M NaCl. We used filtration through DNA-cellulose columns and treatment with high salt to prepare pulse-labeled immunoreactive viral chromatin. The viral DNA was digested before, and in other experiments after, immunoprecipitation with the restriction endonuclease HindIII. We found that SV40 DNA sequences, most probably representing the entire genome, remain in the immunoprecipitate after HindIII digestion, indicating an association of T antigen with origin-distal sections of replicating viral DNA. The results suggest that T antigen in replicating chromatin may be bound to regions close to replicating points. We performed control experiments with in vitro-formed complexes of T antigen and SV40 DNA. When these complexes were immunoprecipitated and HindIII digested we found, in agreement with previous studies, that only the origin containing the HindIII C fragment carried bound T antigen.

DNA binding properties of simian virus 40 temperature-sensitive A proteins

Wild-type simian virus 40 A protein (large T antigen) bound to three tandem regions of simian virus 40 DNA. The binding regions were defined by the ability of A protein to protect simian virus 40 DNA from digestion with limited (footprint assay) or excess (fragment assay) amounts of DNase I. At low concentrations, protein first bound to region I, which maps 30 to 45 base pairs to the early side of the origin of replication. At higher concentrations, A protein also protected region II and then region III. Region II spanned approximately 65 base pairs and corresponded in location to the functional origin of replication that contains a unique BglI site along with an adjacent adenine-thymine-rich region. Region III was adjacent to the late boundary of region II, but its distal limit was not well defined. Twelve distinct temperature-sensitive (ts) A proteins were purified and examined for their ability to bind in regions I to III. Three classes of tsA protein were defined on the basis of thermal stability. Class I tsA protein displayed wild-type binding either with or without a heat shock. Unheated class II tsA protein exhibited wild-type binding, but after a heat shock bound very poorly to the origin of replication. Class III tsA protein was defective in its binding even without a heat shock and only protected region I. Classes II and III were coded by mutants mapping in two distinct regions of the genome. For all of the tsA proteins examined, there was a positive correlation between the thermolability of origin binding in vitro and the temperature sensitivity of these mutants for DNA replication and transcriptional autoregulation in vivo. This correlation adds support to the essential role of origin binding by A protein in viral DNA replication and early transcription repression.

Methylation of simian virus 40 Hpa II site affects late, but not early, viral gene expression

DNA methylation has been correlated with reduced gene expression in a number of studies, although evidence for a casual link between the two events has been lacking. Because microinjection of simian virus 40 (SV40) DNA into the nucleus of Xenopus laevis oocytes results in the synthesis of both early and late viral gene products, it was possible to test whether a specific methylation event can affect gene expression. The single SV40 Hpa II site at 0.72 SV40 map units was specifically methylated with Hpa II methylase. When this DNA was injected into oocytes, there was a marked reduction in the synthesis of the major late viral capsid protein VP-1, relative to the synthesis by an unmethylated control. However, production of the early proteins (the large and small tumor antigens) was not affected by Hpa II methylation. Therefore, methylation at a single site on the viral DNA located near the 5' end of the late region can specifically repress late gene expression. The possible mechanisms by which this repression is mediated are discussed.

A small subclass of SV40 T antigen binds to the viral origin of replication

We examined the affinities of SV40 large T antigen for unique viral DNA sequences by binding SV40 Bst NI DNA fragments in extracts of infected or transformed cells, and then immunoprecipitating the T antigen-DNA complex. The G fragment, which spans the viral origin of replication (ori) was quantitatively bound to T antigen. A T-antigen-specific monoclonal antibody (McI 7), which recognized only 5%-10% of the T antigen from infected or transformed cells, immunoprecipitated the majority of the ori-binding activity. This suggests that only a minor subclass of wild-type T antigen is active in binding to the origin. C6 cells contain a replication-defective mutant T antigen that when tested in the DNA-binding immunoassay, showed no affinity for the ori fragment. McI 7 not only failed to immunoprecipitate ori binding in C6 cells, but also did not detect any labeled C6 T antigen whatever. Thus McI 7 recognizes an immunologically distinct subset of wild-type 7 antigen that comprises the origin-binding form of the viral protein, which is absent in the C6 T antigen population. McI 122, which recognizes a 53 kilodalton host protein that complexes with T antigen, immunoprecipitated ori-binding activity from extracts of infected or transformed cells, but not from C6 cells. Thus wild-type T antigen can bind ori sequences even when complexed to the host protein. These data suggest that T antigen consists of different subpopulations with different functions.

Simian virus 40 large tumor antigen: a "RNA binding protein"?

Simian virus 40 large tumor antigen was isolated by immunoaffinity chromatography from monkey or mouse cell cultures undergoing lytic or transforming infection. RNase-treated gel-purified large tumor antigen, on hydrolysis with alkali, gave about equimolar amounts of AMP, GMP, CMP, and UMP. Furthermore, RNA fragments of approximately 45 nucleotides could be isolated from large tumor antigen purified by the same procedure. Mapping of the T1 oligonucleotides showed a high complexity, as indicated by the presence of unique sequences of 15-30 nucleotides and of poly(A). This is compatible with the hypothesis that these RNA fragments are derived from cellular pre-mRNAs or mRNAs. Our results suggest that Simian virus 40 large tumor antigen is a RNA-binding protein and might possibly be involved in regulation of synthesis, maturation, or translation of cellular mRNAs.

Transforming genes and gene products of polyoma and SV40

The small DNA-containing viruses, SV40 and polyoma, transform cells in vitro and induce tumors in vivo. For both viruses two genes required for transformation have been found. The genes required for transformation are also involved in productive infection. Although the two viruses are similar in their effects on cells, the organization of the transforming genes and gene products is different. The purpose of this review is to compare what is known about the biology and the biochemistry of the early regions of the two viruses. The genetic and biochemical studies defining the sequences important for transformation will be reviewed. Then, the products of the transforming genes, called T antigens, will be discussed in detail. There is a substantial body of descriptive information on those products, and studies on the function of the T antigens have also begun.

Mapping the in vivo arrangement of nucleosomes on simian virus 40 chromatin by the photoaddition of radioactive hydroxymethyltrimethylpsoralen

Intracellular simian virus 40 (SV40) chromatin was photoreacted with a 3H-labeled psoralen derivative, hydroxymethyltrimethylpsoralen (HMT), at 48 h postinfection. Psoralen compounds have been shown to readily penetrate intact cells and, in the presence of long-wavelength UV light, form covalent adducts to DNA, preferentially at regions unprotected by nucleosomes. The average distribution pattern of [3H]HMT on the SV40 genome was determined by specific activity measurements of the DNA fragments generated by HindIII plus HpaII or by AtuI restriction enzyme digestion. At levels of 1 to 10 [3H]HMT photoadducts per SV40 molecule, the radiolabel was found to be distributed nonrandomly. Comparison of the labeling pattern in vivo with that of purified SV40 DNA labeled in vitro revealed one major difference. A region of approximately 400 base pairs, located between 0.65 and 0.73 on the physical map, was preferentially labeled under in vivo conditions. This finding strongly suggests that the highly accessible region near the origin of replication, previously observed on isolated SV40 "minichromosomes," exists on SV40 chromatin in vivo during a lytic infection.

Radioimmunoassay of the cellular protein p53 in mouse and human cell lines

We have developed quantitative radioimmunological solid phase assays for the host protein p53 from mouse cells and from human cells. The first assay, for mouse p53, depends on having two monoclonal antibodies reacting with different determinants on the p53 molecule. With this assay we have shown that SV40-transformed cells have approximately 100-fold more p53 than untransformed mouse cells and that other transformed cells have intermediate levels. Embryonal carcinoma cell lines have approximately 50-fold less p53 than SV40-transformed cells. This is in contrast to the high levels of incorporation of [35S]methionine into p53 in these cells and indicates that metabolic labelling is not a valid approach for measuring p53 levels. The second assay, for human p53, required a different approach and made use of the anti-p53 antibodies detected in the sera of some breast cancer patients. Human tumour cell lines contained amounts of p53 varying from the high level seen in SV40-transformed human fibroblasts down to less than one hundredth of this amount. Normal human cells showed low levels of p53. The data confirm that many, but not all, human tumour cell lines contain more p53 than normal cells.

Ultraviolet irradiation inhibits encapsidation of simian virus 40 chromatin

During normal maturation and majority of pulse-labeled simian virus 40 DNA progresses from chromatin to previrions and virions within 5 h. UV light inhibits this progression. In heavily irradiated cultures (108 J m-2) most of the simian virus 40 DNA synthesized immediately before irradiation remains as chromatin for at least 5 h. This inhibition of maturation seems to be a result of the inhibition of protein synthesis. The data suggest that the pool of proteins required for maturation is sufficient to convert one-third of the simian virus 40 DNA molecules labeled in a 10-min pulse (at 33 h postinfection) from chromatin to previrions and virions and is exhausted within 1 h.

Replication of viral DNA sequences integrated within the chromatin of SV40-transformed Chinese hamster lung cells

To determine when during S phase integrated viral DNA sequences in several tsA SV40-transformed Chinese hamster cell clones replicate, we pulse-labeled cultures with BrdUrd and subsequently collected mitotic cells during sequential time intervals. Restriction endonuclease mapping indicated that each of the three SV40-transformed Chinese hamster lung cell clones contained a single viral DNA sequence at a different, but in each case unique, chromosomal site. DNA was extracted from each population of mitotic cells and then was resolved into dense, BrdUrd-containing and light, unsubstituted DNA fractions by cesium chloride gradient centrifugation. In each pair of samples obtained, we measured viral DNA sequences by solution hybridization using single-stranded SV40 32P-labeled DNA probes. Our results support the conclusions that specific genes within a mammalian DNA are programmed to replicate at particular times during S phase, and that the SV40 A gene product, large T antigen, programs integrated viral DNA sequences to replicate very early in S phase. The fractions of viral DNA replicated early in S phase appeared to correlate with each clone's content of functional large T antigen at permissive and nonpermissive culture temperatures.

Papovavirus chromatin associated cellular endonuclease which introduces one double-strand cut in superhelical deoxyribonucleic acid

Nuclear extracts from SV40-infected CV-1 monkey kidney cells and from polyoma-infected 3T3 mouse cells contain an endonucleolytic activity which cleaves circular viral DNA within the chromatin to full-length linear rods [Waldeck, W., Föhring, B., Chowdhury, K., Gruss, P., & Sauer, G, (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 5964-5968; Scott, W. A., & Wigmore, D. J. (1978) Cell (Cambridge, Mass.) 15, 1511-1518]. Sedimentation of the nuclear extracts through sucrose density gradients revealed a preferential binding of the endonuclease to the viral chromatin. Deproteinized exogenous covalently closed superhelical DNA substrates such as SV40 and polyoma as well as Col E1 and PM2 DNAs were linearized by the endonuclease by introduction of one double-strand break per molecule. The reaction products, FOIII unit length rods, were shown to be devoid of single-strand nicks by electrophoresis in denaturing agarose gels. The double-strand break was randomly located within the various substrates since redigestion of the FOIII with single-cut restriction endonucleases failed to generate discrete pairs of reaction products. Neither linear double-stranded nor nicked circular FOII DNA structures were accepted as substrates. The endonucleolytic activity does not require the presence of ATP but is sensitive to EDTA. The enzyme activity is of cellular origin since nuclear extracts from uninfected CV-1 cells converted exogenous superhelical DNA to FOIII structures with the same properties as those described above. The biological properties of the endonuclease are discussed in the light of its possible function in permitting genetic exchange between different circular genomes. Further, it may play an essential role late during the replication of papovavirus DNA when the catenated daughter molecules are liberated from each other by an as yet unidentified mechanism.

Cessation of reentry of simian virus 40 DNA into replication and its simultaneous appearance in nucleoprotein complexes of the maturation pathway

Newly synthesized SV40 DNA is used as a template for further DNA synthesis (reenters replication) or as a substrate in the assembly of virions (maturation pathway). The time courses of reentry into replication and progression along the maturation pathway were both determined on identical samples. DNA, synthesized during a 20-min pulse, reentered replication over a period of several hours and then was removed from the pool of molecules available for replication. The cessation of reentry coincided with the maturation of this DNA from the chromatin form to previrion and virion forms. More reentry and less maturation was observed at 24 h postinfection than at 42 h postinfection. The data are consistent with the hypothesis that the factor(s) responsible for cessation of reentry is also responsible for initiation of the maturation pathway.

Two deletions within genes for simian virus 40 structural proteins VP2 and VP3 lead to formation of abnormal transcriptional complexes

The procedure developed by R. M. Fernandez-Muñoz et al. (J. Virol. 29:612-623, 1979) for isolating simian virus 40 (SV 40) chromatin free of disrupted previrions was optimized for preparing late transcriptional complexes, and these complexes were partially characterized. Transcriptional complexes derived from wild-type virus and from several deletion and temperature-sensitive mutants could be activated more than five-fold either by the anionic detergent Sarkosyl or by 300 mM ammonium sulfate, in agreement with the properties of SV40 transcriptional complexes prepared by other procedures. In contrast, complexes from cells infected with deletion mutants dl1261 or dl1262 were not activated at all by a high salt concentration, even though the extent of their activation by Sarkosyl was normal. Mutants dl1261 and dl1262 carry deletions of 54 and 36 base pairs, respectively, at an approximate map position of 0.91, which is within the overlapping genes for the virion proteins VP2 and VP3. The effects of these deletions on transcription in vitro indicate that VP2 or VP3 or both are bound to late transcriptional complexes in a way that affects the progress of initiated RNA polymerase. The properties of late transcriptional complexes derived from wild-type SV40 can be explained by the presence of the following two different kinds of complexes: (i) a minority class (about 20%), which is free of VP2 or VP3, active at low concentrations of ammonium sulfate in vitro, and responsible for late transcription in vivo, and (ii) a majority class (about 80%) with VP2 or VP3 bound, which is inactive at low salt concentrations both in vitro and in vivo but capable of being activated by high salt concentrations or by Sarkosyl. We propose that mutant VP2 and VP3 proteins from dl1261 and dl1262 bind to the majority class of late transcriptional complexes in a way that can be reversed by Sarkosyl but not by a high salt concentration.

Immunological detection of specific proteins in total cell extracts by fractionation in gels and transfer to diazophenylthioether paper

We describe a sensitive immunological procedure for the detection of specific proteins in total cell extracts and for the comparison of antigenically related polypeptides. Proteins are fractionated in polyacrylamide gels and transferred electrophoretically to diazophenylthioether paper, to which they bind covalently. Specific proteins are identified by incubation with specific antibody and 125 I-labeled protein A from Staphylococcus aureus, followed by autoradiography. High-resolution separation of proteins prior to transfer is achieved by polyacrylamide gradient gel electrophoresis in the presence of sodium dodecyl sulfate or by nonequilibrium pH gradient electrophoresis, followed by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Further information can be obtained by limited enzymatic proteolysis of the proteins in the gel following polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and analysis of the cleavage products by gel electrophoresis at right angles to the first gel. We show the application of this technique to the detection and comparison in extracts from infected cells of proteins related immunologically to the simian virus 40 capsid proteins VP1 and VP3.

Identification and initial characterization of a new low-molecular-weight virus-encoded T antigen in a line of simian virus 40-transformed cells

SV80 cells, a simian virus 40 (SV40)-transformed derivative of a strain of human fibroblasts, synthesize an 8-kilodalton anti-T reactive polypeptide in addition to large T and small t antigens. Although not observed during lytic infection carried out under a variety of conditions, an anti-T reactive molecule which comigrated with the SV80 8-kilodalton protein during sodium dodecyl sulfate-polyacrylamide gel electrophoresis was synthesized by one of five other SV40-transformed cell lines studied. The SV40 8-kilodalton protein was present in lysates of cells exposed to a brief pulse of radioactive methionine and did not accumulate during an extended chase period. This polypeptide could not by generated by mixing an unlabeled extract of SV80 cells with a labeled extract of infected monkey cells. The 8-kilodalton molecule reacts with antibody raised against homogeneous large T antigen, is present only in the cytoplasm, is not complexed with T, lacks DNA-binding properties, and is not phosphorylated. This protein could be translated in a cell-free system programmed by SV40-specific mRNA. At least two messenger species (approximately 19S and approximately 22S) directed its synthesis. Tryptic peptide analysis of [35S]methionine-labeled proteins demonstrated that the 8-kilodalton protein contains all eight of the common T/t peptides and one additional peptide not present in the maps of t or T. It lacks both of the t-unique peptides. The organization of the integrated viral sequences which encode this molecule was determined by restriction endonuclease analysis. In particular, SV80 cells contain at least two integrated SV40 genomes which are oriented in tandem, with an intervening cellular sequence..

A histone-specific acetyltransferase is associated with simian-virus-40 chromatin

[14C]Thymidine-labeled simian virus 40 nucleoprotein complexes were prepared from nuclei of lytically infected African green monkey kidney cells. The nucleoprotein complexes were further purified by sucrose gradient centrifugation and then incubated in the presence of [3H]acetyl-coenzyme A. We observed a transfer of [3H]acetyl groups to the endogenous histones H2B, H3 and H4. The enzyme was solubilized in the presence of 0.5 M NaCl and showed properties described for the DNA-binding acetyltransferase (J. Böhm, E. J. Schlaeger and R. Knippers, preceding paper in this journal).

Association of polyoma T antigen and DNA with the nuclear matrix from lytically infected 3T6 cells

Nuclear matrix prepared from mouse 3T6 cells lytically infected with polyoma virus retained significant amounts of the 100K T antigen and intact viral genomes. Bound T antigen was resistant to the extraction by high salt (2 M NaCl), detergent (1% Triton X-100) and exhaustive DNAase treatment. Only conditions sufficient to disrupt the integrity of the matrix itself solubilized the matrix T antigen. During the time period of 16-30 hr after infection, both the accumulation (in microgram) and the incorporation of 35S-methionine into T antigen increased steadily in cell extracts to a peak at 26 hr and then declined. In contrast, the amount of labeled T antigen retained by the matrix was relatively constant over the same time period. Matrix-bound T antigen was more highly phosphorylated and newly synthesized compared with the extractable T antigen. Viral DNA steadily accumulates in nuclei and on the matrix from 18 to 30 hr after infection. The fraction of viral DNA retained by the matrix was greatest early in infection (25% at 16 hr), declining to less than 10% by 24 hr. These data are consistent with the existence of a fixed (and limited) number of sites for T antigen (more highly phosphorylated) on the matrix and implicate the nuclear matrix as a site of viral DNA replication and possibly encapsidation.

Two-dimensional analysis of proteins sedimenting with simian virus 40 chromosomes

The nonhistone proteins sedimenting in low-salt glycerol gradients with simian virus 40 chromosomes were analyzed by two-dimensional gel electrophoresis, utilizing nonequilibrium pH gradients as the first dimension and sodium dodecyl sulfate-gel electrophoresis as the second dimension. By densitometric quantitation of the radiolabeled proteins present in each fraction of the gradients, it was possible to identify sedimenting with all or a fraction of the simian virus 40 chromosomes. VP-1 sedimented with simian virus 40 chromosomes; additional evidence for its binding to chromosomes was obtained by immunochemical techniques. Four proteins (Mr 25,000, pI 6.0; Mr 32,000, pI 7.2; Mr 35,000, pI 8.5; and Mr 80,000, pI 7.2) sedimented with specific subsets of chromosomes.

Simian virus 40 T-antigen-related cell surface antigen: serological demonstration on simian virus 40-transformed monolayer cells in situ

Simian virus 40 (SV40)-transformed monolayer cells were analyzed in situ by indirect immunofluorescence microscopy for the postulated cell surface location of SV40 T-antigen-related molecules. With antisera prepared against purified, sodium dodecyl sulfate-denatured SV40 T-antigen, positive surface staining was obtained when the cells had been treated with formaldehyde before immunofluorescence analysis. In contrast, living SV40-transformed cells analyzed in monolayer were surface fluorescence negative. The fixation procedure developed in this study combined with a double staining immunofluorescence technique allowed the simultaneous analysis of the same cells for the expression of both SV40 T-antigen-related surface antigen and nuclear T-antigen. The localization of SV40 T-antigen-related surface antigen on the outer surface of the plasma membrane of formaldehyde-fixed SV40-transformed cells was demonstrated directly by the protein A-mediated binding of Staphylococcus aureus bacteria on formaldehyde-fixed SV40-transformed cells precoated with antiserum against sodium dodecyl sulfate-denatured T-antigen. Both cell surface staining and S. aureus binding were found to be highly specific for SV40 T-antigen-related binding sites. These results indicate that T-antigen-related molecules in a cryptic form are located on the surface of SV40-transformed monolayer cells and can be detected in situ after modification of the cell surface architecture.