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

A Decade of Discovery-Eukaryotic Replisome Disassembly at Replication Termination

The eukaryotic replicative helicase (CMG complex) is assembled during DNA replication initiation in a highly regulated manner, which is described in depth by other manuscripts in this Issue. During DNA replication, the replicative helicase moves through the chromatin, unwinding DNA and facilitating nascent DNA synthesis by polymerases. Once the duplication of a replicon is complete, the CMG helicase and the remaining components of the replisome need to be removed from the chromatin. Research carried out over the last ten years has produced a breakthrough in our understanding, revealing that replication termination, and more specifically replisome disassembly, is indeed a highly regulated process. This review brings together our current understanding of these processes and highlights elements of the mechanism that are conserved or have undergone divergence throughout evolution. Finally, we discuss events beyond the classic termination of DNA replication in S-phase and go over the known mechanisms of replicative helicase removal from chromatin in these particular situations.

Mechanisms of DNA replication termination

Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation. We briefly review the mechanism of termination in the bacterium Escherichia coli and in simian virus 40 (SV40) and also focus on recent advances in eukaryotic replication termination. In particular, we discuss the recently discovered E3 ubiquitin ligases that control replisome disassembly in yeast and higher eukaryotes, and how their activity is regulated to avoid genome instability.

The mechanism of DNA replication termination in vertebrates

Eukaryotic DNA replication terminates when replisomes from adjacent replication origins converge. Termination involves local completion of DNA synthesis, decatenation of daughter molecules, and replisome disassembly. Termination has been difficult to study because termination events are generally asynchronous and sequence non-specific. To overcome these challenges, we paused converging replisomes with a site-specific barrier in Xenopus egg extracts. Upon removal of the barrier, forks underwent synchronous and site-specific termination, allowing mechanistic dissection of this process. We show that DNA synthesis does not slow detectably as forks approach each other and that leading strands pass each other unhindered before undergoing ligation to downstream lagging strands. Dissociation of CMG helicases occurs only after the final ligation step, and is not required for completion of DNA synthesis, strongly suggesting that converging CMGs pass one another and dissociate from double-stranded DNA. This termination mechanism allows rapid completion of DNA synthesis while avoiding premature replisome disassembly

The nuclear matrix and virus function

Replication of the small DNA tumor virus, simian virus 40 (SV40), is largely dependent on host cell functions, because SV40, in addition to virion proteins, codes only for a few regulatory proteins, the most important one being the SV40 large tumor antigen (T-antigen). This renders SV40 an excellent tool for studying complex cellular and viral processes. In this review we summarize and discuss data providing evidence for virtually all major viral processes during the life cycle of SV40 from viral DNA replication to virion formation, being performed at or within structural systems of the nucleus, in particular the chromatin and the nuclear matrix. These data further support the concept that viral replication in the nucleus is structurally organized and demonstrate that viruses are excellent tools for analyzing the underlying cellular processes. The analysis of viral replication at nuclear structures might also provide a means for specifically interfering with viral processes without interfering with the corresponding cellular functions.

Structural topography of simian virus 40 DNA replication

Applying an in situ cell fractionation procedure, we analyzed structural systems of the cell nucleus for the presence of mature and replicating simian virus 40 (SV40) DNA. Replicating SV40 DNA intermediates were tightly and quantitatively associated with the nuclear matrix, indicating that elongation processes of SV40 DNA replication proceed at this structure. Isolated nuclei as well as nuclear matrices were able to continue SV40 DNA elongation under replication conditions in situ, arguing for a coordinated and functional association of SV40 DNA and large T molecules at nuclear structures. SV40 DNA replication also was terminated at the nuclear matrix. While the bulk of newly synthesized, mature SV40 DNA molecules then remained at this structure, some left the nuclear matrix and accumulated at the chromatin.

Characterization of SV40 T antigen associated with the nuclear matrix

Simian virus 40 (SV40) T antigen associated with the nuclear matrix of SV40-infected TC7 cells has been characterized. Pulse-chase studies on the turnover of T antigen in the different subcellular fractions show that T antigen turns over most rapidly in its association with the purified SV40 nucleoprotein complexes (NPCs) and undergoes a slower rate of turnover in its association with the nuclear matrix. In contrast, turnover of SV40 T antigen in its association with the other subcellular fractions is not detected during the same period of time. Tryptic peptide maps establish that NPC-associated T antigen and nuclear matrix-associated T antigen are chemically related, in that they have two additional methionine-containing peptides that are not found in the majority of T antigen molecules. The association of T antigen with the nuclear matrix is independent of SV40 DNA replication since T antigen is still present in the nuclear matrix after a 1-hr shift-up of tsA58-infected cells to the nonpermissive temperature. In addition, T antigen is associated with the nuclear matrices of both C6 and Cos7 transformed cells, indicating that the association of T antigen with the nuclear matrix is independent of its ability to initiate and support SV40 DNA replication.

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.

Differential increase in topoisomerase II in simian virus 40-infected cells

The time course of expression of topoisomerase I, topoisomerase II, and simian virus 40 (SV40) large tumor (T) antigen was determined in whole-cell extracts of uninfected versus SV40-infected TC7 cells. After a minor increase, the level of topoisomerase I remained fairly constant throughout the time course in both uninfected and SV40-infected cells. In contrast, the level of topoisomerase II increased markedly in SV40-infected cells but not in uninfected cells following the appearance of SV40 T antigen.

Programmed factor binding to simian virus 40 GC-box replication and transcription control sequences

Nuclear footprinting revealed a temporal program involving factor binding to the repetitive GC-box DNA elements present in the simian virus 40 regulatory region. This program specified ordered and directional binding to these tandem regulatory sequences in vivo during the late phase of infection. The program was interrupted by the DNA replication inhibitor aphidicolin or by inactivation of the viral replication factor simian virus 40 T antigen, suggesting a link between viral DNA replication and new factor binding. Measurements of DNA accumulation in viruses lacking either the distal or proximal halves of the GC-box region suggested that the region has a dual role in replication control. Overall, the data point to important relationships between DNA replication and factor binding to the GC-box DNA, a multifunctional regulatory region.

A transcription factor from simian virus 40 chromosomes which activates the viral late promoter in vitro

We have characterized a transcription factor, obtained from simian virus 40 (SV40) chromosomes, which activates transcription from the SV40 late promoter in vitro. The late promoter-activating factor was distinct from SV40 T antigen as judged by its behavior on chromatography on hydroxylapatite; it was not recognized by anti-T antibodies, while T antigen itself was recognized. T antigen from SV40 chromosomes, on the other hand, abolished transcription in vitro from the early promoter. In DNase I footprinting experiments, a partially purified late promoter-activating factor preparation protected a region of DNA centered on SV40 nucleotide 270, which is between the repeated 72-base-pair enhancer and the major late RNA start site. Proteins from HeLa cells did not give the same footprint at this position. Gel mobility shift assays showed that proteins from SV40-infected CV-1 cells form a complex with DNA containing this binding site. The complex has a different rate of gel migration and a higher stability than complexes formed with proteins from uninfected cells.

Characterization of simian virus 40 large T antigen by using different monoclonal antibodies: T-p53 complexes are preferentially ATPase active and adenylylated

We used 21 monoclonal antibodies (PAbs 100 to 117, 405, 419, and KT3) specific for different determinants in simian virus 40 (SV40) large T antigen (T) and one antibody specific for p53 that coprecipitates T complexed with p53 (T-p53) to analyze T in SV40-infected CV1 cells. We measured the ATPase specific activity, extent of adenylylation, and p53 content of T precipitated by antibodies directed against the N-terminal region I (0.65 to 0.62 map units), the midregion III (0.43 to 0.28 map units) containing both the ATPase- and nucleotide-binding sites, and the C-terminal region IV (0.28 to 0.17 map units) of T. Lytic T appeared to exist in three different forms with respect to p53 binding and ATPase activity. The most ATPase-active form of T was that precipitated by PAb 122. This T-p53 complex contained only 6% of the total T but contributed 35% of the ATPase activity, on average. Free p53 isolated from 3T6, Ann-1, or L929 cells had no apparent ATPase activity. A second form of T precipitated by several antibodies had little associated p53 but appreciable ATPase activity, accounting for 15 to 20% of total T and 60 to 70% of the ATPase activity. The rest of T constituted the third form and was also depleted in p53 but had a decreased ATPase specific activity. Thus, the remaining 75 to 80% of T had 15 to 20% of the ATPase specific activity. Antibodies specific for region III precipitated T with both altered ATPase activity and altered amounts of bound p53. PAbs 104 and 114 reacted with ATPase-active T but inhibited ADP hydrolysis, suggesting that they were inactivating antibodies. T that was preferentially adenylylated in vitro corresponded to T that was also preferentially ATPase active. T bound to p53 was adenylylated to a higher specific activity than total T. In addition, p53 itself was significantly adenylylated under these conditions. The results suggest that ATPase activity and p53 binding are structurally and functionally related and that p53 alters biochemical activities of T and plays a role in productive infection.

Unwinding of duplex DNA from the SV40 origin of replication by T antigen

The T antigen specified by SV40 virus is the only viral-encoded protein required for replication of SV40 DNA. T antigen has two activities that appear to be essential for viral DNA replication: specific binding to duplex DNA at the origin of replication and helicase activity that unwinds the two DNA strands. As judged by electron microscopy, DNA unwinding is initiated at the origin of replication and proceeds bidirectionally. Either linear or circular DNA molecules containing the origin of replication are effective substrates; with closed circular DNA, a topoisomerase capable of removing positive superhelical turns is required for an efficient reaction. Presence of an origin sequence on duplex DNA and a single-strand DNA-binding protein appear to be the only requirements for T antigen to catalyze unwinding. This reaction mediated by T antigen defines a likely pathway to precise initiation of DNA replication: (i) the sequence-specific binding activity locates the origin sequence, (ii) the duplex DNA is unwound at this site, and (iii) the DNA polymerase and primase begin DNA replication. A similar pathway has been inferred for the localized initiation of DNA replication by bacteriophage lambda and by Escherichia coli in which a sequence-specific binding protein locates the origin and directs the DnaB helicase to this site. Observations with the SV40 system indicate that localized initiation of duplex DNA replication may be similar for prokaryotes and eukaryotes.

In vivo characterization of the poly(ADP-ribosylation) of SV40 chromatin and large T antigen by immunofractionation

We have confirmed the poly(ADP-ribosylation) of large T antigen of SV40 by using antibodies to both large T antigen and poly(ADP-ribose) and consequently have begun to characterize how this post-translational nuclear modification of the viral protein modulates its biological functions. SV40 minichromosomal subpopulation containing replicative intermediate DNA was shown to have a significantly higher affinity for anti-poly(ADP-Rib)-Sepharose than viral chromatin fractions containing mature minichromosomal DNA. An anti-large T-Sepharose column was used to isolate T antigen from crude extracts by two different approaches: (1) large T antigen was labeled with [35S]methionine in vivo and the infected cell extract was immunofractionated to isolate large T antigen and (2) large T antigen from infected cell extracts was immunofractionated followed by immunostaining. Using these techniques, 1-10% of the total T antigen from infected cells was found to be poly(ADP-ribosylated). Minichromosome preparations per se were also subjected to immunofractionation on anti-large T-Sepharose. The high level of retention of poly(ADP-ribosylated) species of minichromosomes on this matrix suggested that this post-translational modification of viral chromatin may be related to those steps in viral replication and transcription under regulation by large T antigen.

Factor interactions at simian virus 40 GC-box promoter elements in intact nuclei

Primer extension footprinting was used to probe late simian virus 40 regulatory elements in intact infected cell nuclei. Specific protection was observed over the viral "GC-box" transcription elements. The participation of the bound templates in gene activation is addressed by quantitation that shows that their abundance greatly exceeds that of transcription complexes but is comparable to that of open chromatin.

Factor interactions at simian virus 40 GC-box promoter elements in intact nuclei

Primer extension footprinting was used to probe late simian virus 40 regulatory elements in intact infected cell nuclei. Specific protection was observed over the viral "GC-box" transcription elements. The participation of the bound templates in gene activation is addressed by quantitation that shows that their abundance greatly exceeds that of transcription complexes but is comparable to that of open chromatin.

Initiation of simian virus 40 DNA replication in vitro: aphidicolin causes accumulation of early-replicating intermediates and allows determination of the initial direction of DNA synthesis

Aphidicolin, a specific inhibitor of DNA polymerase alpha, provided a novel method for distinguishing between initiation of DNA synthesis at the simian virus 40 (SV40) origin of replication (ori) and continuation of replication beyond ori. In the presence of sufficient aphidicolin to inhibit total DNA synthesis by 50%, initiation of DNA replication in SV40 chromosomes or ori-containing plasmids continued in vitro, whereas DNA synthesis in the bulk of SV40 replicative intermediate DNA (RI) that had initiated replication in vivo was rapidly inhibited. This resulted in accumulation of early RI in which most nascent DNA was localized within a 600- to 700-base-pair region centered at ori. Accumulation of early RI was observed only under conditions that permitted initiation of SV40 ori-dependent, T-antigen-dependent DNA replication and only when aphidicolin was added to the in vitro system. Increasing aphidicolin concentrations revealed that DNA synthesis in the ori region was not completely resistant to aphidicolin but simply less sensitive than DNA synthesis at forks that were farther away. Since DNA synthesized in the presence of aphidicolin was concentrated in the 300 base pairs on the early gene side of ori, we conclude that the initial direction of DNA synthesis was the same as that of early mRNA synthesis, consistent with the model proposed by Hay and DePamphilis (Cell 28:767-779, 1982). The data were also consistent with initiation of the first DNA chains in ori by CV-1 cell DNA primase-DNA polymerase alpha. Synthesis of pppA/G(pN)6-8(pdN)21-23 chains on a single-stranded DNA template by a purified preparation of this enzyme was completely resistant to aphidicolin, and further incorporation of deoxynucleotide monophosphates was inhibited. Therefore, in the presence of aphidicolin, this enzyme could initiate RNA-primed DNA synthesis at ori first in the early gene direction and then in the late gene direction, but could not continue DNA synthesis for an extended distance.

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.

Initiation of simian virus 40 DNA replication in vitro: aphidicolin causes accumulation of early-replicating intermediates and allows determination of the initial direction of DNA synthesis

Aphidicolin, a specific inhibitor of DNA polymerase alpha, provided a novel method for distinguishing between initiation of DNA synthesis at the simian virus 40 (SV40) origin of replication (ori) and continuation of replication beyond ori. In the presence of sufficient aphidicolin to inhibit total DNA synthesis by 50%, initiation of DNA replication in SV40 chromosomes or ori-containing plasmids continued in vitro, whereas DNA synthesis in the bulk of SV40 replicative intermediate DNA (RI) that had initiated replication in vivo was rapidly inhibited. This resulted in accumulation of early RI in which most nascent DNA was localized within a 600- to 700-base-pair region centered at ori. Accumulation of early RI was observed only under conditions that permitted initiation of SV40 ori-dependent, T-antigen-dependent DNA replication and only when aphidicolin was added to the in vitro system. Increasing aphidicolin concentrations revealed that DNA synthesis in the ori region was not completely resistant to aphidicolin but simply less sensitive than DNA synthesis at forks that were farther away. Since DNA synthesized in the presence of aphidicolin was concentrated in the 300 base pairs on the early gene side of ori, we conclude that the initial direction of DNA synthesis was the same as that of early mRNA synthesis, consistent with the model proposed by Hay and DePamphilis (Cell 28:767-779, 1982). The data were also consistent with initiation of the first DNA chains in ori by CV-1 cell DNA primase-DNA polymerase alpha. Synthesis of pppA/G(pN)6-8(pdN)21-23 chains on a single-stranded DNA template by a purified preparation of this enzyme was completely resistant to aphidicolin, and further incorporation of deoxynucleotide monophosphates was inhibited. Therefore, in the presence of aphidicolin, this enzyme could initiate RNA-primed DNA synthesis at ori first in the early gene direction and then in the late gene direction, but could not continue DNA synthesis for an extended distance.

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.

Structure of transcriptionally active chromatin

Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.

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.

Both trans-acting factors and chromatin structure are involved in the regulation of transcription from the early and late promoters in simian virus 40 chromosomes

We isolated simian virus 40 (SV40) chromosomes from lytically infected CV-1 cells at various times during the late phase and transcribed them in vitro with either whole-cell or nuclear extracts of HeLa cells. The late promoter was 3- to 10-fold more active than the early promoter. With bare SV40 DNA templates, the early promoter was up to 10-fold stronger than the late promoter. The relative strengths of the early and late promoters on SV40 chromosomes were essentially independent of template concentration or length of the replicative phase of the infection. When monoclonal antibodies or antisera against T antigen (T Ag) were added to SV40 chromosomes or when T Ag, both free and chromatin bound, was removed by immunoprecipitation with anti-T, the activity of the late promoter remained essentially unchanged. Washing with 0.4 M NaCl removed T Ag from more than 90% of the mature chromosomes associated with T Ag. Transcription from the late promoter still predominated in the salt-washed T Ag-depleted chromosomes, even though there was a marked increase in early promoter activity. The depression of the early promoter could be reversed by adding the T Ag-containing extract back to the depleted chromosomes. Extraction of SV40 chromosomes with 1.5 M NaCl resulted in a decrease in the activity of the late promoter and a further increase in the activity of the early promoter so that the relative amounts of early and late RNA synthesized were similar to those for bare SV40 DNA templates. Late RNA synthesis from bare SV40 DNA templates was stimulated by high-speed supernatants prepared from nuclear extracts of SV40-infected cells but not from those of uninfected cells. Pretreatment of the supernatants with anti-T did not alter the result. Our findings indicate that the activity of the early and late SV40 promoters is regulated by at least two different mechanisms at the chromosomal level. One is mediated by a subclass of T Ag bound to SV40 chromosomes which represses early SV40 transcription but has no effect on late transcription. A second level of regulation, involving a tightly bound trans-acting chromosomal factor and a stable nucleoprotein structure, favors the late promoter over the early promoter by up to 10-fold.