Topoisomerase I is preferentially associated with normal SV40 replicative intermediates, but is associated with both replicating and nonreplicating SV40 DNAs which are deficient in histones

A model for the formation of the duplicated enhancers found in polyomavirus regulatory regions

When purified from persistent infections, the genomes of most human polyomaviruses contain single enhancers. However, when isolated from productively infected cells from immunocompromised individuals, the genomes of several polyomaviruses contain duplicated enhancers that promote a number of polyoma-based diseases. The mechanism(s) that gives rise to the duplicated enhancers in the polyomaviruses is, however, not known. Herein we propose a model for the duplication of the enhancers that is based on recent advances in our understanding of; 1) the initiation of polyomavirus DNA replication, 2) the formation of long flaps via displacement synthesis and 3) the subsequent generation of duplicated enhancers via double stranded break repair. Finally, we discuss the possibility that the polyomavirus based replication dependent enhancer duplication model may be relevant to the enhancer-associated rearrangements detected in human genomes that are associated with various diseases, including cancers.

The SV40 large T-antigen origin binding domain directly participates in DNA unwinding

The origin binding domain (OBD) of SV40 large T-ag serves a critical role during initiation of DNA replication to position T-ag on the origin. After origin recognition, T-ag forms a double hexamer over the origin. Within each hexamer, the OBD adopts a lock washer structure where the origin recognizing A1 and B2 loops face toward the helicase domain and likely become unavailable for binding DNA. In this study, we investigated the role of the central channel of the OBD hexamer in DNA replication by analyzing the effects of mutations of residues lining the channel. All mutants showed binding defects with origin DNA and ssDNA especially at low protein concentrations, but only half were defective at supporting DNA replication in vitro. All mutants were normal in unwinding linear origin DNA fragments. However, replication defective mutants failed to unwind a small origin containing circular DNA whereas replication competent mutants did so normally. The presence of RPA and/or pol/prim restored circular DNA unwinding activity of compromised mutants probably by interacting with the separated DNA strands on the T-ag surface. We interpret these results to indicate a role for the OBD central channel in binding and threading ssDNA during unwinding of circular SV40 DNA. Mixing experiments suggested that only one monomer in an OBD hexamer was necessary for DNA unwinding. We present a model of DNA threading through the T-ag complex illustrating how single-stranded DNA could pass close to a trough generated by key residues in one monomer of the OBD hexamer.

Mutational analysis of the preferential binding of human topoisomerase I to supercoiled DNA

Human topoisomerase I binds DNA in a topology-dependent fashion with a strong preference for supercoiled DNAs of either sign over relaxed circular DNA. One hypothesis to account for this preference is that a second DNA-binding site exists on the enzyme that mediates an association with the nodes present in supercoiled DNA. The failure of the enzyme to dimerize, even in the presence of DNA, appears to rule out the hypothesis that two binding sites are generated by dimerization of the protein. A series of mutant protein constructs was generated to test the hypotheses that the homeodomain-like core subdomain II (residues 233-319) provides a second DNA-binding site, or that the linker or basic residues in core subdomain III are involved in the preferential binding to supercoiled DNAs. When putative DNA contact points within core subdomain II were altered or the domain was removed altogether, there was no effect on the ability of the enzyme to recognize supercoiled DNA, as measured by both a gel shift assay and a competition binding assay. However, the preference for supercoils was noticeably reduced for a form of the enzyme lacking the coiled-coil linker region or when pairs of lysines were changed to glutamic acids in core subdomain III. The results obtained implicate the linker and solvent-exposed basic residues in core subdomain III in the preferential binding of human topoisomerase I to supercoiled DNA.

Topoisomerase I associates specifically with simian virus 40 large-T-antigen double hexamer-origin complexes

Topoisomerase I (topo I) is required for releasing torsional stress during simian virus 40 (SV40) DNA replication. Recently, it has been demonstrated that topo I participates in initiation of replication as well as in elongation. Although T antigen and topo I can bind to one another in vitro, there is no direct evidence that topo I is a component of the replication initiation complex. We demonstrate in this report that topo I associates with T-antigen double hexamers bound to SV40 origin DNA (T(DH)) but not to single hexamers. This association has the same nucleotide and DNA requirements as those for the formation of double hexamers on DNA. Interestingly, topo I prefers to bind to fully formed T(DH) complexes over other oligomerized forms of T antigen associated with the origin. High ratios of topo I to origin DNA destabilize T(DH). The partial unwinding of a small-circular-DNA substrate is dependent on the presence of both T antigen and topo I but is inhibited at high topo I concentrations. Competition experiments with a topo I-binding fragment of T antigen indicate that an interaction between T antigen and topo I occurs during the unwinding reaction. We propose that topo I is recruited to the initiation complex after the assembly of T(DH) and before unwinding to facilitate DNA replication.

Human topoisomerase I promotes initiation of simian virus 40 DNA replication in vitro

Addition of purified human topoisomerase I (topo I) to simian virus 40 T antigen-driven in vitro DNA replication reactions performed with topo I-deficient extracts results in a greater than 10-fold stimulation of completed molecules as well as a more than 3-fold enhancement of overall DNA replication. To further characterize this stimulation, we first demonstrate that bovine topo I but not Escherichia coli topo I can also enhance DNA replication. By using several human topo I mutants, we show that a catalytically active form of topo I is required. To delineate whether topo I influences the initiation or the elongation step of replication, we performed delayed pulse, pulse-chase, and delayed pulse-chase experiments. The results illustrate that topo I cannot promote the completion of partially replicated molecules but is needed from the beginning of the reaction to initiate replication. Competitive inhibition experiments with the topo I binding T antigen fragment 1-246T and a catalytically inactive topo I mutant suggest that part of topo I's stimulation of replication is mediated through a direct interaction with T antigen. Collectively, our data indicate that topo I enhances the synthesis of fully replicated DNA molecules by forming essential interactions with T antigen and stimulating initiation.

Involvement of topoisomerases in the initiation of simian virus 40 minichromosome replication

Topoisomerases provide the unlinking activity necessary for replication fork movement during DNA replication. It is uncertain, however, whether topoisomerases are also required for the initiation of replication. To investigate this point, we have performed pulse-chase experiments with SV40 minichromosomes as template to distinguish between the initiation and the elongation of replication. Using an unfractionated cytosolic extract as a source of replication functions, we found that the addition of topoisomerases at the initiation step significantly increased the number of active chromatin templates, whereas addition of topoisomerases at the elongation step had only minor effects. Minichromosomes with an extended chromatin structure as well as protein-free DNA required less topoisomerase for effective replication initiation. We could exclude the possibility that topoisomerases enhance the origin binding of T antigen, the SV40 replication initiator, and propose instead that the arrangement of nucleosomes influences the diffusion of supercoils during initial DNA unwinding. Efficient initiation therefore requires a high local concentration of topoisomerases to relax the torsional stress.

Topoisomerase I stimulates SV40 T antigen-mediated DNA replication and inhibits T antigen's ability to unwind DNA at nonorigin sites

We have previously found that purified SV40 T antigen and topoisomerase I (topo I) bind to one another in vitro. In this report, we determined the effects of human topo I on T antigen-mediated DNA replication and investigated whether it altered T antigen's biochemical activities. Topo I stimulates DNA replication and especially increases the amounts of finished circular molecules. This protein had no effect on T antigen's ability to bind, distort, or unwind the origin of replication. However, unwinding of DNA by T antigen was strongly inhibited by topo I when it was initiated at sites other than the origin. We demonstrate that the presence of T antigen binding sites in DNA interfere with inhibition of unwinding by topo I. These results indicate that topo I may increase the specificity of unwinding by inhibiting the reaction at non-origin sites. Fragments of T antigen that bind to topo I abrogate topo I's inhibition of non-origin-dependent unwinding, indicating that topo I inhibits unwinding through a direct interaction with T antigen. We propose a model whereby T antigen and topo I function together at the origin to specifically unwind it and initiate DNA replication.

Accessibility to topoisomerases I and II regulates the replication efficiency of simian virus 40 minichromosomes

We determined the effects of chromatin structure on template accessibility to replication factors and used three different templates as substrates for simian virus 40 (SV40) DNA replication in vitro: native and salt-treated SV40 minichromosomes and protein-free SV40 DNA. Native minichromosomes contain histone H1 and numerous nonhistone proteins in addition to the core histones, whereas salt-treated minichromosomes carry essentially only core histones. We reasoned that the less densely packed salt-treated minichromosomes should be more effective replication templates due to their more extended configuration. However, contrary to this expectation, we found that native minichromosomes replicated with significantly higher efficiency than salt-treated minichromosomes, while protein-free DNA was most active as a replication template. The higher replication efficiency of native minichromosomes was due to two activities bound to the chromatin, which were identified as DNA topoisomerases I and II. By using chromatin substrates of different general configurations, we also showed that the overall chromatin structure determines accessibility to topoisomerases I and II and thereby the efficiency of replicative chain elongation.

T cell proliferative response induced by DNA topoisomerase I in patients with systemic sclerosis and healthy donors

The in vitro T cell proliferative response to DNA topoisomerase I (topo I) was examined in 26 systemic sclerosis (SSc) patients with anti-topo I antibody, 10 SSc patients without anti-topo I antibody, and 21 healthy donors. Using recombinant fusion proteins encompassing the entire human topo I amino acid sequence, a topo I-specific proliferative response was detected in PBMC cultures from 25 (96%) anti-topo I-positive SSc patients, 4 (40%) anti-topo I-negative SSc patients, and 13 (62%) healthy donors. Molecular typing at MHC class II loci revealed that all SSc patients and healthy donors having either DRB1*1501,2 (DR15), DRB1*1101,3,4 (DR11), or DRB1*07 (DR7) were responders. Characterization of the topo I-induced T cell proliferative response showed that (a) the responding cells were CD4+ T cells; (b) antigen-presenting cells were necessary for the response; (c) the response was restricted by HLA-DR, and to a lesser extent by HLA-DQ; and (d) the estimated frequency of the responding T cells determined by limiting dilution analysis was 1/9,277-1/24,853. PBMC cultures from anti-topo I-positive SSc patients showed a high T cell proliferative response after only 3 d of culture with topo I. Anti-topo I-negative SSc patients and healthy donors had no proliferative response after 3 d, but did respond after 7 d of culture. T cell proliferative responses to six truncated topo I fragments tested individually showed different patterns of T cell proliferation that were dependent upon the responder's HLA-DR alleles. These results indicate that T cells reactive with topo I are components of the normal T cell repertoire, and that the topo I-specific T cell proliferative response is not associated with the presence or absence of SSc or anti-topo I antibody, but is restricted by MHC class II alleles.

Purification of Caenorhabditis elegans DNA topoisomerase I

DNA topoisomerase I was partially purified from Caenorhabditis elegans worms. The enzyme is a 95 kDa polypeptide and its proteolytically degraded form of 70 kDa was also observed. The enzyme removed not only negative but also positive DNA supercoils. The optimum salt concentration for the DNA relaxation activity was 100 mM KCl, and divalent cations were not required but stimulated the activity. The DNA relaxation activity was weakly sensitive to 125 microM camptothecin but was completely inhibited by 125 microM berenil.