Intra- and intermolecular strand transfer by HeLa DNA topoisomerase I

DNA topoisomerase I from rat brain neurons

The DNA topoisomerase I has been isolated from neurons of rat cerebral cortex. The most homogeneous fraction purified contains only one polypeptide of Mr approx. 100 000. The enzyme relaxes supercoiled DNA in the absence of ATP or Mg2+. The optimum monovalent cation concentration for the relaxation of superhelical DNA under conditions of DNA excess is found to be 175-200 mM. The neuron enzyme is similar to other mammalian type I DNA topoisomerases in that it links to the 3' ends of the broken DNA strands. Like calf thymus DNA topoisomerase I, the neuron topoisomerase can be selectively inhibited by poly(dG) but not by other homopolymerical deoxyribonucleotides.

Association of crossover points with topoisomerase I cleavage sites: a model for nonhomologous recombination

Nonhomologous DNA recombination is frequently observed in somatic cells upon the introduction of DNA into cells or in chromosomal events involving sequences already stably carried by the genome. In this report, the DNA sequences at the crossover points for excision of SV40 from chromosomes were shown to be associated with eukaryotic topoisomerase I cleavage sites in vitro. The precise location of the cleavage sites relative to the crossover points has suggested a general model for nonhomologous recombination mediated by topoisomerase I.

DNA elements are asymmetrically joined during the site-specific recombination of kappa immunoglobulin genes

Immunoglobulin K genes are constructed during lymphocyte differentiation by the joining of two DNA elements, VK and JK, to form both a VKJK coding unit and a reciprocal recombination product. The two products formed in single VK-to-JK joining events can be directly isolated through the use of a retrovirally introduced recombination substrate. The structural analysis of a number of recombinants and the derivation of secondary recombination products define some of the basic features of the mechanism of immunoglobulin gene assembly.

Breakage of single-stranded DNA by eukaryotic type 1 topoisomerase occurs only at regions with the potential for base-pairing

Eukaryotic type 1 DNA topoisomerases break single-stranded DNA at specific sites. A preferred site for rat liver topoisomerase breakage in single-stranded phi X174 DNA was located within a region of the DNA with the potential for duplex formation. To investigate the relationship between sites of breakage in duplex and single-stranded DNA, a restriction fragment containing sequences from the transcriptional regulatory and enhancer region of the simian virus 40 genome was used as a substrate for topoisomerase. While different patterns of breakage in the native and denatured forms of the DNA were observed, some sites of breakage were common to both forms. The break sites in the denatured DNA were a subset of the break sites in the duplex DNA and were located in regions which had the potential for intrastrand base-pairing due to distal complementary sequences. A series of single-stranded fragments were generated with the distal complementary sequences deleted and these fragments were used as substrates for topoisomerase breakage. The lack of detectable breakage at a site when the complementary sequence was deleted, suggests that topoisomerase acts at duplex regions in the single-stranded DNA and that it is not active on regions of single-stranded DNA that are not base-paired.

Alternate domains of neuron DNA topoisomerase I in developing rat brain

The DNA topoisomerase found in rat brain neurons relaxes supercoiled DNA in the absence of ATP or Mg2+. The estimated content of the active enzyme per nucleus of nerve cell is constant during development from a fetal proliferating neuroblast at the embryonic stage of 18 days to the terminally differentiated neuron (postnatal age of 60 days). The salt stability of DNA topoisomerase association with chromatin varies with the stage of development of nerve cells: at 300 mM NaCl most of the enzyme activity (greater than 90% of the removed activity) elutes from differentiated neuron chromatin, whereas only approx. 25% of the enzyme activity elutes from neuroblast chromatin.

DNA strand breakage by wheat germ type 1 topoisomerase

Properties of strand breakage in duplex and single-stranded DNA by the wheat germ type 1 DNA topoisomerase were investigated. Strand breakage in duplex DNA is dependent upon the use of denaturing conditions to inactivate the enzyme and terminate the reaction, whereas breakage of single-stranded DNA occurs under the normal reaction conditions and is not dependent upon denaturation. Breakage generates a free 5' hydroxyl group and enzyme bound to the 3' side of the break, presumably via the 3' phosphate group. The location of sites of breakage with both duplex and single-stranded DNA is not random. In all these respects the wheat germ enzyme closely resembles the rat liver type 1 topoisomerase. A comparison of the locations of the sites of breakage in duplex DNA generated by the topoisomerases from wheat germ and rat liver indicates a number of common sites, although the patterns of breakage are not identical.

DNA sequence studies of simian virus 40 chromosomal excision and integration in rat cells

Cell fusion between simian CV1 cells and the simian virus 40-transformed rat cell line 14B, which contains a single copy of integrated simian virus 40 DNA, results in chromosomal excision of viral DNA. A heterogeneous population of circular molecules containing both viral and cellular DNA is detected in the replicating pool. We present the DNA sequences across six novel junctions created by these excision events and use this information to define the parental genomic sequences involved in this form of "illegitimate" recombination. The data were analyzed to discover whether any common structural feature(s) could be detected at these sites. In each case a redundancy of either two or three base-pairs was found at the precise points of cross-over in both parental DNA molecules. The cross-over points were further distinguished by the presence of at least one copy of the sequence 5'Pyr-T-T3' in either of the homologous sequences that define the cross-over points. Additional stretches of homology are found extending from the homologous cross-over points. To explore the possibility that the selection of the cross-over sites is determined by the free energy of base-pairing, we have used the program of Zuker & Stiegler (1981) to form model heteroduplexes between single-stranded parental DNA molecules. In some cases model heteroduplexes were formed that paired the cross-over points, although these structures were of dubious thermodynamic stability. We therefore conclude that, while the redundancies at the cross-over points must play some role in these processes, other factors aside from simple base-pairing across replicating structures must also be involved. In order to expand our analysis of the recombination events that accompany transformation of rat cells by simian virus 40, we determined the DNA sequences across one of the sites on the rat genome that served as the target for the integration event that engendered the 14B line. Our analysis of this DNA showed that: (1) viral and chromosomal DNA share three base-pairs of homology at the site of cross-over; (2) the cross-over site in the rat genome is adjacent to the trinucleotide 5'Pyr-T-T3'; and (3) the homology shared by the virus and chromosome does not resemble the homology reported at another integration locus, but is similar in that it is flanked on one side by alternating purine and pyrimidine nucleotides.

Poly (ADP-ribosylation) and DNA topoisomerase I in different cell lines

The modification of DNA topoisomerase I activity by poly (ADP-ribosylation) is a potentially important control mechanism for this ubiquitous enzyme which is widely believed to play a role in replication (2, 3). Our studies of the phenomenon so far suggest that DNA topoisomerase I activity may be regulated in response to the state of the DNA in the nucleus since the modification enzyme, poly (ADP-ribose) synthetase, is sensitive to interruptions in the normal double helical structure of DNA (10). Although this phenomenon has been most extensively characterized for the purified enzymes from calf thymus (5), preliminary evidence for poly (ADP-ribosylation) of topoisomerase I is presented in a nonthymic system, the mammalian cell line CHO EM9. Attempts to detect poly (ADP-ribosylation) in yeast cells have so far proven to be unsuccessful.

The mechanism of phage lambda site-specific recombination: site-specific breakage of DNA by Int topoisomerase

We demonstrate that the topoisomerase activity of bacteriophage lambda Int protein introduces single-strand breaks into duplex DNA at specific sites. Strand breakage is accompanied by the covalent linkage of Int to DNA. The linkage connects a residue in Int to the 3' phosphate of DNA at the site of breakage; the other breakage product has a 5' OH terminus. Int is the first procaryotic topoisomerase shown to break DNA in this manner. We find that in att sites, Int breaks DNA within the 15 bp homologous core. These sites of Int topoisomerase action result from the interaction of Int with "junction-type" recognition sequences (CAACTTNNT), and Int topoisomerase acts between the 7th and 8th bases of this sequence. The sites of breakage within the cores of attP and attB coincide exactly with positions where breakage and reunion occur during Int-dependent recombination. These results indicate that Int topoisomerase executes strand exchange during recombination.

Topoisomerase I from chicken erythrocytes: purification, characterization, and detection by a deoxyribonucleic acid binding assay

We have purified a deoxyribonucleic acid topoisomerase to near homogeneity from the nuclei of mature chicken erythrocytes. The enzyme relaxes supercoiled DNA in the absence of ATP or Mg2+. It is unable to resolve topologically knotted circular duplex DNA. These properties resemble those of type I eukaryotic topoisomerases capable of breaking and rejoining one strand of duplex DNA at a time. The sedimentation value of the protein is 4.4 S. The molecular weight of the reduced, denatured protein is 100K. After elution from sodium dodecyl sulfate (NaDodSO4) gels and renaturation, topoisomerase activity is found in the band at 100K and in minor bands at 95K, 78K, and 73K. The minor bands are likely to be proteolytic fragments since the Mr 100K protein is cleaved by trypsin to fragments of similar or even smaller size with retention of activity. At KCl concentrations suboptimal for the 100K form, the trypsin cleaved form is severalfold more active than the 100K form. Single-stranded DNA, but not duplex DNA or RNA, inhibits DNA relaxing activity, presumably by forming a covalent complex at the enzyme active site. Preincubation of the enzyme with single-stranded DNA leads to the depletion, in NaDodSO4-polyacrylamide gels, of protein bands corresponding to the 100K topoisomerase, its putative proteolytic fragments, and its tryptic fragments. The reaction which leads to band depletion requires active topoisomerase and conditions where single-stranded DNA inhibits relaxing activity. The band depletion technique provides a convenient assay for the polynucleotide binding activity of topoisomerases and possibly other proteins. The function of the enzyme in the inactive nuclei of mature chicken erythrocytes is unclear. The estimated content of chicken erythrocyte topoisomerase per unit DNA is comparable to that in nuclei active in replication and transcription.