An omega protein from Drosophila melanogaster

Generation of double-stranded breaks in hypernegatively supercoiled DNA by Drosophila topoisomerase IIIbeta, a type IA enzyme

Drosophila topoisomerase (topo) IIIbeta is a member of the type IA family of DNA topoisomerases, which generates a single-stranded break to form a covalent complex with the 5'-end of DNA. We show here that a purified preparation of topo IIIbeta is able to convert a hypernegatively supercoiled substrate into primarily nicked, but also linear, DNA at enzyme/DNA molar ratios of 5:1 or greater. Although the optimal temperature for the relaxation activity is between 37 and 45 degrees C, maximal cleavage occurs between 23 and 30 degrees C, a temperature range that is more physiologically relevant for fruit flies. The cleavage products require protease treatment to enter the gel, they are stable over time, they are reversible, and they are not observed with a Y332F active site mutant, which further supports the idea that topo IIIbeta possesses an endonucleolytic cleavage activity. This cleavage activity appears to be specific for highly unwound, or single strand-containing substrates. Southern blot analysis of the cleavage products demonstrates that the topo IIIbeta cleavage activity is concentrated primarily in highly A/T-rich regions. These results suggest that topo IIIbeta may function as a reversible endonuclease in vivo by recognizing and cleaving/rejoining DNA structures with single-stranded character.

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.

Isolation and characterization of a gene encoding DNA topoisomerase I in Drosophila melanogaster

We synthesized a DNA probe specific for the gene encoding eucaryotic DNA topoisomerase I by the polymerase chain reaction. The sequences of the primers for this reaction were deduced from the regions with extensive homology among the enzymes from the fission and budding yeasts, and the human. From the clones isolated by screening a Drosophila cDNA library with this DNA probe, two cDNA clones of 3.8 and 5.2 kb were characterized and completely sequenced. Both cDNA sequences contain an identical open reading frame for 972 amino acid residues. The 3.8 kb messenger RNA is likely generated by using a polyadenylation site 5' upstream to that used in generating the 5.2 kb mRNA. The predicted amino acid sequence shows that a segment of 420 amino acid residues at the amino terminus is hydrophilic, similar to the amino terminal 200 residues in the yeast and human enzymes. Furthermore, the Drosophila enzyme is unique in that the amino terminal 200 residues are enriched in serine and histidine residues; most of them are present in clusters. The rest of the Drosophila sequence is highly homologous to those from yeast and human enzymes. The evolutionarily conserved residues are identified and are likely the critical elements for the structure and function of this enzyme. A plasmid vector containing the cloned cDNA was constructed for the expression of Drosophila protein in Escherichia coli. The enzymatic and immunochemical analysis of the polypeptide produced in this heterologous expression system demonstrated that the expressed protein shares similar enzymatic properties and antigenic epitopes with DNA topoisomerase I purified from Drosophila embryos or tissue culture cells, thus establishing the bacterial expression system being useful for the future structure/function analysis of the Drosophila enzyme.

Regulation of the function of eukaryotic DNA topoisomerase I: topological conditions for inactivity

The effects of supercoiling on the cleavage reaction by eukaryotic DNA topoisomerases I (wheat germ, chicken erythrocyte, and calf thymus) have been analyzed on DNA fragments (0.96 and 2.3 kilobases) encompassing an immunoglobulin kappa light-chain promoter. In one topological condition of the substrate, the absolutely relaxed state, cleavage was found to be impeded. This finding defines the topology-dependent step of the eukaryotic DNA topoisomerase I reaction and shows that for the cleavage reaction topology is more critical than sequence effects. These findings suggest a simple model for the regulation of the DNA topoisomerase I reaction based on topological factors, which may explain the regulatory function of the enzyme in in vivo eukaryotic transcription.

Expression of yeast DNA topoisomerase I can complement a conditional-lethal DNA topoisomerase I mutation in Escherichia coli

We show that, despite differences in primary structure, substrate preference, and mechanism of catalysis, yeast DNA topoisomerase I can functionally substitute for Escherichia coli DNA topoisomerase I. A family of plasmids expressing the yeast TOP1 gene or 5'-deletion mutations of it were used to complement the temperature-sensitive phenotype of an E. coli topA mutant. These plasmids were then isolated from the cells by a rapid lysis procedure and examined for their degrees of supercoiling. Functional complementation of a conditional-lethal mutation in topA, which encodes E. coli DNA topoisomerase I, correlates with the expression of a catalytically active yeast enzyme that reduces the degree of negative supercoiling of intracellular DNA. We also show that approximately 130 amino acids of the amino-terminal portion of the yeast enzyme can be deleted without affecting its activity in vitro; activity of the enzyme inside E. coli, however, is more sensitive to such deletions.

Localization of specific topoisomerase I interactions within the transcribed region of active heat shock genes by using the inhibitor camptothecin

Camptothecin stabilizes the topoisomerase I-DNA covalent intermediate that forms during the relaxation of torsionally strained DNA. By mapping the position of the resultant DNA nicks, we analyzed the distribution of the covalent intermediates formed on heat shock genes in cultured Drosophila melanogaster cells. Topoisomerase I was found to interact with the transcriptionally active genes hsp22, hsp23, hsp26, and hsp28 after heat shock but not with the inactive genes before heat shock. The interaction occurred predominantly within the transcribed region, with specific sites occurring on both the transcribed and nontranscribed strands of the DNA. Little interaction was seen with nontranscribed flanking sequences. Camptothecin only partially inhibited transcription of the hsp28 gene during heat shock, causing a reduced level of transcripts which were nonetheless full length. Topoisomerase I also interacted with the DNA throughout the transcriptionally active hsp83 gene, including an intron, in both heat-shocked and non-heat-shocked cells. The results point to a dynamic set of interactions at the active locus.

Localization of specific topoisomerase I interactions within the transcribed region of active heat shock genes by using the inhibitor camptothecin

Camptothecin stabilizes the topoisomerase I-DNA covalent intermediate that forms during the relaxation of torsionally strained DNA. By mapping the position of the resultant DNA nicks, we analyzed the distribution of the covalent intermediates formed on heat shock genes in cultured Drosophila melanogaster cells. Topoisomerase I was found to interact with the transcriptionally active genes hsp22, hsp23, hsp26, and hsp28 after heat shock but not with the inactive genes before heat shock. The interaction occurred predominantly within the transcribed region, with specific sites occurring on both the transcribed and nontranscribed strands of the DNA. Little interaction was seen with nontranscribed flanking sequences. Camptothecin only partially inhibited transcription of the hsp28 gene during heat shock, causing a reduced level of transcripts which were nonetheless full length. Topoisomerase I also interacted with the DNA throughout the transcriptionally active hsp83 gene, including an intron, in both heat-shocked and non-heat-shocked cells. The results point to a dynamic set of interactions at the active locus.

Complete nucleotide sequence of the topA gene encoding Escherichia coli DNA topoisomerase I

The nucleotide sequence of a 4071 base-pair long segment containing the gene topA encoding Escherichia coli DNA topoisomerase I and its flanking regions has been determined. The gene encodes a total of 864 amino acids from the ATG start to a TAA termination codon, of which the first f-Met appears to be removed after translation; the calculated molecular weight of the translated protein is 97,413. Mapping of promoters by deletion of sequences upstream from the ATG initiation codon indicates the existence of at least two promoters that direct transcription into topA.

Topoisomerase-II activity in human leukemic and lymphoblastoid cells

Topoisomerase-II activity was analyzed in various human leukemic and lymphoblastoid cell-lines with comparison to normal human peripheral blood lymphocytes. All of the examined tumor cells contained this enzyme in both the nuclear and cytoplasmic fractions, whereas no appreciable activity of the enzyme was detected in either fraction of the resting normal lymphocytes. Using pBR322 plasmid as a substrate, undialyzed extracts of the tumor cells exhibited the typical ATP-dependent relaxation of supercoiled circles and formation of linear and catenated structures, as well as the ATP-independent knotting activity. On the other hand, dialyzed extracts exerted only the ATP-dependent supercoil relaxation. Novobiocin inhibited the linearization and catenation but not the supercoil relaxing or knotting activities. This study provides indications for an excessive level of a structurally abnormal topoisomerase-II in these tumor cell-lines.

DNA topoisomerase I and II activities during cell proliferation and the cell cycle in cultured mouse embryo fibroblast (C3H 10T1/2) cells

We have used C3H 10T1/2 cells to examine the regulation of topoisomerase activities during cell proliferation and the cell cycle. The specific activity of topoisomerase I was about 4-fold greater in proliferating (log phase) cells than in non-proliferating (confluent) cells. In synchronized cells, the bulk of the increased activity occurred during or just prior to S phase, depending upon the method of synchronization. A smaller increase in activity also occurred during G1 phase. The increase in activity during S phase was not altered by a hydroxyurea block at the G1/S phase boundary indicating that it is not directly coupled to DNA synthesis and is not the result of topoisomerase I gene dosage. The increase was inhibited by blocking cells at mid-G1 phase using isoleucine deprivation. Thus, the increase in activity during S phase is dependent on events occurring during mid- to late G1 phase. In contrast to the changes in topoisomerase I levels, the specific activity of topoisomerase II showed no detectable difference in proliferating vs non-proliferating cells. In addition, no detectable difference in topoisomerase II specific activity was seen in G1, S and M phases of the cell cycle. The differences in the activity profiles of the topoisomerases I and II during the cell cycle suggest that the two activities are regulated independently and may be required for different functions.

Chromatin assembly in Xenopus oocytes: in vitro studies

We describe and characterize a complex reaction that catalyzes DNA supercoiling and chromatin assembly in vitro. A Xenopus oocyte extract supplemented with ATP and Mg++ converts DNA circles into minichromosomes that display a native, 200 bp periodicity. When supercoiled DNA is added to this extract it undergoes a time-dependent series of topological changes, which precisely mimic those found when the DNA is microinjected into oocytes. As judged by the conformation of the subsequently deproteinized DNA, the supercoiled DNA is first relaxed, in a reaction that takes 4 min, and then it is resupercoiled in a slower process that takes 4 hr. The relaxation is partially inhibited by EDTA, to an extent that suggests that that it is catalyzed by a type I DNA topoisomerase. The resupercoiling , on the other hand, requires ATP and Mg++, is completely inhibited by EDTA, and is inhibited by novobiocin in a manner that suggests it is catalyzed by a type II DNA topoisomerase. These findings, and the ones reported in the preceding paper ( Ryoji and Worcel , 1984), lead us to propose that chromatin assembly is an active, ATP-driven process.

Epidermal growth factor-induced topoisomerase(s). Intracellular translocation and relation to DNA synthesis

We have used epidermal growth factor (EGF) to investigate the relationship between eukaryotic topoisomerases and DNA synthesis. We found that EGF stimulates topoisomerase activity in human fibroblasts and Swiss/3T3 mouse fibroblasts. The first increase is seen in the cytoplasm, followed by increased activity in the nucleus. The nuclear increases correspond to increases in DNA synthesis. A type II topoisomerase is stimulated as indicated by the ATP dependence of the relaxing reaction and by the formation of catenanes. We have also found that the topoisomerase activity in the cytoplasm is sedimentable indicating that it is either membrane-associated or in a supramolecular complex. The stimulation of topoisomerase activity by EGF may represent a key step in the process by which EGF induces DNA synthesis and cell division.

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.

Drosophila topoisomerase I: isolation, purification and characterization

We have purified and characterized topoisomerase I from Drosophila melanogaster. The molecular weight of the enzyme is 135,000; 100,000, 90,000, and 65,000 molecular weight products result from degradation of the enzyme. The enzyme relaxes both positive and negative supercoiled DNA. Mg++ is not absolutely required, but stimulates the enzymatic activity considerably.

Type I DNA topoisomerases from mammalian cell nuclei interlock strains and promote renaturation of denatured closed circular PM2 DNA

Type I DNA topoisomerases from mouse ascites cell nuclei and from rat liver cell nuclei act on denatured viral closed circular PM2 DNA to produce molecules with a highly contracted structure as well as fully duplex non-supercoiled covalently closed circular molecules. Highly contracted DNA molecules contain a novel type of topological linkage in which a strand in one region of the double-stranded molecule passes between the strands in another region of the circular molecule one or more times. Since it is also found that the action of the topoisomerase promotes renaturation of complementary strands in denatured closed circular DNA, it is suggested that formation of contracted DNA structures proceeds through renatured, duplex intermediates with highly negative superhelix densities that contain small single-stranded regions.

Ribonucleic acid and other polyanions facilitate chromatin assembly in vitro

Crude extracts of Drosophila embryos are a rich source of both DNA topoisomerase I and chromatin assembly activity [Nelson, T., Hsieh, T., & Brutlag, D.L. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 5510-5514; Hseih, T., & Brutlag, D. L. (1980) Cell (Cambridge, Mass.) 21, 115-125]. Purified topoisomerase I from Drosophila embryos, however, is not sufficient for chromatin assembly. Rather, the ability of Drosophila embryo extracts to mediate chromatin assembly in vitro requires an anionic fraction which we demonstrate to be RNA. Exogenous natural and homopolymer RNAs, if of sufficient length, can also mediate chromatin assembly in vitro. The RNA acts stoichiometrically in assembly, being required in amounts at least equal in weight to the amount of histones present. Natural and homopolymer DNAs, whether single or double stranded, are inactive under the same conditions. The arginine-rich histones H3 and H4 or histone H4 alone is sufficient to produce nucleoprotein complexes with physiological numbers of supertwists in the DNA. Complexes containing these subsets of the core histones also resemble assembled complexes containing all four core histones with respect to some patterns of nuclease sensitivity, although complexes containing all four core histones more closely resemble native chromatin in nuclease digestions.

The androgenic regulation of superhelical-DNA nicking-closing enzyme in rat ventral prostate

The activity of superhelical-DNA nicking-closing enzyme (NC enzyme) was measured in nuclei from rat ventral prostate by a fluorimetric assay based on the binding of ethidium bromide to supercoiled phage-PM2 DNA. The nuclear concentration of NC-enzyme activity declined rapidly after castration, although this response could be prevented by daily administration of dihydrotestosterone. The low NC-enzyme activity in involuted prostates (10% of normal) was restored to normal after 8-10 days of treatment with androgen. In the regenerating prostate the time course of restoration of NC-enzyme activity was not in phase with that of DNA synthesis. Examination of nucleosome repeat lengths and the arrangement of nucleosomes along the chromatin fibre revealed no differences in the structural organization of chromatin in prostates with high or low NC-enzyme activity. Together, these results suggest that the major role of NC enzyme is related to the onset and maintenance of differentiation in the prostate and that the activity of this enzyme is not expressed through gross alterations in chromatin structure.

ATP-dependent DNA topoisonmerase from D. melanogaster reversibly catenates duplex DNA rings

Extracts of Drosophila embryos contain an enzymatic activity that converts circular DNAs into huge networks of catenated rings in an ATP-dependent fashion. The catenated activity is resolved into two protein components during purification. One component is a novel DNA topoisomerase that requires the presence of ATP in order to relax supercoiled DNA. We have shown that the ATP-dependent DNA topoisomerase relaxes DNA by a mechanism distinct from that of nicking-closing enzymes. The Drosophila ATP-dependent topoisomerase allows one segment of a circular DNA to pass through transient breaks in both strands at another site on the DNA circle without any relative rotation between the ends at the transient break. This mechanism can convert negative supertwists to positive twists and vice versa until a relaxed equilibrium state is reached. The formation of catenated rings is mediated by an analogous bimolecular reaction which can occur between two nonhomologous DNA circles. The catenation reaction is fully reversible: in the presence of the second protein component, circular DNA is converted quantitatively into catenated forms; in its absence, the ATP-dependent topoisomerase resolves catenated networks back into monomer circles. The Drosophila ATP-dependent topoisomerase appears to be closely related to E. coli DNA gyrase in that both use a similar mechanism to change the topology of DNA, both require ATP and both are inhibited by the antibiotic novobiocin. The presence of an enzyme that allows one DNA helix to pass freely through another could not only be useful in relaxation of topological constraints, but also may be involved in the folding and unfolding of eucaryotic chromosomes.

Postreplication repair in mammalian cells after ultraviolet irradiation: a model

A model is presented for bypass of ultraviolet-induced damage in DNA during replication. The overall process is initiated by the introduction of a single-strand break into parental DNA near the point of arrest of synthesis, followed by a transient crossing-over step similar to that envisaged in genetic recombination. The mechanism proposed provides an alternative explanation to existing models and is entirely consistent with available data on postreplication repair in mammalian cells. In addition the model explains the low level of recombination repair observed in mammalian cells.

Biochemical analysis of genetic recombination in eukaryotes

Recent studies concerning molecular mechanisms of genetic recombination in eukaryotes are reviewed. Since many of these studies have focused on the testable predictions arising from the hybrid DNA theory of genetic recombination, this theory is summarised. Experiments to determine the time of meiotic crossing-over and the structure of the synaptonemal complex which facilitates meiotic crossing-over are described. Investigations of DNA nicking and repair events implicated in recombination are discussed. Properties of proteins which may facilitate hybrid DNA formation, and biochemical evidence for hybrid DNA formation are presented. Finally, a nuclease which has been implicated in gene conversion is described.

DNA swivel enzyme activity in a nuclear membrane fraction

DNA swivel (nicking-rejoining) enzyme activity has been studied in various cell fractions of a human lymphoid cell line. Swivel activity is found only in chromatin and in a nuclear membrane fraction containing DNA and possessing endogenous DNA synthesizing activity. Twenty percent of the total swivel activity and less than one percent of the total DNA are in the membrane fraction. The swivel enzyme is more tightly bound to the membrane fraction than to the chromatin fraction. These observations suggest that the swivel enzyme may be a replication factor, specifically bound to replicating DNA in the membrane fraction.

A model for chromatin based upon two symmetrically paired half-nucleosomes

We propose that the basic unit of chromatin is constructed of two isologously paired heterotypic protein tetramers each containing one molecule of H2A, H2B, H3, and H4 histone. These proteins form a core that holds 140 base pairs (bp) of DNA in a single left-handed, non-interwound DNA super-coil approximately 95 bp in circumference, creating a nucleosome particle (DNA and protein) organized about a dyad axis of symmetry. Such a nucleosome can open up into its separate half-nucleosomes to allow genetic readout without requiring histone displacement.

Evidence for an intermediate with a single-strand break in the reaction catalyzed by the DNA untwisting enzyme

The DNA untwisting enzyme relaxes covalently closed circylar DNAs by the sequential breaking (nicking) and closure of one strand of the duplex. The use of highly purified enzyme from rat liver nuclei at very high protein concentrations has permitted the detection of the nicked intermediate in the reaction. The nicking of closed circular simian virus 40 DNA was measured by alkaline sucrose gradient sedimentation or by equilibrium centrifugation in CsCl gradients containing propidium diiodide. The following observations support the hypothesis that the nicked DNA represents an intermediate in the untwisting reaction. The extent of nicking does not increase with time. Nicking is observed in the range of salt concentrations where the enzyme is active (0.01-0.25 M KCl), but is not observed at 0.50 Mkdl, where enzyme activity is undetectable. The nicked DNA that is generated during the reaction carried out in low salt rapidly disappears if the KCl concentration is raised to 0.50 M. At constant enzyme concentration, the number of nicks in the reaction mixture is independent of DNA concentration in the range from 3 to 14 mug/ml. The addition of an excess of unlabeled DNA to a reaction initially containing labeled nicked DNA partially chases the label from the nicked intermediate into covalently closed circular DNA.

Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers

Highly purified nicking-closing enzyme from mouse cells in 20-fold enzyme/substrate excess converts closed circular native PM2, ColE1, and Minicol DNA into limit product sets of DNAs. Each set has a mean degree of supercoiling of approximately zero. The individual species in the sets differ by deltatau = +/-1, +/-2, etc., and the relative masses fit a Boltzmann distribution. It was also demonstrated that "nonsupercoiled" closed circular duplex molecules serve as substrates for the nicking-closing enzyme, and that a distribution of topological isomers is generated. Polynucleotide ligase, acting on nicked circular DNA, forms under the same conditions, the same set of closed DNAs. The latter enzyme freezes the population into sets of molecules otherwise in configurational equilibrium in solution.

Isolation and partial characterisation of the relaxation protein from nuclei of cultured mouse and human cells

A protein, called relaxation protein because of its ability to remove superhelical turns in closed-circular DNA, has been isolated and partially characterized from the nuclei of LA9 mouse and HeLa cells. The purification was facilitated by an assay method, with PM2 DNA, which used the fluorescence enhancement of the intercalating dye ethidium bromide upon binding to the closed-circular DNA. The amount of dye bound depends upon the degree of the superhelix density of the DNA. The relaxation products were analysed by the buoyant separation method in CsCl containing ethidium bromide and were shown to be completely relaxed. The purification resulted in a single band in a dodecylsulfate gel electrophoresis with an apparent molecular weight of 37000. The pH optimum is 7.0 and the optimal salt concentration is 0.2 M NaCl. The relaxation protein removes negative as well as positive supercoils, the latter generated by the interaction of ethidium bromide with closed-circular DNA. Relaxation of positive supercoils results, after removal of the dye, in the formation of molecules with superhelix densities exceeding that of native PM2 DNA (0.054). The highest negative superhelix density observed was -0.098 +/- 0.001. The corresponding positive superhelix density has been calculated to be + 0.023. A nicking--swivelling--closing mechanism is postulated, but nicked intermediates have so far not been demonstrated. The relaxation protein is not inhibited by known mammalian endonuclease I inhibitors, except for denatured DNA, and does not possess a conventional polynucleotide ligase activity. The relaxation activity was found to be predominantly in the nuclei, with only small amounts present in the cytoplasm and mitochondria. The biological function of transient swivels induced by the relaxation protein is not known. However, transient swivels are considered necessary or useful in the replication of closed-circular DNA or long linear DNA, respectively. Relaxation protein could replace the combined action of an endonuclease and a ligase ahead of the replication fork. Alternatively, transient swivels could be involved in the transcription process.