HMG17 protein facilitates the DNA catenation reaction catalyzed by DNA topoisomerases

DNA-Stimulated Liquid-Liquid phase separation by eukaryotic topoisomerase ii modulates catalytic function

Type II topoisomerases modulate chromosome supercoiling, condensation, and catenation by moving one double-stranded DNA segment through a transient break in a second duplex. How DNA strands are chosen and selectively passed to yield appropriate topological outcomes - for example, decatenation vs. catenation - is poorly understood. Here, we show that at physiological enzyme concentrations, eukaryotic type IIA topoisomerases (topo IIs) readily coalesce into condensed bodies. DNA stimulates condensation and fluidizes these assemblies to impart liquid-like behavior. Condensation induces both budding yeast and human topo IIs to switch from DNA unlinking to active DNA catenation, and depends on an unstructured C-terminal region, the loss of which leads to high levels of knotting and reduced catenation. Our findings establish that local protein concentration and phase separation can regulate how topo II creates or dissolves DNA links, behaviors that can account for the varied roles of the enzyme in supporting transcription, replication, and chromosome compaction.

Mechanism of catalysis by eukaryotic DNA topoisomerase I

The elucidation of the chemistry of the topo I reaction has provided the first example of how a phosphodiester bond in DNA can be temporarily broken and the energy for reclosure stored in a covalent linkage between the end of the broken strand and the enzyme (Champoux, 1977a, 1981). This type of reaction offers several advantages to the cell. First, unnecessary exposure of DNA ends to nucleolytic attack is prevented. Second, breakage and reclosure of DNA strands can occur without an expenditure of ATP energy. Third, the combined breakage and rejoining reactions can be both spatially and temporally coordinated with other cellular activities by regulating the activity of a single protein molecule. This general mechanism has not only been extended to type II topoisomerases (see Chapters 3 and 5), but also to the specialized single-stranded phage replication proteins (e.g., phi X174 gene A protein) (Ikeda et al., 1976; Eisenberg et al., 1977) and to site-specific recombinases such as the bacteriophage lambda integrase (Craig and Nash, 1983), the delta gamma and Tn3 resolvases (Reed, 1981; Reed and Grindley, 1981; Krasnow and Cozzarelli, 1983; Hatfull and Grindley, 1986), and the yeast 2-microns circle FLP recombinase (Andrews et al., 1985; Gronostajski and Sadowski, 1985). Since the site-specific recombinases attach the broken strand to a different terminus rather than simply restoring the original phosphodiester bond as conventional topoisomerases do, they have been referred to as DNA strand transferases. It is conceivable that a similar mechanism applies to the rearrangement of immunoglobulin genes (Schatz et al., 1990) and to other specific genomic rearrangements that might occur during development (Matsuoka et al., 1991).

Characterization of Ustilago maydis DNA binding protein one (UBP1)

The DNA binding properties of a protein from the lower eukaryote Ustilago maydis have been characterized. Using both filter binding and gel retention assays, we demonstrate that this protein, termed UBP1 (Ustilago binding protein one), binds preferentially to DNA molecules lacking chain interruptions. The introduction of DNA breaks by a restriction enzyme or a purified nuclease, from Ustilago maydis, causes the dissociation of protein-DNA complexes. UBP1 stimulates the relaxation of negatively supercoiled DNA, mediated by Ustilago type I topoisomerase, through a mechanism most likely involving the association of UBP1 with the DNA rather than with the topoisomerase. The prebinding of UBP1 to DNA templates, subsequently assembled into minichromosomes, results in the development of a disorganized nucleosomal array. Possible roles for UBP1 in processes that involve changes in DNA topology, such as chromatin assembly, are discussed.

HMG 14 and protamine enhance ligation of linear DNA to form linear multimers: phosphorylation of HMG 14 at Ser 20 specifically inhibits intermolecular DNA ligation

HMG 14 and protamine can be used to enhance intermolecular ligation of low concentrations of linear DNA. Adding HMG 14 (50 moles per mole DNA) caused 50% of blunt-ended DNA to form predominantly dimers, and all cohesive-ended DNA to form multimers (greater than 6-mer) in response to T4 ligase. Protamine was maximally effective at 40:1, producing mostly dimers and trimers. Adding higher concentrations of HMG 14 did not affect the ligation pattern of cohesive-ended DNA, while higher concentrations of protamine inhibit the formation of multimers. Phosphorylation of HMG 14 at Ser 20 by Ca(++)-phospholipid dependent protein kinase abolished the ability of HMG 14 to stimulate intermolecular ligation, but did not substantially interfere with intramolecular ligation, or the binding of HMG 14 to linear or circular DNA as assessed by gel mobility. Thus Ser 20, which is located in the amino terminal DNA-binding domain of HMG 14, appears to modulate DNA-DNA interactions.

Binding of HMG 17 to mononucleosomes of the avian beta-globin gene cluster in erythroid and non-erythroid cells

The binding of HMG 17 to stripped core mononucleosomes containing DNA from the avian beta-globin gene cluster was examined to determine whether binding in vitro in this developmentally-regulated gene domain was associated with transcriptional activity or DNaseI-sensitivity in intact nuclei. Mononucleosomes were prepared from primitive and definitive stage embryonic red blood cells of chick embryos, adult reticulocytes, adult reticulocytes in which embryonic rho-globin transcription was induced, and adult thymus cells. Preferential binding by HMG 17 to mononucleosomes containing the beta-globin gene cluster was confined to erythroid-derived mononucleosomes that contain the embryonic rho-globin gene, the adult beta-globin gene, and DNA sequences located between these two genes, but not to those that contain the embryonic epsilon-globin gene. Comparison of these results to the known patterns of transcription and DNaseI-sensitivity within the beta-globin gene cluster shows that HMG 17 binding, although tissue-specific, does not correlate directly with either DNaseI-sensitivity or active gene transcription, but is dependent on other factors present in core mononucleosomes from this active gene domain.

In vitro assays used to measure the activity of topoisomerases

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Protection of doxorubicin cytotoxicity by cycloheximide

The effect of cycloheximide (an inhibitor of cellular protein synthesis) on doxorubicin-induced cytotoxicity in V79 (rodent fibroblasts) cells was investigated. Cycloheximide is a potent protector of doxorubicin-induced cytotoxicity at concentrations paralleling those required for protein synthesis inhibition. The greatest protective effect was achieved at 10 microM cycloheximide; this concentration correlated with 95% inhibition of protein synthesis. A 15 minute cycloheximide (10 microM) exposure resulted in maximal protein synthesis inhibition; however, 4-6 hr of pretreatment with cycloheximide (10 microM) was required to maximally protect cells from doxorubicin. These results suggest that a time-dependent depletion of a protein is required for cycloheximide's protective effect. Cycloheximide treatments were found to decrease intracellular accumulation of doxorubicin by 35-50% but this decrease accounts for only a small fraction of the total protective effect. When corrections were made for differences in doxorubicin accumulation, cycloheximide had no effect on the formation of DNA-protein crosslinks (DNA-topoisomerase II complexes revealed as single strand DNA breaks in alkaline elution studies). These studies suggest that cycloheximide confers protection from doxorubicin cytotoxicity by a step which occurs following the stabilization of DNA-topoisomerase II complexes.

DNA topoisomerase I from Leydig cells is modulated by luteinizing hormone and cyclic adenosine monophosphate

The action of luteinizing hormone on topoisomerase I activity from rat Leydig cells was studied. Stimulation of the enzyme was observed after long-term (24 and 48 h) gonadotrophin treatment in in vivo experiments. No change could be detected for shorter times than 12 h using two different experimental approaches. Topoisomerase I was stimulated by cAMP in a whole cell extract in a phosphorylation-dependent manner. These results suggest that topoisomerase I could be a target for nuclear events induced by peptide hormone action.

DNA topoisomerase II: a primer on the enzyme and its unique role as a multidrug target in cancer chemotherapy

Based on the weight of evidence accrued in the past eight years, there is little question that the nuclear enzyme, topoisomerase II, serves as a common intracellular target for the cytotoxic effect of drugs of widely varying structure. The enzyme appears to be unique as a chemotherapy target in that it is recruited into a lethal process under the influence of drug. Its role contrasts sharply with other more classical chemotherapy targets, such as dihydrofolate reductase, whose activity must be successfully inhibited for the expression of cytotoxicity. Resistance to inhibitors of this enzyme frequently results from marked elevations in intracellular enzyme content. In contrast, the presence of topoisomerase is required for drug effect, and, in general, the greater the cellular content of the enzyme, the more sensitive the cell will be to these agents. However, important issues remain unresolved. The biochemical events that are initiated by cleavable complex formation and result in cell death must be more fully defined. It is likely a better understanding of the drug-enzyme interaction will be required for rational drug development. Finally, those aspects of the drug-topoisomerase interaction that confer therapeutic selectivity and/or clinical resistance are of paramount importance if the phenomenon is ever to be fully exploited.

Adenovirus infection elevates levels of cellular topoisomerase I

We have developed a specific, sensitive, and quantitative assay for topoisomerase I, which is based on the formation of a covalent enzyme-DNA intermediate. Our assay measures the quantitative transfer of 32P radioactivity from 32P-labeled DNA to topoisomerase I. Since 32P-labeled topoisomerase molecules are resolved by NaDodSO4/PAGE, HeLa topoisomerase I (100 kDa) and calf thymus topoisomerase I (82 kDa) can be quantitatively assayed in the same reaction mixture. The assay can detect at least 0.3 ng (3 fmol) of topoisomerase I. We have used our assay to measure the levels of topoisomerase I activity in crude extracts of nuclei prepared from uninfected, adenovirus-infected, and adenovirus-transformed human cells. The evidence suggests that an adenovirus early gene product, presumably a protein encoded in early region 1A (E1A), increases cellular topoisomerase I activity at least 10-fold. Immunoblotting analysis with antiserum against calf thymus topoisomerase I shows that the increase in activity is due to an increase in the amount of enzyme.

Effect of concentration on the subsequent fate of plasmid DNA in human fibroblasts

The physical fate of plasmid DNA after entry into human fibroblasts was studied using Southern hybridisation and electron microscopy. Exposure of the cells (5 X 10(5) per well) to pC194 DNA-CaPi, containing 50 micrograms plasmid DNA, resulted in the occasional formation of interlocked molecules. Exposure to a co-precipitate containing 100 micrograms pC194 plasmid DNA per well resulted in an increase of interlocked molecules by a factor of 10-20 relative to the number of monomers. In addition, new classes of molecules were observed. After prolonged incubation of the cells exposed to the higher DNA concentration, the plasmid DNA was partly contained in structures with a very low electrophoretic mobility. Upon restriction endonuclease digestion of the re-extracted DNA, a pattern of bands was observed, suggesting the involvement of illegitimate recombination between non-random plasmid DNA sequences in the formation of the new classes of molecules.