DNA topoisomerases

Regulation of RNA polymerase I transcription in yeast and vertebrates

This article focuses on what is currently known about the regulation of transcription by RNA polymerase I (pol I) in eukaryotic organisms at opposite ends of the evolutionary spectrum--a yeast, Saccharomyces cerevisiae, and vertebrates, including mice, frogs, and man. Contemporary studies that have defined the DNA sequence elements are described, as well as the majority of the basal transcription factors essential for pol I transcription. Situations in which pol I transcription is known to be regulated are reviewed and possible regulatory mechanisms are critically discussed. Some aspects of basal pol I transcription machinery appear to have been conserved from fungi to vertebrates, but other aspects have evolved, perhaps to meet the needs of a metazoan organism. Different parts of the pol I transcription machinery are regulatory targets depending on different physiological stimuli. This suggests that multiple signaling pathways may also be involved. The involvement of ribosomal genes and their transcripts in events such as mitosis, cancer, and aging is discussed.

Effects of nucleosomes and anti-tumor drugs on the catalytic activity of type II DNA topoisomerase from rat testis

To gain insight into the relative catalytic efficiencies of mammalian type I and type II DNA topoisomerases, in the cellular context, we have used naked DNA and DNA incorporated into nucleosomes as substrates. We observed that the relaxation activity of both the enzymes declined with DNA containing increasing densities of nucleosomes; however, kinetic analysis revealed that topoisomerase I seemed less affected than topoisomerase II. The addition of histone H1, in stoichiometric amounts, to naked DNA or minichromosomes lessened the activity of topoisomerase II, and required 7-fold less for complete inhibition when the latter was used as the substrate. To ascertain if the observed differences are specific to topoisomerase II from testis, we examined the effect of nucleosomes on the catalytic efficiency of its isoform from liver. Interestingly, the suppression of relaxation activity of liver topoisomerase II required substrates containing higher mass ratios of histone octamer/DNA. Studies on the effect of nucleosomes on the action of teniposide displayed significant differences in the kinetics of the reaction, in its IC50 values, and have provided biochemical evidence for the first time that nucleosomes increased inhibition caused by teniposide. Further, this feature appears to be specific for topoisomerase II-directed drugs and is not shared by the generic class of either DNA-intercalating or non-DNA-intercalating ligands.

Purification and functional characterization of type II DNA topoisomerase from rat testis and comparison with topoisomerase II from liver

A number of studies in yeast have shown that DNA topoisomerase II is essential for chromosome condensation and disjunction during mitosis at the metaphase/anaphase transition and meiosis I. Accordingly, kinetic and mechanistic studies have implied a role for topoisomerase II in chromosome disjunction. As a step toward understanding the nature and role of topoisomerase II in a mammalian germline in vivo, we have purified topoisomerase II from rat testis to homogeneity and ascertained several of its catalytic activities in conjunction with that of the purified enzyme from liver. The purified enzymes appeared to be monomers under denaturing conditions; however, they differed in their relative molecular mass. Topoisomerase II from testis and liver have apparent molecular masses of 150 +/- 10 kDa and 160 +/- 10 kDa, respectively. The native molecular mass of testis topoisomerase II as assayed by immunoblot analysis of cell-free extracts, prepared in the presence of SDS and a number of protease inhibitors, corroborated with the size of the purified enzyme. Both enzymes are able to promote decatenation and relax supercoiled DNA substrates in an ATP and Mg(2+)-dependent manner. However, quantitative comparison of catalytic properties of topoisomerase II from testis with that of the enzyme from liver displayed significant differences in their efficiencies. Optimal pH values for testis enzyme are 6.5 to 8.5 while they are 6 to 7.5 for the liver enzyme. Intriguingly, the relaxation activity of liver topoisomerase II was inhibited by potassium glutamate at 1 M, whereas testis enzyme required about half its concentration. These findings argue that topoisomerase II from rat testis is structurally distinct from that of its somatic form and the functional differences between the two enzymes parallels with the physiological environment that is unique to these two tissues.

Casein kinase II stimulates Xenopus laevis DNA topoisomerase I by physical association

A Xenopus laevis casein kinase II-like activity copurified with X. laevis DNA topoisomerase I activity during chromatography on DEAE-cellulose, phosphocellulose, and hydroxylapatite, but the two activities were resolved by chromatography on DNA-agarose [Kaiserman, H. B., Ingebritsen, T. S., & Benbow, R. M. (1988) Biochemistry 27, 3216-3222]. Phosphorylation of the catalytic polypeptides of dephosphorylated X. laevis DNA topoisomerase I by the endogenous X. laevis casein kinase II-like activity apparently resulted in a severalfold increase in catalytic activity. In this study, we show that incubation of purified X. laevis DNA topoisomerase I with electrophoretically homogeneous bovine brain casein kinase II and ATP strongly stimulated catalytic activity. Surprisingly, purified bovine casein kinase II stimulated X. laevis DNA topoisomerase I activity by more than an order of magnitude in the absence of ATP, although ATP resulted in additional stimulation. Other basic proteins, such as histone H1 and HMG proteins, also stimulated X. laevis DNA topoisomerase I catalytic activity 2-3-fold in the absence of ATP. Modulation of catalytic activity by direct physical association (protein-protein interactions) must, therefore, be considered in addition to phosphorylation in assessing the physiological role of casein kinase II and other basic proteins during regulation of X. laevis DNA topoisomerase I activity in vivo.

Structure and function of type II DNA topoisomerases

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Phosphorylation of DNA topoisomerase I is increased during the response of mammalian cells to mitogenic stimuli

DNA topoisomerase I is phosphorylated after mitogenic stimulation of 3T3-L1 mouse fibroblasts by 12-O-tetradecanoylphorbol 13-acetate (TPA), a phorbol ester tumor promoter. In vivo labeling with [32P]orthophosphate and immunoprecipitation with an anti-DNA topoisomerase I antibody has demonstrated an increase in the phosphorylation of DNA topoisomerase I in Swiss/3T3 mouse fibroblasts treated with epidermal growth factor (EGF) and H35 rat hepatoma cells treated with insulin. The only phosphorylated form of DNA topoisomerase I observed was the 100-kDa protein Digestion of DNA topoisomerase I with trypsin revealed two phosphopeptides. In addition, VT-1, a non-responsive genetic variant of 3T3-L1, and the DNA topoisomerase I inhibitor camptothecin were used to further study TPA-induced DNA topoisomerase I phosphorylation. Our results indicate that the phosphorylation of DNA topoisomerase I may be an ubiquitous response of cultured mammalian cells to mitogenic agents, even in the absence of DNA replication.

The predominant form of mammalian DNA topoisomerase I in vivo has a molecular mass of 100 kDa

DNA topoisomerase I was purified to apparent homogeneity from human HeLa cells as a single polypeptide with a molecular mass of 100 kDa, as assayed by both gel filtration column chromatography and SDS-polyacrylamide gel electrophoresis. No smaller forms of the enzyme were detected in the purified fraction. Therefore, smaller forms, which have been observed by other investigators, are likely to be the result of proteolysis during isolation and are not relevant to the in vivo activity of DNA topoisomerase I.

The localization of topoisomerase II cleavage sites on DNA in the presence of antitumor drugs

Type II topoisomerase are enzymes that break and religate DNA phosphodiester bonds while crossing over DNA strands and altering DNA topology. They also are structural proteins that play a role in the spatial organization of chromatin and are involved in several crucial biological functions, such as DNA replication and transcription, chromosome segregation and recombination. Many drugs interfere with type II topoisomerases and can be assigned to two groups. Coumarin derivatives and synthetic quinolones act at the level of ATP binding or hydrolysis and are used for controlling bacterial infections. Drugs belonging to the second group produce DNA lesions by trapping a "cleavable complex" consisting of the normal transient topoisomerase II-DNA reaction intermediate in which the enzyme and the DNA are joined by two covalent bonds. There are four main categories of antitumour drugs that form cleavable complexes in eukaryotes: acridines, anthracyclines, ellipticines and epipodophyllotoxins. These drugs are cytotoxic and many--but not all--are endowed with antitumoral properties. The mechanisms of this pharmacological activity are not understood. Topoisomerase II-induced DNA breaks generated from cleavable complexes display different levels of cytotoxicity depending on their localization on DNA. The primary structure of DNA is not the only parameter that determines this localization. The spatial organization of the enzyme-DNA complex and both the topology and the structure of the underlying chromatin fiber constitute additional critical factors. It, therefore, may be unrealistic to expect that the actual pharmacological potency of antitumor drugs that act on type II topoisomerases can be accurately predicted solely on the basis of simple in vitro test tube experiments carried out using pure enzymes and naked DNA.

Scaffold-associated regions: cis-acting determinants of chromatin structural loops and functional domains

It has been proposed that scaffold-associated regions are DNA elements that form the bases of chromatin loops in eukaryotic cells. Recent evidence supports a role for these elements as cis-acting 'handlers' of both structural and functional chromatin domains.

Chromatin condensation: does histone H1 dephosphorylation play a role?

In this article we describe three distinct biological systems where histone H1 phosphorylation is uncoupled from mitosis and highly condensed chromatin is enriched in dephosphorylated forms of H1: the amitotic macronucleus of Tetrahymena, terminally differentiated avian erythrocytes and sea urchin sperm. Each system offers informative contrasts to the idea that H1 hyperphosphorylation is causally related to mitotic chromosome condensation. Assuming that higher order chromatin folding is primarily driven by electrostatic interactions between H1 and DNA, an alternative model is presented for the role of H1 phosphorylation in chromatin condensation.

Posttreatment exposure to camptothecin enhances the lethal effects of x-rays on radioresistant human malignant melanoma cells

Little is known about the molecular mechanisms responsible for the survival recovery process(es) (known as potentially lethal damage repair), which occurs in mammalian cells following ionizing radiation. Previously, we presented data indicating a role for the DNA unwinding enzyme, topoisomerase I, in DNA repair. We now demonstrate that camptothecin, a specific inhibitor of topoisomerase I, causes dramatic radiosensitization of an extremely resistant human melanoma (U1-Mel) cell line. Camptothecin radiosensitized U1-Mel cells when it was administered either during or immediately following x-irradiation. U1-Mel cells were optimally radiosensitized with 4 microM camptothecin for a period of 4-6 hrs after x-irradiation. Enhanced cell killing by camptothecin was proportional to the initial extent of damage created by x-irradiation; the higher the dose of ionizing radiation, the greater the radiosensitization. The apparent synergy observed with camptothecin and x-rays was irreversible; camptothecin-treated U1-Mel cells were not able to carry out PLDR in a 48 hr period after the drug was removed. We hypothesize that the administration of camptothecin causes lesion modification through a topoisomerase I-mediated mechanism. These data support a role for topoisomerase I in DNA repair and indicate that camptothecin, or more effective derivatives, may have clinical use.

Chromosome assembly in vitro: topoisomerase II is required for condensation

The role of topoisomerase II (topo II) in chromosome condensation was studied in a mitotic extract derived from Xenopus eggs by specific immunodepletion. HeLa nuclei, which have a high complement of endogenous topo II, are converted to mitotic chromosomes in the topo II-depleted extract equally well as in the control. Chicken erythrocyte nuclei, however, which have a very low content of topo II, do not convert to condensed chromosomes in the depleted extract, although their condensation is normal upon addition of purified topo II. Dosage experiments support the possible notion of a structural involvement of topo II in chromosome condensation. In the topo II-depleted extract the erythrocyte nuclei progress to precondensation chromosomes, which lack the nuclear membrane-lamina complex and consist of a cluster of swollen chromatids.

Developmental regulation of Drosophila DNA topoisomerase II

Affinity-purified polyclonal antibodies were used to quantitate steady-state levels of DNA topoisomerase II (topo II) throughout Drosophila development. Although wide fluctuations were recorded at different stages, these fluctuations were paralleled by changes in levels of the nuclear lamin, a nuclear structural protein used as an internal standard. The exception to this was adult males where lamin levels were significantly elevated relative to topo II. Northern blot analyses of topo II and lamin mRNA, performed in conjunction with immunoblot analyses of protein revealed fluctuations in levels of the two different messages that paralleled changes in each other and in their respective translation products. Biochemical and immunochemical analyses were complemented by indirect immunofluorescence and immunoperoxidase experiments performed in situ. topo II was found distributed throughout nuclei in most but not all cell types examined. These results for Drosophila topo II are apparently at odds with those obtained by others working in vertebrate systems (see, for example, Heck, M. M. S. and W. C. Earnshaw. 1986. J. Cell Biol. 103:2569-2581; Heck, M. M. S., W. N. Hittelman, and W. C. Earnshaw. 1988. Proc. Natl. Acad. Sci. USA. 85:1086-1090) and suggest that in Drosophila, topo II may not be a useful marker for the proliferative state.

Paranemic structures of DNA and their role in DNA unwinding

A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.