DNA supercoiling and relaxation by ATP-dependent DNA topoisomerases

1992 ◽  
Vol 336 (1276) ◽  
pp. 83-91 ◽  
Keyword(s):  
Topoisomerase Ii ◽  
Atp Hydrolysis ◽  
Energy Coupling ◽  
Dna Supercoiling ◽  
Dna Topoisomerases ◽  
Functional Conservation ◽  
Negative Supercoiling ◽  
Topo Ii ◽  
Type Ii Dna Topoisomerases

Bacterial DNA gyrase and the eukaryotic type II DNA topoisomerases are ATPases that catalyse the introduction or removal of DNA supercoils and the formation and resolution of DNA knots and catenanes. Gyrase is unique in using ATP to drive the energetically unfavourable negative supercoiling of DNA, an example of mechanochemical coupling: in contrast, eukaryotic topoisomerase II relaxes DNA in an ATP-requiring reaction. In each case, the enzyme-DNA complex acts as a ‘gate’ mediating the passage of a DNA segment through a transient enzyme-bridged double-strand DNA break. We are using a variety of genetic and enzymic approaches to probe the nature of these complexes and their mechanism of action. Recent studies will be described focusing on the role of DNA wrapping on the A 2 B 2 gyrase complex, subunit activities uncovered by using ATP analogues and the coumarin and quinolone inhibitors, and the identification and functions of discrete subunit domains. Homology between gyrase subunits and the A 2 homodimer of eukaryotic topo II suggests functional conservation between these proteins. The role of ATP hydrolysis by these topoisomerases will be discussed in regard to other energy coupling systems.

Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases

2005 ◽  
Vol 33 (6) ◽  
pp. 1460-1464 ◽  
Author(s):  
A. Maxwell ◽  
L. Costenaro ◽  
S. Mitelheiser ◽  
A.D. Bates
Keyword(s):  
Atp Hydrolysis ◽  
Dna Gyrase ◽  
Energy Coupling ◽  
Dna Topoisomerases ◽  
Structural Work ◽  
Structural Details ◽  
Negative Supercoiling ◽  
Topo Ii ◽  
Dna Strand ◽  
Strand Passage

Type IIA topos (topoisomerases) catalyse topological conversions of DNA through the passage of one double strand through a transient break in another. In the case of the archetypal enzyme, DNA gyrase, it has always been apparent that the enzyme couples the free energy of ATP hydrolysis to the introduction of negative supercoiling, and the structural details of this process are now becoming clearer. The homologous type IIA enzymes such as topo IV and eukaryotic topo II also require ATP and it has more recently been shown that the energy of hydrolysis is coupled to a reduction of supercoiling or catenation (linking) beyond equilibrium. The mechanism behind this effect is less clear. We review the energy coupling process in both classes of enzyme and describe recent mechanistic and structural work on gyrase that addresses the mechanism of energy coupling.

The role of ATP in the reactions of type II DNA topoisomerases

2010 ◽  
Vol 38 (2) ◽  
pp. 438-442 ◽  
Author(s):  
Andrew D. Bates ◽  
Anthony Maxwell
Keyword(s):  
Atp Hydrolysis ◽  
Dna Gyrase ◽  
Dna Topology ◽  
Type Ii ◽  
Free Energies ◽  
Dna Topoisomerases ◽  
Type Ii Dna Topoisomerases ◽  
Topology Simplification ◽  
Hydrolysis Of

Type II DNA topoisomerases catalyse changes in DNA topology in reactions coupled to the hydrolysis of ATP. In the case of DNA gyrase, which can introduce supercoils into DNA, the requirement for free energy is clear. However, the non-supercoiling type II enzymes carry out reactions that are apparently energetically favourable, so their requirement for ATP hydrolysis is not so obvious. It has been shown that many of these enzymes (the type IIA family) can simplify the topology of their DNA substrates to a level beyond that expected at equilibrium. Although this seems to explain their usage of ATP, we show that the free energies involved in topology simplification are very small (<0.2% of that available from ATP) and we argue that topology simplification may simply be an evolutionary relic.

Ultrastructural localization of DNA topoisomerase II in oral squamous cell carcinoma utilizing immunogold EM

1992 ◽  
Vol 50 (1) ◽  
pp. 644-645
Author(s):  
M D'Andrea ◽  
P Farber ◽  
D Foglesong
Keyword(s):  
Topoisomerase I ◽  
Topoisomerase Ii ◽  
Essential Role ◽  
Ultrastructural Localization ◽  
Dna Topoisomerase Ii ◽  
Dna Topoisomerase ◽  
Dna Topoisomerases ◽  
Dividing Cells ◽  
Topo Ii

DNA topoisomerases are enzymes which insert transient breaks into duplex DNA and are important in DNA replication, transcription and recombination. There are two forms of the enzyme, Topoisomerase I which breaks and rejoins only one of the two strands of DNA and Topoisomerase II (Topo II) which breaks and rejoins both of the DNA duplex strands. The essential role of Topo II in cell proliferation is reflected in its abundance in dividing cells, including normal and neoplastic cells.

scholarly journals Plasmid DNA Supercoiling and Survival in Long-Term Cultures of Escherichia coli: Role of NaCl

2003 ◽  
Vol 185 (17) ◽  
pp. 5324-5327 ◽  
Author(s):  
Annie Conter
Keyword(s):  
Escherichia Coli ◽  
Dna Supercoiling ◽  
Luria Bertani ◽  
Plasmid Pbr322 ◽  
E Coli ◽  
Topological State ◽  
Negative Supercoiling ◽  
The Relationship

ABSTRACT The relationship between the survival of Escherichia coli during long-term starvation in rich medium and the supercoiling of a reporter plasmid (pBR322) has been studied. In aerated continuously shaken cultures, E. coli lost the ability to form colonies earlier in rich NaCl-free Luria-Bertani medium than in NaCl-containing medium, and the negative supercoiling of plasmid pBR322 declined more rapidly in the absence of NaCl. Addition of NaCl at the 24th hour restored both viability and negative supercoiling in proportion to the concentration of added NaCl. Addition of ofloxacin, a quinolone inhibitor of gyrase, abolished rescue by added NaCl in proportion to the ofloxacin added. This observation raises the possibility that cells had the ability to recover plasmid supercoiling even if nutrients were not available and could survive during long-term starvation in a manner linked, at least in part, to the topological state of DNA and gyrase activity.

scholarly journals Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA

2019 ◽  
Vol 47 (13) ◽  
pp. 6946-6955 ◽  
Author(s):  
Antonio Valdés ◽  
Lucia Coronel ◽  
Belén Martínez-García ◽  
Joana Segura ◽  
Sílvia Dyson ◽  
...  
Keyword(s):  
Dna Replication ◽  
Crucial Role ◽  
Topoisomerase Ii ◽  
Chromatin Condensation ◽  
Chromatin Dynamics ◽  
Eukaryotic Chromatin ◽  
Topo Ii ◽  
Inversion Mechanism

AbstractRecent studies have revealed that the DNA cross-inversion mechanism of topoisomerase II (topo II) not only removes DNA supercoils and DNA replication intertwines, but also produces small amounts of DNA knots within the clusters of nucleosomes that conform to eukaryotic chromatin. Here, we examine how transcriptional supercoiling of intracellular DNA affects the occurrence of these knots. We show that although (−) supercoiling does not change the basal DNA knotting probability, (+) supercoiling of DNA generated in front of the transcribing complexes increases DNA knot formation over 25-fold. The increase of topo II-mediated DNA knotting occurs both upon accumulation of (+) supercoiling in topoisomerase-deficient cells and during normal transcriptional supercoiling of DNA in TOP1 TOP2 cells. We also show that the high knotting probability (Pkn ≥ 0.5) of (+) supercoiled DNA reflects a 5-fold volume compaction of the nucleosomal fibers in vivo. Our findings indicate that topo II-mediated DNA knotting could be inherent to transcriptional supercoiling of DNA and other chromatin condensation processes and establish, therefore, a new crucial role of topoisomerase II in resetting the knotting–unknotting homeostasis of DNA during chromatin dynamics.

Multifactorial resistance to antineoplastic agents in drug-resistant P388 murine leukemia, Chinese hamster ovary, and human HeLa cells, with emphasis on the role of DNA topoisomerase II

1992 ◽  
Vol 70 (5) ◽  
pp. 354-364 ◽  
Author(s):  
Abdul M. Deffie ◽  
J. Peter McPherson ◽  
Radhey S. Gupta ◽  
David W. Hedley ◽  
Gerald J. Goldenberg
Keyword(s):  
Hela Cells ◽  
Cho Cells ◽  
Topoisomerase Ii ◽  
Chinese Hamster ◽  
Dna Topoisomerase Ii ◽  
Dna Topoisomerase ◽  
Catalytic Activities ◽  
Topo Ii ◽  
Posttranscriptional Level

The role of DNA topoisomerase II in multifactorial resistance to antineoplastic agents is reviewed. We have previously observed that in Adriamycin (ADR) resistant P388 murine leukemia cells, DNA topoisomerase II enzyme content and cleavage and catalytic activities were all reduced and correlated with drug sensitivity. A subsequent study provided evidence for an allelic mutation of the gene for DNA topoisomerase II as a possible molecular mechanism underlying the enzyme alterations. To ascertain how universal were these observations, a study was undertaken of DNA topoisomerase II (topo II) in other cell lines resistant either to ADR or another topo-II-interactive drug, mitoxantrone. In ADR-resistant Chinese hamster ovary (CHO) cells, topo II cleavage and catalytic activities and the gene product were all reduced; however, only cleavage activity correlated with drug sensitivity. No differences were noted between ADR-sensitive and -resistant CHO cells by Northern or Southern blot analysis, raising the possibility that the enzyme in resistant cells may be regulated at a posttranscriptional level. Findings on a gel retardation or immunoblot band depletion assay showed that the enzyme in CHO/ADR-1 cells failed to bind to the DNA–drug–enzyme complex, suggesting a qualitative as well as quantitative enzyme alteration in those cells. Mitoxantrone-resistant HeLa cells (Mito-1) displayed not only a lower level of cleavage activity but also of enzyme content and catalytic activity, relative to the parental drug-sensitive HeLa cells. As with the CHO cells, no differences were noted between mitoxantrone-sensitive and -resistant HeLa cells on Northern and Southern blot analyses, suggesting that enzyme regulation in these resistant cells may also be at a posttranscriptional level. There was no evidence of enzyme binding to DNA–drug–enzyme complex in resistant HeLa/Mito-1 cells, once again suggesting the presence of a qualitative enzyme alteration. The findings in both ADR-resistant CHO cells and mitoxantrone-resistant HeLa cells do not exclude the possibility that subtle changes in the topoisomerase II gene, such as point mutations, may account for these enzyme changes. The apparent qualitative changes observed in enzyme may result from posttranslational modifications such as phosphorylation.Key words: drug resistance, DNA topoisomerase II, Adriamycin, mitoxantrone.

scholarly journals Topoisomerase II as a target for anticancer chemotherapy.

1995 ◽  
Vol 42 (4) ◽  
pp. 381-393
Author(s):  
S H Kaufmann ◽  
R Hancock
Keyword(s):  
Anticancer Agents ◽  
Topoisomerase Ii ◽  
Current Knowledge ◽  
Chemotherapeutic Agents ◽  
Cytotoxic Agents ◽  
Type Ii ◽  
Dna Topoisomerases ◽  
Anticancer Chemotherapy ◽  
The Subject ◽  
Type Ii Dna Topoisomerases

Type II DNA topoisomerases are required for the segregation of genomic DNA at cell division in prokaryotic and eukaryotic cells, and inhibitors of these enzymes are potential cytotoxic agents in both prokaryotes and eukaryotes. The bacterial member of the topoisomerase II family, DNA gyrase, and the chemotherapeutic agents which target it are the subject of a recent review (Maxwell, A. et al., 1993, in Molecular Biology of DNA Topoisomerases, Andoh, T. et al., eds., pp. 21-30, CRC Press, Boca Raton). Here we present an overview of current knowledge of eukaryotic topoisomerase II and the anticancer agents which target this enzyme, focussing predominantly on new observations and recent reports and reviews.

scholarly journals Modulated control of DNA supercoiling balance by the DNA-wrapping domain of bacterial gyrase

2020 ◽  
Vol 48 (4) ◽  
pp. 2035-2049
Author(s):  
Matthew J Hobson ◽  
Zev Bryant ◽  
James M Berger
Keyword(s):  
Atp Hydrolysis ◽  
Dna Supercoiling ◽  
Thermodynamic Efficiency ◽  
Futile Cycling ◽  
Negative Supercoiling ◽  
The Stability ◽  
Species Specific ◽  
Supercoil Relaxation ◽  
Strand Passage ◽  
Dna Wrapping

Abstract Negative supercoiling by DNA gyrase is essential for maintaining chromosomal compaction, transcriptional programming, and genetic integrity in bacteria. Questions remain as to how gyrases from different species have evolved profound differences in their kinetics, efficiency, and extent of negative supercoiling. To explore this issue, we analyzed homology-directed mutations in the C-terminal, DNA-wrapping domain of the GyrA subunit of Escherichia coli gyrase (the ‘CTD’). The addition or removal of select, conserved basic residues markedly impacts both nucleotide-dependent DNA wrapping and supercoiling by the enzyme. Weakening CTD–DNA interactions slows supercoiling, impairs DNA-dependent ATP hydrolysis, and limits the extent of DNA supercoiling, while simultaneously enhancing decatenation and supercoil relaxation. Conversely, strengthening DNA wrapping does not result in a more extensively supercoiled DNA product, but partially uncouples ATP turnover from strand passage, manifesting in futile cycling. Our findings indicate that the catalytic cycle of E. coli gyrase operates at high thermodynamic efficiency, and that the stability of DNA wrapping by the CTD provides one limit to DNA supercoil introduction, beyond which strand passage competes with ATP-dependent supercoil relaxation. These results highlight a means by which gyrase can evolve distinct homeostatic supercoiling setpoints in a species-specific manner.

scholarly journals A role of topoisomerase II in linking DNA replication to chromosome condensation

2003 ◽  
Vol 160 (5) ◽  
pp. 645-655 ◽  
Author(s):  
Olivier Cuvier ◽  
Tatsuya Hirano
Keyword(s):  
Dna Replication ◽  
Topoisomerase Ii ◽  
Atp Hydrolysis ◽  
Early Stage ◽  
Chromosome Condensation ◽  
Binding Property ◽  
Dependent Manner ◽  
Mitotic Chromosomes ◽  
Topo Ii

The condensin complex and topoisomerase II (topo II) have different biochemical activities in vitro, and both are required for mitotic chromosome condensation. We have used Xenopus egg extracts to investigate the functional interplay between condensin and topo II in chromosome condensation. When unreplicated chromatin is directly converted into chromosomes with single chromatids, the two proteins must function together, although they are independently targeted to chromosomes. In contrast, the requirement for topo II is temporarily separable from that of condensin when chromosome assembly is induced after DNA replication. This experimental setting allows us to find that, in the absence of condensin, topo II becomes enriched in an axial structure within uncondensed chromatin. Subsequent addition of condensin converts this structure into mitotic chromosomes in an ATP hydrolysis–dependent manner. Strikingly, preventing DNA replication by the addition of geminin or aphidicolin disturbs the formation of topo II–containing axes and alters the binding property of topo II with chromatin. Our results suggest that topo II plays an important role in an early stage of chromosome condensation, and that this function of topo II is tightly coupled with prior DNA replication.

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