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DNA Topoisomerases

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 November 2017) | Viewed by 74991

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Special Issue Editors

Prof. Caroline Austin

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Guest Editor

Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
Interests: DNA topoisomerase; transcription

Dr. Ian Cowell

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Co-Guest Editor

Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
Interests: DNA topoisomerase; transcription
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Special Issue Information

Dear Colleagues,

We are planning a Special Issue in the International Journal of Molecular Sciences, focusing on the topic of DNA topoisomerases. DNA topoisomerases are essential enzymes that modulate DNA topology. They alter DNA topology by transiently cleaving and re-joining cellular DNA. There are two main classes: Type I enzymes that enzymatically cleave a single DNA strand and type II enzymes that can cleave both DNA strands. Mammals have two type II DNA topoisomerases, TOP2A and TOP2B. Bacteria have two type II DNA topoisomerases, DNA gyrase and DNA topoisomerase IV. DNA topoisomerases are targets for both anti-bacterial agents and anti-cancer agents. Mechanistic understanding of these enzymes has been advanced by solving crystal structures for domains of the enzymes. Processes, such as transcription and replication, require DNA topoisomerases. New methodologies utilizing next generation sequencing, such as ChIP seq, RNA seq and 3C, are enabling the elucidation of the mechanisms of actions of DNA topoisomerases. In this Special Issue, we wish to review advances in our understanding of these exciting enzymes.

Professor Caroline Austin
Guest Editor
Dr. Ian Cowell
Co-Guest Editor

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Keywords

DNA topoisomerase
DNA topology
Transcription
R–loops
ChIP-seq
nuclear organization
topological domains
CTCF

Published Papers (12 papers)

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15 pages, 2673 KiB

Open AccessArticle

Effect of TDP2 on the Level of TOP2-DNA Complexes and SUMOylated TOP2-DNA Complexes

by Ka Cheong Lee, Rebecca L. Swan, Zbyslaw Sondka, Kay Padget, Ian G. Cowell and Caroline A. Austin

Int. J. Mol. Sci. 2018, 19(7), 2056; https://doi.org/10.3390/ijms19072056 - 14 Jul 2018

Cited by 16 | Viewed by 4188

Abstract

DNA topoisomerase II (TOP2) activity involves a normally transient double-strand break intermediate in which the enzyme is coupled to DNA via a 5′-phosphotyrosyl bond. However, etoposide and other topoisomerase drugs poison the enzyme by stabilising this enzyme-bridged break, resulting in the accumulation of TOP2-DNA covalent complexes with cytotoxic consequences. The phosphotyrosyl diesterase TDP2 appears to be required for efficient repair of this unusual type of DNA damage and can remove 5′-tyrosine adducts from a double-stranded oligonucleotide substrate. Here, we adapt the trapped in agarose DNA immunostaining (TARDIS) assay to investigate the role of TDP2 in the removal of TOP2-DNA complexes in vitro and in cells. We report that TDP2 alone does not remove TOP2-DNA complexes from genomic DNA in vitro and that depletion of TDP2 in cells does not slow the removal of TOP2-DNA complexes. Thus, if TDP2 is involved in repairing TOP2 adducts, there must be one or more prior steps in which the protein-DNA complex is processed before TDP2 removes the remaining 5′ tyrosine DNA adducts. While this is partly achieved through the degradation of TOP2 adducts by the proteasome, a proteasome-independent mechanism has also been described involving the SUMOylation of TOP2 by the ZATT E3 SUMO ligase. The TARDIS assay was also adapted to measure the effect of TDP2 knockdown on levels of SUMOylated TOP2-DNA complexes, which together with levels of double strand breaks were unaffected in K562 cells following etoposide exposure and proteasomal inhibition. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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12 pages, 5527 KiB

Open AccessArticle

Biochemical Basis of E. coli Topoisomerase I Relaxation Activity Reduction by Nonenzymatic Lysine Acetylation

by Qingxuan Zhou, Mario E. Gomez Hernandez, Francisco Fernandez-Lima and Yuk-Ching Tse-Dinh

Int. J. Mol. Sci. 2018, 19(5), 1439; https://doi.org/10.3390/ijms19051439 - 11 May 2018

Cited by 11 | Viewed by 3823

Abstract

The relaxation activity of E. coli topoisomerase I is required for regulation of global and local DNA supercoiling. The in vivo topoisomerase I enzyme activity is sensitive to lysine acetylation–deacetylation and can affect DNA supercoiling and growth as a result. Nonenzymatic lysine acetylation by acetyl phosphate has been shown to reduce the relaxation activity of E. coli topoisomerase I. In this work, the biochemical consequence of topoisomerase I modification by acetyl phosphate with enzymatic assays was studied. Results showed that noncovalent binding to DNA and DNA cleavage by the enzyme were reduced as a result of the acetylation, with greater effect on DNA cleavage. Four lysine acetylation sites were identified using bottom-up proteomics: Lys13, Lys45, Lys346, and Lys488. The Lys13 residue modified by acetyl phosphate has not been reported previously as a lysine acetylation site for E. coli topoisomerase I. We discuss the potential biochemical consequence of lysine acetylation at this strictly conserved lysine and other lysine residues on the enzyme based on available genetic and structural information. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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19 pages, 12860 KiB

Open AccessArticle

Site-Specific Cleavage by Topoisomerase 2: A Mark of the Core Centromere

by Walter E. Mills, Jennifer M. Spence, Tatsuo Fukagawa and Christine J. Farr

Int. J. Mol. Sci. 2018, 19(2), 534; https://doi.org/10.3390/ijms19020534 - 10 Feb 2018

Cited by 7 | Viewed by 4157

Abstract

In addition to its roles in transcription and replication, topoisomerase 2 (topo 2) is crucial in shaping mitotic chromosomes and in ensuring the orderly separation of sister chromatids. As well as its recruitment throughout the length of the mitotic chromosome, topo 2 accumulates at the primary constriction. Here, following cohesin release, the enzymatic activity of topo 2 acts to remove residual sister catenations. Intriguingly, topo 2 does not bind and cleave all sites in the genome equally; one preferred site of cleavage is within the core centromere. Discrete topo 2-centromeric cleavage sites have been identified in α-satellite DNA arrays of active human centromeres and in the centromere regions of some protozoans. In this study, we show that topo 2 cleavage sites are also a feature of the centromere in Schizosaccharomyces pombe, the metazoan Drosophila melanogaster and in another vertebrate species, Gallus gallus (chicken). In vertebrates, we show that this site-specific cleavage is diminished by depletion of CENP-I, an essential constitutive centromere protein. The presence, within the core centromere of a wide range of eukaryotes, of precise sites hypersensitive to topo 2 cleavage suggests that these mark a fundamental and conserved aspect of this functional domain, such as a non-canonical secondary structure. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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12 pages, 2337 KiB

Open AccessArticle

Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site

by Sebastian Franco-Ulloa, Giuseppina La Sala, Gian Pietro Miscione and Marco De Vivo

Int. J. Mol. Sci. 2018, 19(2), 453; https://doi.org/10.3390/ijms19020453 - 03 Feb 2018

Cited by 14 | Viewed by 5662

Abstract

DNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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Review

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18 pages, 552 KiB

Open AccessReview

Anthracyclines as Topoisomerase II Poisons: From Early Studies to New Perspectives

by Jessica Marinello, Maria Delcuratolo and Giovanni Capranico

Int. J. Mol. Sci. 2018, 19(11), 3480; https://doi.org/10.3390/ijms19113480 - 06 Nov 2018

Cited by 151 | Viewed by 7889

Abstract

Mammalian DNA topoisomerases II are targets of anticancer anthracyclines that act by stabilizing enzyme-DNA complexes wherein DNA strands are cut and covalently linked to the protein. This molecular mechanism is the molecular basis of anthracycline anticancer activity as well as the toxic effects such as cardiomyopathy and induction of secondary cancers. Even though anthracyclines have been used in the clinic for more than 50 years for solid and blood cancers, the search of breakthrough analogs has substantially failed. The recent developments of personalized medicine, availability of individual genomic information, and immune therapy are expected to change significantly human cancer therapy. Here, we discuss the knowledge of anthracyclines as Topoisomerase II poisons, their molecular and cellular effects and toxicity along with current efforts to improve the therapeutic index. Then, we discuss the contribution of the immune system in the anticancer activity of anthracyclines, and the need to increase our knowledge of molecular mechanisms connecting the drug targets to the immune stimulatory pathways in cancer cells. We propose that the complete definition of the molecular interaction of anthracyclines with the immune system may open up more effective and safer ways to treat patients with these drugs. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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21 pages, 2228 KiB

Open AccessReview

TOP2B: The First Thirty Years

by Caroline A. Austin, Ka C. Lee, Rebecca L. Swan, Mushtaq M. Khazeem, Catriona M. Manville, Peter Cridland, Achim Treumann, Andrew Porter, Nick J. Morris and Ian G. Cowell

Int. J. Mol. Sci. 2018, 19(9), 2765; https://doi.org/10.3390/ijms19092765 - 14 Sep 2018

Cited by 69 | Viewed by 7724

Abstract

Type II DNA topoisomerases (EC 5.99.1.3) are enzymes that catalyse topological changes in DNA in an ATP dependent manner. Strand passage reactions involve passing one double stranded DNA duplex (transported helix) through a transient enzyme-bridged break in another (gated helix). This activity is required for a range of cellular processes including transcription. Vertebrates have two isoforms: topoisomerase IIα and β. Topoisomerase IIβ was first reported in 1987. Here we review the research on DNA topoisomerase IIβ over the 30 years since its discovery. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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15 pages, 977 KiB

Open AccessReview

The Roles of DNA Topoisomerase IIβ in Transcription

by Ram Madabhushi

Int. J. Mol. Sci. 2018, 19(7), 1917; https://doi.org/10.3390/ijms19071917 - 29 Jun 2018

Cited by 39 | Viewed by 7182

Abstract

Type IIA topoisomerases allow DNA double helical strands to pass through each other by generating transient DNA double strand breaks βDSBs), and in so doing, resolve torsional strain that accumulates during transcription, DNA replication, chromosome condensation, chromosome segregation and recombination. Whereas most eukaryotes possess a single type IIA enzyme, vertebrates possess two distinct type IIA topoisomerases, Topo IIα and Topo IIβ. Although the roles of Topo IIα, especially in the context of chromosome condensation and segregation, have been well-studied, the roles of Topo IIβ are only beginning to be illuminated. This review begins with a summary of the initial studies surrounding the discovery and characterization of Topo IIβ and then focuses on the insights gained from more recent studies that have elaborated important functions for Topo IIβ in transcriptional regulation. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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15 pages, 1534 KiB

Open AccessReview

Why Two? On the Role of (A-)Symmetry in Negative Supercoiling of DNA by Gyrase

by Dagmar Klostermeier

Int. J. Mol. Sci. 2018, 19(5), 1489; https://doi.org/10.3390/ijms19051489 - 16 May 2018

Cited by 21 | Viewed by 5112

Abstract

Gyrase is a type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme consists of two GyrA and two GyrB subunits. It is believed to introduce negative supercoils into DNA by converting a positive DNA node into a negative node through strand passage: First, it cleaves both DNA strands of a double-stranded DNA, termed the G-segment, and then it passes a second segment of the same DNA molecule, termed the T-segment, through the gap created. As a two-fold symmetric enzyme, gyrase contains two copies of all elements that are key for the supercoiling reaction: The GyrB subunits provide two active sites for ATP binding and hydrolysis. The GyrA subunits contain two C-terminal domains (CTDs) for DNA binding and wrapping to stabilize the positive DNA node, and two catalytic tyrosines for DNA cleavage. While the presence of two catalytic tyrosines has been ascribed to the necessity of cleaving both strands of the G-segment to enable strand passage, the role of the two ATP hydrolysis events and of the two CTDs has been less clear. This review summarizes recent results on the role of these duplicate elements for individual steps of the supercoiling reaction, and discusses the implications for the mechanism of DNA supercoiling. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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13 pages, 2046 KiB

Open AccessReview

Structure and Chromosomal Organization of Yeast Genes Regulated by Topoisomerase II

by Ricky S. Joshi, Christoforos Nikolaou and Joaquim Roca

Int. J. Mol. Sci. 2018, 19(1), 134; https://doi.org/10.3390/ijms19010134 - 03 Jan 2018

Cited by 9 | Viewed by 5076

Abstract

Cellular DNA topoisomerases (topo I and topo II) are highly conserved enzymes that regulate the topology of DNA during normal genome transactions, such as DNA transcription and replication. In budding yeast, topo I is dispensable whereas topo II is essential, suggesting fundamental and exclusive roles for topo II, which might include the functions of the topo IIa and topo IIb isoforms found in mammalian cells. In this review, we discuss major findings of the structure and chromosomal organization of genes regulated by topo II in budding yeast. Experimental data was derived from short (10 min) and long term (120 min) responses to topo II inactivation in top-2 ts mutants. First, we discuss how short term responses reveal a subset of yeast genes that are regulated by topo II depending on their promoter architecture. These short term responses also uncovered topo II regulation of transcription across multi-gene clusters, plausibly by common DNA topology management. Finally, we examine the effects of deactivated topo II on the elongation of RNA transcripts. Each study provides an insight into the particular chromatin structure that interacts with the activity of topo II. These findings are of notable clinical interest as numerous anti-cancer therapies interfere with topo II activity. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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2962 KiB

Open AccessReview

A Topology-Centric View on Mitotic Chromosome Architecture

by Ewa Piskadlo and Raquel A. Oliveira

Int. J. Mol. Sci. 2017, 18(12), 2751; https://doi.org/10.3390/ijms18122751 - 18 Dec 2017

Cited by 26 | Viewed by 8299

Abstract

Mitotic chromosomes are long-known structures, but their internal organization and the exact process by which they are assembled are still a great mystery in biology. Topoisomerase II is crucial for various aspects of mitotic chromosome organization. The unique ability of this enzyme to untangle topologically intertwined DNA molecules (catenations) is of utmost importance for the resolution of sister chromatid intertwines. Although still controversial, topoisomerase II has also been proposed to directly contribute to chromosome compaction, possibly by promoting chromosome self-entanglements. These two functions raise a strong directionality issue towards topoisomerase II reactions that are able to disentangle sister DNA molecules (in trans) while compacting the same DNA molecule (in cis). Here, we review the current knowledge on topoisomerase II role specifically during mitosis, and the mechanisms that directly or indirectly regulate its activity to ensure faithful chromosome segregation. In particular, we discuss how the activity or directionality of this enzyme could be regulated by the SMC (structural maintenance of chromosomes) complexes, predominantly cohesin and condensin, throughout mitosis. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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1267 KiB

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Non-Catalytic Roles of the Topoisomerase IIα C-Terminal Domain

by Duncan J. Clarke and Yoshiaki Azuma

Int. J. Mol. Sci. 2017, 18(11), 2438; https://doi.org/10.3390/ijms18112438 - 17 Nov 2017

Cited by 15 | Viewed by 6337

Abstract

DNA Topoisomerase IIα (Topo IIα) is a ubiquitous enzyme in eukaryotes that performs the strand passage reaction where a double helix of DNA is passed through a second double helix. This unique reaction is critical for numerous cellular processes. However, the enzyme also possesses a C-terminal domain (CTD) that is largely dispensable for the strand passage reaction but is nevertheless important for the fidelity of cell division. Recent studies have expanded our understanding of the roles of the Topo IIα CTD, in particular in mitotic mechanisms where the CTD is modified by Small Ubiquitin-like Modifier (SUMO), which in turn provides binding sites for key regulators of mitosis. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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Other

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11 pages, 773 KiB

Open AccessOpinion

DNA Supercoiling, Topoisomerases, and Cohesin: Partners in Regulating Chromatin Architecture?

by Camilla Björkegren and Laura Baranello

Int. J. Mol. Sci. 2018, 19(3), 884; https://doi.org/10.3390/ijms19030884 - 16 Mar 2018

Cited by 21 | Viewed by 7648

Abstract

Although our knowledge of chromatin organization has advanced significantly in recent years, much about the relationships between different features of genome architecture is still unknown. Folding of mammalian genomes into spatial domains is thought to depend on architectural proteins, other DNA-binding proteins, and different forms of RNA. In addition, emerging evidence points towards the possibility that the three-dimensional organisation of the genome is controlled by DNA topology. In this scenario, cohesin, CCCTC-binding factor (CTCF), transcription, DNA supercoiling, and topoisomerases are integrated to dictate different layers of genome organization, and the contribution of all four to gene control is an important direction of future studies. In this perspective, we review recent studies that give new insight on how DNA supercoiling shape chromatin structure. Full article

(This article belongs to the Special Issue DNA Topoisomerases)

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