The response of eukaryotic topoisomerases to DNA damage

doi:10.1016/S0167-4781(98)00138-9

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression

Volume 1400, Issues 1–3, 1 October 1998, Pages 223-232

https://doi.org/10.1016/S0167-4781(98)00138-9 Get rights and content

Abstract

Beyond the known mutagenic properties of DNA lesions, recent evidence indicates that several forms of genomic damage dramatically influence the catalytic activities of DNA topoisomerases. Apurinic sites, apyrimidinic sites, base mismatches, and ultraviolet photoproducts all enhance topoisomerase I-mediated DNA cleavage when they are located in close proximity to the point of scission. Furthermore, when located between the points of scission of a topoisomerase II cleavage site, these same lesions (with the exception of ultraviolet photoproducts) greatly stimulate the cleavage activity of the type II enzyme. Thus, as found for anticancer drugs, lesions have the capacity to convert topoisomerases from essential cellular enzymes to potent DNA toxins. These findings raise exciting new questions regarding the mechanism of anticancer drugs, the physiological functions of topoisomerases, and the processing of DNA damage in the cell.

Introduction

Topological relationships within the genetic material, such as over- and underwinding, knotting, and tangling, profoundly affect virtually every aspect of DNA metabolism [1, 2]. In order to regulate these critical relationships, eukaryotic cells have evolved ubiquitous enzymes, known as DNA topoisomerases, that freely pass one nucleic acid segment through another [1, 2, 3, 4, 5, 6]. Topoisomerases are required for the viability of proliferating cells and play essential roles in a number of fundamental nuclear processes, including DNA replication, transcription, and recombination, as well as chromosome organization and segregation [1, 2, 3, 4].

There are two classes of topoisomerases that are distinguished by their catalytic mechanisms. Type I topoisomerases alter DNA topology by facilitating the rotation of DNA about a transient single-stranded break (or potentially by passing a single strand of DNA through a break that they generate in the complementary strand) [5, 6, 7, 8]. Type II topoisomerases act by passing an intact DNA helix through a transient double-stranded break that they generate in a separate helix [1, 2, 3, 4, 7].

As a result of their DNA passage reactions, topoisomerases render nucleic acids invisible to themselves [1, 2]. However, in order to confer this ethereal property on DNA, topoisomerases must generate breaks in the genetic material [9, 10, 11, 12]. Since these breaks are fleeting intermediates in the strand passage reaction, they normally are present at low steady-state levels and are tolerated by the cell. However, conditions that significantly increase the physiological concentration of topoisomerase-mediated DNA breaks trigger mutagenic events, such as insertions, deletions, translocations, and chromosomal breaks [2, 13, 14, 15, 16, 17, 18]. Furthermore, when present in sufficient numbers, these breaks initiate a programmed series of events that ultimately culminates in cell death. Several clinically relevant anticancer drugs exploit this deleterious aspect of topoisomerase mechanism and kill malignant cells by increasing levels of enzyme–DNA cleavage complexes [5, 13, 14, 16, 17, 18, 19, 20, 21].

Beyond the known genomic functions of topoisomerases, there is an emerging body of literature that suggests that these enzymes have specific interactions with damaged DNA. Several commonly formed DNA lesions dramatically stimulate topoisomerase-mediated DNA scission [22, 23, 24, 25, 26, 27, 28, 29, 30]. Thus, as found for anticancer drugs, lesions have the capacity to convert topoisomerases from essential cellular enzymes to potent DNA toxins. Since interactions between topoisomerases and DNA damage may have significant physiological ramifications and reveal novel cellular roles for these enzymes, this review will focus on the response of topoisomerases to DNA damage.

Section snippets

The generation of DNA damage

Cells are constantly subjected to forces that damage the genetic material. Although the source of this damage can be either spontaneous (i.e. endogenous) or environmental in nature, the ensuing chemical alterations that occur are often similar [31]. Some of the most common DNA lesions formed are apurinic/apyrimidinic sites (i.e. abasic sites), deaminated cytosine residues (which produces uracil:guanine mismatches), base mismatches, and ultraviolet-induced photoproducts [31, 32, 33]. To

Ultraviolet-induced photoproducts

In addition to its effects on DNA replication, treatment of cells with ultraviolet radiation has long been known to induce covalent protein-DNA crosslinks as well as single-stranded breaks in the genetic material [34, 35, 36, 37]. Recent evidence strongly suggests that topoisomerase I is the enzyme primarily responsible for the generation of these chromosomal aberrations. This conclusion is based on two findings. First, levels of topoisomerase I-generated chromosomal breaks increase

Ultraviolet-induced DNA photoproducts

Exposure of DNA to ultraviolet radiation inhibits the catalytic DNA strand passage cycle of topoisomerase II [41]. The inclusion of 10–20 photoproducts per pBR322 plasmid (∼1 lesion per 200–400 bp) decreases enzyme activity ∼50% (as monitored by the ability to relax negatively supercoiled DNA). This inhibition is due exclusively to the presence of cyclobutane pyrimidine dimers rather than 6,4-dipyrimidine lesions, as full activity is restored by treatment of the irradiated plasmid with DNA

How do DNA lesions enhance topoisomerase-mediated DNA cleavage?

As described above, a variety of DNA lesions stimulate the DNA cleavage activities of topoisomerases I and II. Although a detailed mechanism of action is not known, some clues can be derived from their relative efficacies against the two enzymes.

Within experimental limitations, the relative efficacies of ultraviolet photoproducts, apurinic sites, apyrmidinic sites, and base mismatches against topoisomerase I appear to be similar (reported variations are ≤2-fold) [25, 27, 28]. Given their

Acknowledgments

Work in the senior author’s laboratory was supported by Grants GM33944 and GM53960 from the National Institutes of Health.

References (65)

M. Gupta et al.
Eukaryotic DNA topoisomerase I
Biochim. Biophys. Acta
(1995)
J.J. Champoux
Mechanism of catalysis by eukaryotic DNA topoisomerase I
Adv. Pharmacol.
(1994)
A.H. Andersen et al.
The DNA binding, cleavage, and religation reactions of eukaryotic topoisomerases I and II
Adv. Pharmacol.
(1994)
A. Sharma et al.
DNA topoisomerases
Curr. Opin. Struct. Biol.
(1995)
M. Sander et al.
Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster
J. Biol. Chem.
(1983)
L.F. Liu et al.
Cleavage of DNA by mammalian DNA topoisomerase II
J. Biol. Chem.
(1983)
S.J. Froelich-Ammon et al.
Topoisomerase poisons: harnessing the dark side of enzyme mechanism
J. Biol. Chem.
(1995)
J.L. Nitiss et al.
Antitopoisomerase drug action and resistance
Eur. J. Cancer
(1996)
R.D. Anderson et al.
Mutagenicity and carcinogenicity of topoisomerase-interactive agents
Mutat. Res.
(1994)
P.S. Kingma et al.
Abasic sites stimulate double-stranded DNA cleavage mediated by topoisomerase II: anticancer drugs mimic endogenous DNA lesions
J. Biol. Chem.
(1995)

P.S. Kingma et al.

Spontaneous DNA damage stimulates topoisomerase II-mediated DNA cleavage

J. Biol. Chem.

(1997)

P.S. Kingma et al.

Apurinic sites are position-specific topoisomerase II-poisons

J. Biol. Chem.

(1997)

P. Pourquier et al.

Effects of uracil incorporation, DNA mismatches, and abasic sites on cleavage and religation activities of mammalian topoisomerase I

J. Biol. Chem.

(1997)

A. Lanza et al.

Human DNA topoisomerase I-mediated cleavages stimulated by ultraviolet light-induced DNA damage

J. Biol. Chem.

(1996)

Y.C. Yeh et al.

Mammalian topoisomerase I has base mismatch nicking activity

J. Biol. Chem.

(1994)

T. Stevnsner et al.

Interactions between eukaryotic DNA topoisomerase I and a specific binding sequence

J. Biol. Chem.

(1989)

A.J. Fornace et al.

DNA–protein cross-linking by ultraviolet radiation in normal human and xeroderma pigmentosum fibroblasts

Biochim. Biophys. Acta

(1976)

B.S. Rosenstein et al.

Repair of DNA damage induced in systemic lupus erythematosus skin fibroblasts by simulated sunlight

J. Invest. Dermatol.

(1992)

B.S. Rosenstein et al.

DNA–protein crosslinking in normal and solar UV-sensitive ICR 2A frog cell lines exposed to solar UV-radiation

Mutat. Res.

(1989)

A.H. Corbett et al.

Inhibition of eukaryotic topoisomerase II by ultraviolet-induced cyclobutane pyrimidine dimers

J. Biol. Chem.

(1991)

P. Cuniasse et al.

The abasic site as a challenge to DNA polymerase: a nuclear magnetic resonance study of G, C, and T opposite a model abasic site

J. Mol. Biol.

(1990)

I. Goljer et al.

Refined solution structure of a DNA heteroduplex containing an aldehydic abasic site

J. Biol. Chem.

(1995)

D.A. Burden et al.

Topoisomerase II·etoposide interactions direct the formation of drug-induced enzyme–DNA cleavage complexes

J. Biol. Chem.

(1996)

F.C. Christians et al.

Potential sources of multiple mutations in human cancers

Prevent. Med.

(1995)

J.C. Wang

DNA topoisomerases

Annu. Rev. Biochem.

(1996)

N.R. Cozzarelli, J.C. Wang, DNA Topology and its Biological Effects, Cold Spring Harbor Laboratory Press, Cold Spring...

N. Osheroff et al.

Catalytic function of DNA topoisomerase II

BioEssays

(1991)

P.M. Watt et al.

Structure and function of type II DNA topoisomerases

Biochem. J.

(1994)

D.E. Pulleyblank et al.

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

Proc. Natl. Acad. Sci. USA

(1975)

J.J. Champoux

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

Proc. Natl. Acad. Sci. USA

(1976)

L. Liu, DNA Topoisomerases: Topoisomerase-Targeted Drugs, Vol. 29, Academic Press, New York,...

A.H. Corbett et al.

When good enzymes go bad: conversion of topoisomerase II to a cellular toxin by antineoplastic drugs

Chem. Res. Toxicol.

(1993)

Cited by (81)

Untangling trapped topoisomerases with tyrosyl-DNA phosphodiesterases
2020, DNA Repair
DNA topoisomerases alleviate the torsional stress that is generated by processes that are central to genome metabolism such as transcription and DNA replication. To do so, these enzymes generate an enzyme intermediate known as the cleavage complex in which the topoisomerase is covalently linked to the termini of a DNA single- or double-strand break. Whilst cleavage complexes are normally transient they can occasionally become abortive, creating protein-linked DNA breaks that threaten genome stability and cell survival; a process promoted and exploited in the cancer clinic by the use of topoisomerase ‘poisons’. Here, we review the consequences to genome stability and human health of abortive topoisomerase-induced DNA breakage and the cellular pathways that cells have adopted to mitigate them, with particular focus on an important class of enzymes known as tyrosyl-DNA phosphodiesterases.
Pausing sites of RNA polymerase II on actively transcribed genes are enriched in DNA double-stranded breaks
2020, Journal of Biological Chemistry
DNA double-stranded breaks (DSBs) are strongly associated with active transcription, and promoter-proximal pausing of RNA polymerase II (Pol II) is a critical step in transcriptional regulation. Mapping the distribution of DSBs along actively expressed genes and identifying the location of DSBs relative to pausing sites can provide mechanistic insights into transcriptional regulation. Using genome-wide DNA break mapping/sequencing techniques at single-nucleotide resolution in human cells, we found that DSBs are preferentially located around transcription start sites of highly transcribed and paused genes and that Pol II promoter-proximal pausing sites are enriched in DSBs. We observed that DSB frequency at pausing sites increases as the strength of pausing increases, regardless of whether the pausing sites are near or far from annotated transcription start sites. Inhibition of topoisomerase I and II by camptothecin and etoposide treatment, respectively, increased DSBs at the pausing sites as the concentrations of drugs increased, demonstrating the involvement of topoisomerases in DSB generation at the pausing sites. DNA breaks generated by topoisomerases are short-lived because of the religation activity of these enzymes, which these drugs inhibit; therefore, the observation of increased DSBs with increasing drug doses at pausing sites indicated active recruitment of topoisomerases to these sites. Furthermore, the enrichment and locations of DSBs at pausing sites were shared among different cell types, suggesting that Pol II promoter-proximal pausing is a common regulatory mechanism. Our findings support a model in which topoisomerases participate in Pol II promoter-proximal pausing and indicated that DSBs at pausing sites contribute to transcriptional activation.
DNA Damage by an essential enzyme: A delicate balance act on the tightrope
2019, DNA Repair
Citation Excerpt :
The central role of topoisomerases in DNA metabolism led many investigators to examine whether topoisomerases play roles in DNA repair. In eukaryotes, there are no unequivocal examples of DNA repair that require topoisomerases [89,90], with the exception of ribonucleotide removal from DNA, which is discussed below. This is not to say that topoisomerases have no effect on cell survival following exposure to DNA damage.
DNA topoisomerases are essential for DNA metabolic processes such as replication and transcription. Since DNA is double stranded, the unwinding needed for these processes results in DNA supercoiling and catenation of replicated molecules. Changing the topology of DNA molecules to relieve supercoiling or resolve catenanes requires that DNA be transiently cut. While topoisomerases carry out these processes in ways that minimize the likelihood of genome instability, there are several ways that topoisomerases may fail. Topoisomerases can be induced to fail by therapeutic small molecules such as by fluoroquinolones that target bacterial topoisomerases, or a variety of anti-cancer agents that target the eukaryotic enzymes. Increasingly, there have been a large number of agents and processes, including natural products and their metabolites, DNA damage, and the intrinsic properties of the enzymes that can lead to long-lasting DNA breaks that subsequently lead to genome instability, cancer, and other diseases. Understanding the processes that can interfere with topoisomerases and how cells respond when topoisomerases fail will be important in minimizing the consequences when enzymes need to transiently interfere with DNA integrity.
DNA topoisomerases in mtDNA maintenance and ageing
2014, Experimental Gerontology
Citation Excerpt :
Genistein is highly enriched in certain food supplements, but it is not known whether its bioavailability upon consummation of such supplements is sufficient to induce TOP1-poisoning in humans. In addition to the above chemical compounds, various exogenously induced DNA base modifications can inhibit the ligation step of TOP1 or TOP2 in vitro, when placed next to a strong cleavage site in a synthetic DNA substrate (Deweese and Osheroff, 2009b; Kingma and Osheroff, 1998; Leteurtre et al., 1994; Pourquier et al., 1997, 2000; Sabourin and Osheroff, 2000; Yeh et al., 1994). Thus, ephemeral DNA lesions such as base oxidations or abasic sites that are normally rapidly removed can trigger topoisomerase-linked breaks in the DNA backbone that are not or only slowly repaired.
DNA topoisomerases pass DNA strands through each other, a function essential for all DNA metabolic processes that create supercoils or entanglements of DNA. Topoisomerases play an ambivalent role in nuclear genome maintenance: Deficiency compromises gene transcription, replication and chromosome segregation, while the inherent DNA-cleavage activity of the enzymes endangers DNA integrity. Indeed, many DNA-damaging agents act through enhancing topoisomerase DNA cleavage. Mitochondrial DNA (mtDNA) clearly requires topoisomerase activity for transcription and replication, because it is a closed, double-stranded DNA molecule. Three topoisomerases have so far been found in mammalian mitochondria (I, IIβ, IIIα), but their precise role in mtDNA metabolism, mitochondrial maintenance and respiratory function remains mostly unclear. It is a reasonable surmise that these enzymes exhibit similar ambiguity with respect to genome maintenance and gene transcription as their nuclear counterparts. Here, we review what is known about the physiological roles of mitochondrial topoisomerases and draft three scenarios of how these enzymes possibly contribute to ageing-related mtDNA attrition and respiratory chain dysfunction. These scenarios are: mtDNA attrition by exogenously stimulated topoisomerase DNA cleavage, unbalancing of mitochondrial and nuclear transcription by direct effects on mitochondrial transcription, and contributions to enhanced mtDNA entanglement and recombination.
Tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2)
2014, DNA Repair
TDP1 and TDP2 were discovered and named based on the fact they process 3′- and 5′-DNA ends by excising irreversible protein tyrosyl-DNA complexes involving topoisomerases I and II, respectively. Yet, both enzymes have an extended spectrum of activities. TDP1 not only excises trapped topoisomerases I (Top1 in the nucleus and Top1mt in mitochondria), but also repairs oxidative damage-induced 3′-phosphoglycolates and alkylation damage-induced DNA breaks, and excises chain terminating anticancer and antiviral nucleosides in the nucleus and mitochondria. The repair function of TDP2 is devoted to the excision of topoisomerase II- and potentially topoisomerases III-DNA adducts. TDP2 is also essential for the life cycle of picornaviruses (important human and bovine pathogens) as it unlinks VPg proteins from the 5′-end of the viral RNA genome. Moreover, TDP2 has been involved in signal transduction (under the former names of TTRAP or EAPII). The DNA repair partners of TDP1 include PARP1, XRCC1, ligase III and PNKP from the base excision repair (BER) pathway. By contrast, TDP2 repair functions are coordinated with Ku and ligase IV in the non-homologous end joining pathway (NHEJ). This article summarizes and compares the biochemistry, functions, and post-translational regulation of TDP1 and TDP2, as well as the relevance of TDP1 and TDP2 as determinants of response to anticancer agents. We discuss the rationale for developing TDP inhibitors for combinations with topoisomerase inhibitors (topotecan, irinotecan, doxorubicin, etoposide, mitoxantrone) and DNA damaging agents (temozolomide, bleomycin, cytarabine, and ionizing radiation), and as novel antiviral agents.
Dual topoisomerase i and II poisoning by chiral Ru(II) complexes containing 2-thiophenylimidazo[4,5-f][1,10]phenanthroline derivatives
2014, Journal of Inorganic Biochemistry
Citation Excerpt :
These enzymes transiently break and religate DNA, changing the conformation of a DNA segment and resolving the torsional strain which develops during DNA unwinding and hampers processes such as replication and transcription. Topo I and Topo II are two types of these enzymes, each of which has different mechanisms of action and biological functions [1–5]. Despite variation per tumor tissue in the level of expression of Topo I and/or Topo II, topoisomerases remain a very promising drug target in oncology.
A series of chiral Ru(II) complexes bearing thiophene ligands were synthesized and characterized. Both Ru(II) complexes Δ/Λ-[Ru(bpy)₂(pscl)]^2 + (Δ/Λ-1) and Δ/Λ-[Ru(bpy)₂(psbr)]^2 + (Δ/Λ-2) (bpy = 2,2′-bipyridine, pscl = 2-(5-chlorothiophen-2-yl)imidazo[4,5-f][1,10]phenanthroline, psbr = 2-(5-bromothiophen-2-yl)imidazo[4,5-f][1,10]phenanthroline) showed antitumor activities against A549, HepG2 and BEL-7402 tumor cell lines, especially HeLa tumor cell line. Moreover, Δ enantiomers were more active than Λ enantiomers, accounting for the different cellular uptake. In addition, with the extension of time, these enantiomers could finally accumulate in the nucleus, suggesting that nucleic acids were the cellular target of these enantiomers. The DNA-binding behaviors of complexes were studied using spectroscopic and viscosity measurements. Results suggested that four complexes could bind to DNA in an intercalative mode but no obvious DNA-binding selectivity between the enantiomers was observed. Topoisomerase inhibition and DNA religation assay confirmed that four complexes acted as efficient dual topoisomerase I and II poisons, DNA strand breaks had also been observed from alkaline single cell gel electrophoresis (comet assay). Δ-1 and Δ-2 inhibited the growth of HeLa cells through the induction of apoptotic cell death, as evidenced by the Alexa Fluor® 488 annexin V staining assays and flow cytometry analysis. The results demonstrated that Δ/Λ-1 and Δ/Λ-2 acted as dual topoisomerase I and II poisons and caused DNA damage that could lead to cell cycle arrest by apoptosis.

View all citing articles on Scopus

View full text

ReviewThe response of eukaryotic topoisomerases to DNA damage

Abstract

Introduction

Section snippets

The generation of DNA damage

Ultraviolet-induced photoproducts

Ultraviolet-induced DNA photoproducts

How do DNA lesions enhance topoisomerase-mediated DNA cleavage?

Acknowledgments

Biochim. Biophys. Acta

Adv. Pharmacol.

Adv. Pharmacol.

Curr. Opin. Struct. Biol.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

Eur. J. Cancer

Mutat. Res.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

Biochim. Biophys. Acta

J. Invest. Dermatol.

Mutat. Res.

J. Biol. Chem.

J. Mol. Biol.

J. Biol. Chem.

J. Biol. Chem.

Prevent. Med.

DNA topoisomerases

Annu. Rev. Biochem.

Catalytic function of DNA topoisomerase II

BioEssays

Structure and function of type II DNA topoisomerases

Biochem. J.

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

Proc. Natl. Acad. Sci. USA

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

Proc. Natl. Acad. Sci. USA

When good enzymes go bad: conversion of topoisomerase II to a cellular toxin by antineoplastic drugs

Chem. Res. Toxicol.

Review
The response of eukaryotic topoisomerases to DNA damage