1
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Jian JY, McCarty KD, Byl J, Guengerich FP, Neuman K, Osheroff N. Basis for the discrimination of supercoil handedness during DNA cleavage by human and bacterial type II topoisomerases. Nucleic Acids Res 2023; 51:3888-3902. [PMID: 36999602 PMCID: PMC10164583 DOI: 10.1093/nar/gkad190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 04/01/2023] Open
Abstract
To perform double-stranded DNA passage, type II topoisomerases generate a covalent enzyme-cleaved DNA complex (i.e. cleavage complex). Although this complex is a requisite enzyme intermediate, it is also intrinsically dangerous to genomic stability. Consequently, cleavage complexes are the targets for several clinically relevant anticancer and antibacterial drugs. Human topoisomerase IIα and IIβ and bacterial gyrase maintain higher levels of cleavage complexes with negatively supercoiled over positively supercoiled DNA substrates. Conversely, bacterial topoisomerase IV is less able to distinguish DNA supercoil handedness. Despite the importance of supercoil geometry to the activities of type II topoisomerases, the basis for supercoil handedness recognition during DNA cleavage has not been characterized. Based on the results of benchtop and rapid-quench flow kinetics experiments, the forward rate of cleavage is the determining factor of how topoisomerase IIα/IIβ, gyrase and topoisomerase IV distinguish supercoil handedness in the absence or presence of anticancer/antibacterial drugs. In the presence of drugs, this ability can be enhanced by the formation of more stable cleavage complexes with negatively supercoiled DNA. Finally, rates of enzyme-mediated DNA ligation do not contribute to the recognition of DNA supercoil geometry during cleavage. Our results provide greater insight into how type II topoisomerases recognize their DNA substrates.
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Affiliation(s)
- Jeffrey Y Jian
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20982, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
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2
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Nitiss KC, Nitiss JL, Hanakahi LA. DNA Damage by an essential enzyme: A delicate balance act on the tightrope. DNA Repair (Amst) 2019; 82:102639. [PMID: 31437813 DOI: 10.1016/j.dnarep.2019.102639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/18/2019] [Accepted: 07/01/2019] [Indexed: 01/07/2023]
Abstract
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.
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Affiliation(s)
- Karin C Nitiss
- University of Illinois College of Medicine, Department of Biomedical Sciences, Rockford, IL, 61107, United States; University of Illinois College of Pharmacy, Biopharmaceutical Sciences Department, Rockford IL, 61107, United States
| | - John L Nitiss
- University of Illinois College of Pharmacy, Biopharmaceutical Sciences Department, Rockford IL, 61107, United States.
| | - Leslyn A Hanakahi
- University of Illinois College of Pharmacy, Biopharmaceutical Sciences Department, Rockford IL, 61107, United States.
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3
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Jang Y, Son H, Lee SW, Hwang W, Jung SR, Byl JAW, Osheroff N, Lee S. Selection of DNA Cleavage Sites by Topoisomerase II Results from Enzyme-Induced Flexibility of DNA. Cell Chem Biol 2019; 26:502-511.e3. [PMID: 30713098 DOI: 10.1016/j.chembiol.2018.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 10/04/2018] [Accepted: 12/04/2018] [Indexed: 12/26/2022]
Abstract
Topoisomerase II cleaves DNA at preferred sequences with different efficiencies; however, the mechanism of cleavage site selection is not known. Here we used single-molecule fluorescence assays that monitor several critical steps of DNA-topoisomerase II interactions, including binding/dissociation, bending/straightening, and cleavage/religation, and reveal that the cleavage site is selected mainly during the bending step. Furthermore, despite the sensitivity of the bending rate to the DNA sequence, it is not an intrinsic property of the DNA itself. Rather, it is determined by protein-DNA interactions.
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Affiliation(s)
- Yunsu Jang
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Heyjin Son
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Sang-Wook Lee
- Department of Physics and Astronomy, National Center for Creative Research Initiatives, Seoul National University, Seoul 08826, South Korea
| | - Wonseok Hwang
- Department of Physics and Astronomy, National Center for Creative Research Initiatives, Seoul National University, Seoul 08826, South Korea
| | - Seung-Ryoung Jung
- Department of Physics and Astronomy, National Center for Creative Research Initiatives, Seoul National University, Seoul 08826, South Korea
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA.
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea.
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4
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Qian C, Wu J, Ji L, Chao H. Topoisomerase IIα poisoning and DNA double-strand breaking by chiral ruthenium(ii) complexes containing 2-furanyl-imidazo[4,5-f][1,10]phenanthroline derivatives. Dalton Trans 2016; 45:10546-55. [DOI: 10.1039/c6dt01422d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Some chiral ruthenium(ii) complexes bearing furan ligands were developed to act as topoisomerase IIα poisons and caused DNA double-strand damage that could lead to apoptosis.
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Affiliation(s)
- Chen Qian
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Jingheng Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou
- P. R. China
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5
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Wang YC, Qian C, Peng ZL, Hou XJ, Wang LL, Chao H, Ji LN. Dual topoisomerase I and II poisoning by chiral Ru(II) complexes containing 2-thiophenylimidazo[4,5-f][1,10]phenanthroline derivatives. J Inorg Biochem 2013; 130:15-27. [PMID: 24145066 DOI: 10.1016/j.jinorgbio.2013.09.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 02/02/2023]
Abstract
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.
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Affiliation(s)
- Yu-Chuan Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, State Key Laboratory of Optoelectronic Materials and Technologies, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, PR China
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6
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Janes S, Schmidt U, Ashour Garrido K, Ney N, Concilio S, Zekri M, Caspari T. Heat induction of a novel Rad9 variant from a cryptic translation initiation site reduces mitotic commitment. J Cell Sci 2012; 125:4487-97. [PMID: 22797921 DOI: 10.1242/jcs.104075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Exposure of human cells to heat switches the activating signal of the DNA damage checkpoint from genotoxic to temperature stress. This change reduces mitotic commitment at the expense of DNA break repair. The thermal alterations behind this switch remain elusive despite the successful use of heat to sensitise cancer cells to DNA breaks. Rad9 is a highly conserved subunit of the Rad9-Rad1-Hus1 (9-1-1) checkpoint-clamp that is loaded by Rad17 onto damaged chromatin. At the DNA, Rad9 activates the checkpoint kinases Rad3(ATR) and Chk1 to arrest cells in G2. Using Schizosaccharomyces pombe as a model eukaryote, we discovered a new variant of Rad9, Rad9-M50, whose expression is specifically induced by heat. High temperatures promote alternative translation from a cryptic initiation codon at methionine-50. This process is restricted to cycling cells and is independent of the temperature-sensing mitogen-activated protein kinase (MAPK) pathway. While full-length Rad9 delays mitosis in the presence of DNA lesions, Rad9-M50 functions in a remodelled checkpoint pathway to reduce mitotic commitment at elevated temperatures. This remodelled pathway still relies on Rad1 and Hus1, but acts independently of Rad17. Heat-induction of Rad9-M50 ensures that the kinase Chk1 remains in a hypo-phosphorylated state. Elevated temperatures specifically reverse the DNA-damage-induced modification of Chk1 in a manner dependent on Rad9-M50. Taken together, heat reprogrammes the DNA damage checkpoint at the level of Chk1 by inducing a Rad9 variant that can act outside of the canonical 9-1-1 complex.
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Affiliation(s)
- Simon Janes
- Bangor University, Genome Biology Group, College of Natural Sciences, School of Biological Sciences, Brambell Building, Deiniol Road, Bangor LL57 2UW, UK
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7
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Esselen M, Fritz J, Hutter M, Marko D. Delphinidin Modulates the DNA-Damaging Properties of Topoisomerase II Poisons. Chem Res Toxicol 2009; 22:554-64. [DOI: 10.1021/tx800293v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Melanie Esselen
- Section of Food Toxicology, Institute of Applied Biosciences, Universität Karlsruhe (TH), Adenauerring 20a, 76131 Karlsruhe, Germany
| | - Jessica Fritz
- Section of Food Toxicology, Institute of Applied Biosciences, Universität Karlsruhe (TH), Adenauerring 20a, 76131 Karlsruhe, Germany
| | - Melanie Hutter
- Section of Food Toxicology, Institute of Applied Biosciences, Universität Karlsruhe (TH), Adenauerring 20a, 76131 Karlsruhe, Germany
| | - Doris Marko
- Section of Food Toxicology, Institute of Applied Biosciences, Universität Karlsruhe (TH), Adenauerring 20a, 76131 Karlsruhe, Germany
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8
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Deweese JE, Burgin AB, Osheroff N. Using 3'-bridging phosphorothiolates to isolate the forward DNA cleavage reaction of human topoisomerase IIalpha. Biochemistry 2008; 47:4129-40. [PMID: 18318502 DOI: 10.1021/bi702194x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to cleave DNA is critical to the cellular and pharmacological functions of human type II topoisomerases. However, the low level of cleavage at equilibrium and the tight coupling of the cleavage and ligation reactions make it difficult to characterize the mechanism by which these enzymes cut DNA. Therefore, to establish a system that isolates topoisomerase II-mediated DNA scission from ligation, oligonucleotide substrates were developed that contained a 3'-bridging phosphorothiolate at the scissile bond. Scission of these substrates generates a 3'-terminal -SH moiety that is a poor nucleophile relative to the normal 3'-terminal -OH group. Consequently, topoisomerase II cannot efficiently ligate phosphorothiolate substrates once they are cleaved. The characteristics of topoisomerase IIalpha-mediated cleavage of phosphorothiolate oligonucleotides were identical to those seen with wild-type substrates, except that no ligation was observed. This unidirectional accumulation of cleavage complexes provided critical information regarding coordination of the protomer subunits of topoisomerase IIalpha and the mechanism of action of topoisomerase II poisons. Results indicate that the two enzyme subunits are partially coordinated and that cleavage at one scissile bond increases the degree of cleavage at the other. Furthermore, anticancer drugs such as etoposide and amsacrine that strongly inhibit topoisomerase II-mediated DNA ligation have little effect on the forward scission reaction. In contrast, abasic sites that increase levels of cleavage complexes without affecting ligation stimulate the forward rate of scission. Phosphorothiolate substrates provide significant advantages over traditional "suicide substrates" and should be valuable for future studies on DNA scission and the topoisomerase II-DNA cleavage complex.
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Affiliation(s)
- Joseph E Deweese
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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9
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Štros M, Bačíková A, Polanská E, Štokrová J, Strauss F. HMGB1 interacts with human topoisomerase IIalpha and stimulates its catalytic activity. Nucleic Acids Res 2007; 35:5001-13. [PMID: 17636313 PMCID: PMC1976466 DOI: 10.1093/nar/gkm525] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 06/21/2007] [Accepted: 06/22/2007] [Indexed: 11/21/2022] Open
Abstract
DNA topoisomerase IIalpha (topo IIalpha) is an essential nuclear enzyme and its unique decatenation activity has been implicated in many aspects of chromosome dynamics such as chromosome replication and segregation during mitosis. Here we show that chromatin-associated protein HMGB1 (a member of the large family of HMG-box proteins with possible functions in DNA replication, transcription, recombination and DNA repair) promotes topo IIalpha-mediated catenation of circular DNA, relaxation of negatively supercoiled DNA and decatenation of kinetoplast DNA. HMGB1 interacts with topo IIalpha and this interaction, like the stimulation of the catalytic activity of the enzyme, requires both HMG-box domains of HMGB1. A mutant of HMGB1, which cannot change DNA topology stimulates DNA decatenation by topo IIalpha indistinguishably from the wild-type protein. Although HMGB1 stimulates ATP hydrolysis by topo IIalpha, the DNA cleavage is much more enhanced. The observed abilities of HMGB1 to interact with topo IIalpha and promote topo IIalpha binding to DNA suggest a mechanism by which HMGB1 stimulates the catalytic activity of the enzyme via enhancement of DNA cleavage.
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Affiliation(s)
- Michal Štros
- Laboratory of Analysis of Chromosomal Proteins, Academy of Sciences of the Czech Republic, Institute of Biophysics, Brno, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic and Centre de Recherche des Cordeliers, Université Pierre et Marie Curie, Paris, France
| | - Alena Bačíková
- Laboratory of Analysis of Chromosomal Proteins, Academy of Sciences of the Czech Republic, Institute of Biophysics, Brno, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic and Centre de Recherche des Cordeliers, Université Pierre et Marie Curie, Paris, France
| | - Eva Polanská
- Laboratory of Analysis of Chromosomal Proteins, Academy of Sciences of the Czech Republic, Institute of Biophysics, Brno, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic and Centre de Recherche des Cordeliers, Université Pierre et Marie Curie, Paris, France
| | - Jitka Štokrová
- Laboratory of Analysis of Chromosomal Proteins, Academy of Sciences of the Czech Republic, Institute of Biophysics, Brno, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic and Centre de Recherche des Cordeliers, Université Pierre et Marie Curie, Paris, France
| | - François Strauss
- Laboratory of Analysis of Chromosomal Proteins, Academy of Sciences of the Czech Republic, Institute of Biophysics, Brno, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic and Centre de Recherche des Cordeliers, Université Pierre et Marie Curie, Paris, France
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10
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Prescott TAK, Sadler IH, Kiapranis R, Maciver SK. Lunacridine from Lunasia amara is a DNA intercalating topoisomerase II inhibitor. JOURNAL OF ETHNOPHARMACOLOGY 2007; 109:289-94. [PMID: 16963212 DOI: 10.1016/j.jep.2006.07.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Revised: 06/29/2006] [Accepted: 07/27/2006] [Indexed: 05/11/2023]
Abstract
An ethnobotanical survey of plants used to treat tropical ulcers in Papua New Guinea identified Lunasia amara as possessing anti-Staphylococcus aureus activity. Activity-guided fractionation of the aqueous bark extract resulted in the identification of the quinoline alkaloid lunacridine as the active principle. Lunacridine tends to cyslise at room temperature but the 2'-O-trifluoroacetyl derivative was found to be stable and therefore more suitable for biological assays. The compound exhibited a minimal inhibitory concentration (MIC) of 64 micro g/ml against Staphylococcus aureus NCTC 6571 and activity in the low micromolar range against HeLa and H226 cells; the latter showing signs of caspase-3/7 mediated apoptotic cell death. Experiments with drug resistant strains of Streptococcus pneumoniae suggested topoisomerase as a likely target for the drug in bacteria whilst decatenation assays with human topoisomerase II showed the compound to be a potent inhibitor of this isoform (IC(50)<5 micro M) thus explaining the drug's activity against human cell lines. Both lunacridine and 2'-O-trifluoroacetyl lunacridine exhibited mild DNA intercalation activity giving 50% decrease in ethidium DNA fluorescence at 0.22 and 0.6 mM, respectively, placing the drug amongst the DNA intercalating class of topoisomerase II inhibitors.
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Affiliation(s)
- Thomas A K Prescott
- Centre for Integrative Physiology, College of Medicine, University of Edinburgh, Edinburgh, UK
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11
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Mirault ME, Boucher P, Tremblay A. Nucleotide-resolution mapping of topoisomerase-mediated and apoptotic DNA strand scissions at or near an MLL translocation hotspot. Am J Hum Genet 2006; 79:779-91. [PMID: 17033956 PMCID: PMC1698565 DOI: 10.1086/507791] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Accepted: 07/18/2006] [Indexed: 11/03/2022] Open
Abstract
The emergence of therapy-related acute myeloid leukemia (t-AML) has been associated with DNA topoisomerase II (TOP2)-targeted drug treatments and chromosomal translocations frequently involving the MLL, or ALL-1, gene. Two distinct mechanisms have been implicated as potential triggers of t-AML translocations: TOP2-mediated DNA cleavage and apoptotic higher-order chromatin fragmentation. Assessment of the role of TOP2 in this process has been hampered by a lack of techniques allowing in vivo mapping of TOP2-mediated DNA cleavage at nucleotide resolution in single-copy genes. A novel method, extension ligation-mediated polymerase chain reaction (ELMPCR), was used here for mapping topoisomerase-mediated DNA strand breaks and apoptotic DNA cleavage across a translocation-prone region of MLL in human cells. We report the first genomic map integrating translocation breakpoints and topoisomerase I, TOP2, and apoptotic DNA cleavage sites at nucleotide resolution across an MLL region harboring a t-AML translocation hotspot. This hotspot is flanked by a TOP2 cleavage site and is localized at one extremity of a minor apoptotic cleavage region, where multiple single- and double-strand breaks were induced by caspase-activated apoptotic nucleases. This cleavage pattern was in sharp contrast to that observed approximately 200 bp downstream in the exon 12 region, which displayed much stronger apoptotic cleavage but where no double-strand breaks were detected and no t-AML-associated breakpoints were reported. The localization and remarkable clustering of the t-AML breakpoints cannot be explained simply by the DNA cleavage patterns but might result from potential interactions between TOP2 poisoning, apoptotic DNA cleavage, and DNA repair attempts at specific sites of higher-order chromatin structure in apoptosis-evading cells. ELMPCR provides a new tool for investigating the role of DNA topoisomerases in fundamental genetic processes and translocations associated with cancer treatments involving topoisomerase-targeted drugs.
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Affiliation(s)
- Marc-Edouard Mirault
- Unit of Health and Environment, Centre de Recherche du Centre Hospitalier Universitaire de Quebec-Centre Hospitalier de l'Universite Laval, Quebec City, Quebec, Canada.
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12
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Au TK, Pathania S, Harshey RM. True reversal of Mu integration. EMBO J 2004; 23:3408-20. [PMID: 15282550 PMCID: PMC514517 DOI: 10.1038/sj.emboj.7600344] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Accepted: 07/05/2004] [Indexed: 01/02/2023] Open
Abstract
We describe a high-temperature (75 degrees C) transition in the Mu integration complex that causes efficient and true reversal of the integration reaction. A second reversal pathway, first described as 'foldback' reversal for the HIV integrase, was also observed upon disassembly/reassembly of the Mu complex at normal temperatures. Both true and foldback reversal severed only one or the other of the two integrated Mu ends, and each exhibited distinct metal ion specificities. Our results directly implicate an altered transposase configuration in the Mu strand transfer complex that inhibits reversal, thereby regulating the directionality of transposition.
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Affiliation(s)
- T K Au
- Section of Molecular Genetics and Microbiology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Shailja Pathania
- Section of Molecular Genetics and Microbiology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Rasika M Harshey
- Section of Molecular Genetics and Microbiology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Department of Microbiology, Section of Molecular Genetics and Microbiology, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1095, USA. Tel.: +1 512 471 6881; Fax: +1 512 471 7088; E-mail:
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13
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Whitmarsh RJ, Saginario C, Zhuo Y, Hilgenfeld E, Rappaport EF, Megonigal MD, Carroll M, Liu M, Osheroff N, Cheung NKV, Slater DJ, Ried T, Knutsen T, Blair IA, Felix CA. Reciprocal DNA topoisomerase II cleavage events at 5'-TATTA-3' sequences in MLL and AF-9 create homologous single-stranded overhangs that anneal to form der(11) and der(9) genomic breakpoint junctions in treatment-related AML without further processing. Oncogene 2003; 22:8448-59. [PMID: 14627986 DOI: 10.1038/sj.onc.1207052] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Few t(9;11) translocations in DNA topoisomerase II inhibitor-related leukemias have been studied in detail and the DNA damage mechanism remains controversial. We characterized the der(11) and der(9) genomic breakpoint junctions in a case of AML following etoposide and doxorubicin. Etoposide-, etoposide metabolite- and doxorubicin-induced DNA topoisomerase II cleavage was examined in normal homologues of the MLL and AF-9 breakpoint sequences using an in vitro assay. Induction of DNA topoisomerase II cleavage complexes in CEM and K562 cell lines was investigated using an in vivo complex of enzyme assay. The translocation occurred between identical 5'-TATTA-3' sequences in MLL intron 8 and AF-9 intron 5 without the gain or loss of bases. The 5'-TATTA-3' sequences were reciprocally cleaved by DNA topoisomerase II in the presence of etoposide, etoposide catechol or etoposide quinone, creating homologous 4-base 5' overhangs that would anneal to form both breakpoint junctions without any processing. der(11) and der(4) translocation breakpoints in a treatment-related ALL at the same site in MLL are consistent with a damage hotspot. Etoposide and both etoposide metabolites induced DNA topoisomerase II cleavage complexes in the hematopoietic cell lines. These results favor the model in which the chromosomal breakage leading to MLL translocations in DNA topoisomerase II inhibitor-related leukemias is a consequence of DNA topoisomerase II cleavage.
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MESH Headings
- Adolescent
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Histone-Lysine N-Methyltransferase
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Male
- Molecular Sequence Data
- Myeloid-Lymphoid Leukemia Protein
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Processing, Post-Translational
- Proto-Oncogenes
- Recombination, Genetic
- Transcription Factors
- Translocation, Genetic
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Affiliation(s)
- Ryan J Whitmarsh
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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14
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Bromberg KD, Burgin AB, Osheroff N. A two-drug model for etoposide action against human topoisomerase IIalpha. J Biol Chem 2003; 278:7406-12. [PMID: 12473657 DOI: 10.1074/jbc.m212056200] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The widely used anticancer drug etoposide kills cells by increasing levels of topoisomerase II-mediated DNA breaks. While it is known that the drug acts by inhibiting the ability of topoisomerase II to ligate cleaved DNA molecules, the precise mechanism by which it accomplishes this action is not well understood. Because there are two scissile bonds per enzyme-mediated double-stranded DNA break, it has been assumed that there are two sites for etoposide in every cleavage complex. However, it is not known whether the action of etoposide at only one scissile bond is sufficient to stabilize a double-stranded DNA break or whether both drug sites need to be occupied. An oligonucleotide system was utilized to address this important issue. Results of DNA cleavage and ligation assays support a two-drug model for the action of etoposide against human topoisomerase IIalpha. This model postulates that drug interactions at both scissile bonds are required in order to increase enzyme-mediated double-stranded DNA breaks. Etoposide actions at either of the two scissile bonds appear to be independent of one another, with each individual drug molecule stabilizing a strand-specific nick rather than a double-stranded DNA break. This finding suggests (at least in the presence of drug) that there is little or no communication between the two promoter active sites of topoisomerase II. The two-drug model has implications for cancer chemotherapy, the cellular processing of etoposide-stabilized enzyme-DNA cleavage complexes, and the catalytic mechanism of eukaryotic topoisomerase II.
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Affiliation(s)
- Kenneth D Bromberg
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Bromberg KD, Hendricks C, Burgin AB, Osheroff N. Human topoisomerase IIalpha possesses an intrinsic nucleic acid specificity for DNA ligation. Use of 5' covalently activated oligonucleotide substrates to study enzyme mechanism. J Biol Chem 2002; 277:31201-6. [PMID: 12050172 DOI: 10.1074/jbc.m204741200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite the importance of topoisomerase II-mediated DNA ligation to the essential physiological functions of the enzyme, the mechanistic details of this important reaction are poorly understood. Because topoisomerase II normally does not release cleaved DNA molecules prior to ligation, it is not known whether all of the nucleic acid specificity of its cleavage/ligation cycle is embodied in DNA cleavage or whether ligation also contributes specificity to the enzyme. All currently available ligation assays require that topoisomerase II cleave the initial DNA substrate before rejoining can be monitored. Consequently, it has been impossible to examine the specificity of DNA ligation separately from that of scission. To address this issue, a cleavage-independent topoisomerase II DNA ligation assay was developed. This assay utilizes a nicked oligonucleotide whose 5'-phosphate terminus at the nick has been activated by covalent attachment to the tyrosine mimic, p-nitrophenol. Human topoisomerase IIalpha and enzymes with active-site mutations that abrogated cleavage activity ligated the activated nick by catalyzing the direct attack of the terminal 3'-OH on the activated 5'-phosphate. Results with different DNA sequences indicate that human topoisomerase IIalpha possesses an intrinsic nucleic acid specificity for ligation that parallels its specificity for DNA cleavage.
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Affiliation(s)
- Kenneth D Bromberg
- Department of Biochemistry, Vanderbilt University School of Medicine, 654 Robinson Research Building, Nashville, TN 37232-0146, USA
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