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Gaikwad M, Konkimalla VB, Salunke-Gawali S. Metal complexes as topoisomerase inhibitors. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Orritt KM, Feng L, Newell JF, Sutton JN, Grossman S, Germe T, Abbott LR, Jackson HL, Bury BKL, Maxwell A, McPhillie MJ, Fishwick CWG. De novo design of type II topoisomerase inhibitors as potential antimicrobial agents targeting a novel binding region. RSC Med Chem 2022; 13:831-839. [PMID: 35919336 PMCID: PMC9298182 DOI: 10.1039/d2md00049k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
By 2050, it is predicted that antimicrobial resistance will be responsible for 10 million global deaths annually, more deaths than cancer, costing the world economy $100 trillion. Clearly, strategies to address this problem are essential as bacterial evolution is rendering our current antibiotics ineffective. The discovery of an allosteric binding site on the established antibacterial target DNA gyrase offers a new medicinal chemistry strategy. As this site is distinct from the fluoroquinolone binding site, resistance is not yet documented. Using in silico molecular design methods, we have designed and synthesised a novel series of biphenyl-based inhibitors inspired by a published thiophene-based allosteric inhibitor. This series was evaluated in vitro against Escherichia coli DNA gyrase and E. coli topoisomerase IV with the most potent compounds exhibiting IC50 values towards the low micromolar range for DNA gyrase and only ∼2-fold less active against topoisomerase IV. The structure–activity relationships reported herein suggest insights to further exploit this allosteric site, offering a pathway to overcome developing fluoroquinolone resistance. A computational design, make and test strategy was used to identify antibacterial inhibitors of bacterial DNA gyrase and topoisomerase IV, proposed to bind at a novel allosteric site.![]()
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Affiliation(s)
- Kyle M. Orritt
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Lipeng Feng
- Dept. Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Jack N. Sutton
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Scott Grossman
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Thomas Germe
- Dept. Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Lauren R. Abbott
- Dept. Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Anthony Maxwell
- Dept. Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Ubiquitous Nature of Fluoroquinolones: The Oscillation between Antibacterial and Anticancer Activities. Antibiotics (Basel) 2017; 6:antibiotics6040026. [PMID: 29112154 PMCID: PMC5745469 DOI: 10.3390/antibiotics6040026] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/26/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Fluoroquinolones are synthetic antibacterial agents that stabilize the ternary complex of prokaryotic topoisomerase II enzymes (gyrase and Topo IV), leading to extensive DNA fragmentation and bacteria death. Despite the similar structural folds within the critical regions of prokaryotic and eukaryotic topoisomerases, clinically relevant fluoroquinolones display a remarkable selectivity for prokaryotic topoisomerase II, with excellent safety records in humans. Typical agents that target human topoisomerases (such as etoposide, doxorubicin and mitoxantrone) are associated with significant toxicities and secondary malignancies, whereas clinically relevant fluoroquinolones are not known to exhibit such propensities. Although many fluoroquinolones have been shown to display topoisomerase-independent antiproliferative effects against various human cancer cells, those that are significantly active against eukaryotic topoisomerase show the same DNA damaging properties as other topoisomerase poisons. Empirical models also show that fluoroquinolones mediate some unique immunomodulatory activities of suppressing pro-inflammatory cytokines and super-inducing interleukin-2. This article reviews the extended roles of fluoroquinolones and their prospects as lead for the unmet needs of "small and safe" multimodal-targeting drug scaffolds.
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Sedigh-Shams M, Gholami A, Abbaszadegan A, Yazdanparast R, Saberi Nejad M, Safari A, Nabavizadeh M, Ghasemi Y. Antimicrobial Efficacy and Cytocompatibility of Calcium Hypochlorite Solution as a Root Canal Irrigant: An in Vitro Investigation. IRANIAN ENDODONTIC JOURNAL 2016; 11:169-74. [PMID: 27471525 PMCID: PMC4947838 DOI: 10.7508/iej.2016.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 03/11/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022]
Abstract
INTRODUCTION The purpose of this study was to compare the antimicrobial efficacy of sodium hypochlorite (SH) and calcium hypochlorite (CH) against Enterococcus faecalis (E. faecalis) using quantitative real-time polymerase chain reaction (qPCR) analysis and also to compare their cytocompatibility on L929 murine fibroblasts using Mossman's tetrazolium toxicity (MTT) assay. METHODS AND MATERIALS A broth micro-dilution susceptibility test was used to determine the minimum inhibitory concentration (MIC) of each irrigant against E. faecalis. Then, the root canals of 50 mature extracted human mandibular premolars were contaminated with E. faecalis and were randomly divided into three groups according to the irrigant used (n=20). Canals were irrigated with SH in group I (n=20) and CH in group II (n=20) at their obtained MIC. In group III (n=10), sterile saline was used. Microbial sampling was performed before and after biomechanical preparation. Quantitative PCR was used to quantify E. faecalis in the root canal samples. For cytocompatibility assessment, L929 murine fibroblasts were exposed to various concentrations of the irrigants. RESULTS Irrigation with test materials resulted in significant reduction in colony forming units (CFU) in post-instrumentation samples (with the MIC values of SH and CH against E. faecalis being 0.5% and 5%, respectively). However, the reduction in the normal saline group was not significant (P=0.203). In addition, 5% CH was more effective than 0.5% SH (P=0.006) in eliminating E. faecalis. Among the different concentrations of tested irrigants, 0.5% CH and 5% SH showed the least and the most cytotoxicity, respectively (P<0.001). The cytotoxicity of 5% CH and 0.5% SH was similar (P=0.99), and lower than 2.5% SH (P<0.001). CONCLUSION CH at an MIC of 5% was effective in eliminating E. faecalis in planktonic state and also its biofilm and exhibited comparable cytocompatibility to that of 0.5% SH.
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Affiliation(s)
- Mahdi Sedigh-Shams
- Department of Endodontics, Dental School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Gholami
- Pharmaceutical Sciences Research Center and Department of Pharmaceutical Biotechnology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Abbaszadegan
- Department of Endodontics, Dental School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Roohollah Yazdanparast
- Students' Research Committee, Dental School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Milad Saberi Nejad
- Students' Research Committee, Dental School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Azam Safari
- Pharmaceutical Sciences Research Center and Department of Pharmaceutical Biotechnology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammadreza Nabavizadeh
- Department of Endodontics, Dental School, Shiraz University of Medical Sciences, Shiraz, Iran; ; Prevention of Oral and Dental Diseases Research Center, Dental School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center and Department of Pharmaceutical Biotechnology, Shiraz University of Medical Sciences, Shiraz, Iran
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DNA topoisomerase II is involved in regulation of cyst wall protein genes and differentiation in Giardia lamblia. PLoS Negl Trop Dis 2013; 7:e2218. [PMID: 23696909 PMCID: PMC3656124 DOI: 10.1371/journal.pntd.0002218] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 04/04/2013] [Indexed: 12/16/2022] Open
Abstract
The protozoan Giardia lamblia differentiates into infectious cysts within the human intestinal tract for disease transmission. Expression of the cyst wall protein (cwp) genes increases with similar kinetics during encystation. However, little is known how their gene regulation shares common mechanisms. DNA topoisomerases maintain normal topology of genomic DNA. They are necessary for cell proliferation and tissue development as they are involved in transcription, DNA replication, and chromosome condensation. A putative topoisomerase II (topo II) gene has been identified in the G. lamblia genome. We asked whether Topo II could regulate Giardia encystation. We found that Topo II was present in cell nuclei and its gene was up-regulated during encystation. Topo II has typical ATPase and DNA cleavage activity of type II topoisomerases. Mutation analysis revealed that the catalytic important Tyr residue and cleavage domain are important for Topo II function. We used etoposide-mediated topoisomerase immunoprecipitation assays to confirm the binding of Topo II to the cwp promoters in vivo. Interestingly, Topo II overexpression increased the levels of cwp gene expression and cyst formation. Microarray analysis identified up-regulation of cwp and specific vsp genes by Topo II. We also found that the type II topoisomerase inhibitor etoposide has growth inhibition effect on Giardia. Addition of etoposide significantly decreased the levels of cwp gene expression and cyst formation. Our results suggest that Topo II has been functionally conserved during evolution and that Topo II plays important roles in induction of the cwp genes, which is key to Giardia differentiation into cysts. Giardia lamblia becomes infective by differentiation into water-resistant cysts. During encystation, cyst wall proteins (CWPs) are highly synthesized and are targeted to the cyst wall. However, little is known about the regulation mechanisms of these genes. DNA topoisomerases can resolve the topological problems and are needed for a variety of key cellular functions, including cell proliferation, cell differentiation and organ development in higher eukaryotes. We found that giardial Topo II was highly expressed during encystation. Topo II is present in Giardia nuclei and is associated with the encystation-induced cwp gene promoters. Topo II has typical DNA cleavage activity of type II topoisomerases. Interestingly, overexpression of Topo II can induce cwp gene expression and cyst formation. Addition of a type II topoisomerase inhibitor, etoposide, significantly decreased the levels of cwp gene expression and cyst formation. Etoposide also has growth inhibition effect on Giardia. Our results suggest that Topo II plays an important role in induction of encystation by up-regulation of the cwp gene expression. Our results provide insights into the function of Topo II in parasite differentiation into cysts and help develop ways to interrupt the parasite life cycle.
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Physalin B from Physalis angulata triggers the NOXA-related apoptosis pathway of human melanoma A375 cells. Food Chem Toxicol 2012; 50:619-24. [DOI: 10.1016/j.fct.2011.12.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 11/25/2011] [Accepted: 12/08/2011] [Indexed: 11/22/2022]
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Forterre P. Introduction and Historical Perspective. CANCER DRUG DISCOVERY AND DEVELOPMENT 2012. [DOI: 10.1007/978-1-4614-0323-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Chelouah S, Monod-Wissler C, Bailly C, Barret JM, Guilbaud N, Vispé S, Käs E. An integrated Drosophila model system reveals unique properties for F14512, a novel polyamine-containing anticancer drug that targets topoisomerase II. PLoS One 2011; 6:e23597. [PMID: 21853156 PMCID: PMC3154508 DOI: 10.1371/journal.pone.0023597] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 07/21/2011] [Indexed: 11/19/2022] Open
Abstract
F14512 is a novel anti-tumor molecule based on an epipodophyllotoxin core coupled to a cancer-cell vectoring spermine moiety. This polyamine linkage is assumed to ensure the preferential uptake of F14512 by cancer cells, strong interaction with DNA and potent inhibition of topoisomerase II (Topo II). The antitumor activity of F14512 in human tumor models is significantly higher than that of other epipodophyllotoxins in spite of a lower induction of DNA breakage. Hence, the demonstrated superiority of F14512 over other Topo II poisons might not result solely from its preferential uptake by cancer cells, but could also be due to unique effects on Topo II interactions with DNA. To further dissect the mechanism of action of F14512, we used Drosophila melanogaster mutants whose genetic background leads to an easily scored phenotype that is sensitive to changes in Topo II activity and/or localization. F14512 has antiproliferative properties in Drosophila cells and stabilizes ternary Topo II/DNA cleavable complexes at unique sites located in moderately repeated sequences, suggesting that the drug specifically targets a select and limited subset of genomic sequences. Feeding F14512 to developing mutant Drosophila larvae led to the recovery of flies expressing a striking phenotype, "Eye wide shut," where one eye is replaced by a first thoracic segment. Other recovered F14512-induced gain- and loss-of-function phenotypes similarly correspond to precise genetic dysfunctions. These complex in vivo results obtained in a whole developing organism can be reconciled with known genetic anomalies and constitute a remarkable instance of specific alterations of gene expression by ingestion of a drug. "Drosophila-based anticancer pharmacology" hence reveals unique properties for F14512, demonstrating the usefulness of an assay system that provides a low-cost, rapid and effective complement to mammalian models and permits the elucidation of fundamental mechanisms of action of candidate drugs of therapeutic interest in humans.
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Affiliation(s)
- Sonia Chelouah
- Université de Toulouse, UPS, Université Paul Sabatier, Laboratoire de Biologie Moléculaire Eucaryote; Toulouse; France
- CNRS, Centre National de la Recherche Scientifique, UMR5099, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France
| | - Caroline Monod-Wissler
- Université de Toulouse, UPS, Université Paul Sabatier, Laboratoire de Biologie Moléculaire Eucaryote; Toulouse; France
- CNRS, Centre National de la Recherche Scientifique, UMR5099, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France
| | - Christian Bailly
- Centre de Recherche en Oncologie Expérimentale, Institut de Recherche Pierre Fabre, Toulouse, France
| | - Jean-Marc Barret
- Centre de Recherche en Oncologie Expérimentale, Institut de Recherche Pierre Fabre, Toulouse, France
| | - Nicolas Guilbaud
- Centre de Recherche en Oncologie Expérimentale, Institut de Recherche Pierre Fabre, Toulouse, France
| | - Stéphane Vispé
- Centre de Recherche en Oncologie Expérimentale, Institut de Recherche Pierre Fabre, Toulouse, France
- * E-mail: (EK); (SV)
| | - Emmanuel Käs
- Université de Toulouse, UPS, Université Paul Sabatier, Laboratoire de Biologie Moléculaire Eucaryote; Toulouse; France
- CNRS, Centre National de la Recherche Scientifique, UMR5099, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France
- * E-mail: (EK); (SV)
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Singh PK, Chan PF, Hibbs MJ, Vazquez MJ, Segura DC, Thomas DA, Theobald AJ, Gallagher KT, Hassan NJ. High-yield production and characterization of biologically active GST-tagged human topoisomerase IIα protein in insect cells for the development of a high-throughput assay. Protein Expr Purif 2010; 76:165-72. [PMID: 20709174 DOI: 10.1016/j.pep.2010.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 08/05/2010] [Accepted: 08/05/2010] [Indexed: 10/19/2022]
Abstract
DNA topoisomerase type II enzymes are well-validated targets of anti-bacterial and anti-cancer compounds. In order to facilitate discovery of these types of inhibitors human topoisomerase II in vitro assays can play an important role to support drug discovery processes. Typically, human topoisomerase IIα proteins have been purified from human cell lines or as untagged proteins from yeast cells. This study reports a method for the rapid over-expression and purification of active GST-tagged human topoisomerase IIα using the baculovirus mediated insect cell expression system. Expression of the GST fused protein was observed in the nuclear fraction of insect cells. High yields (40 mg/L i.e. 8 mg/10(9) cells) at >80% purity of this target was achieved by purification using a GST HiTrap column followed by size exclusion chromatography. Functional activity of GST-tagged human topoisomerase IIα was demonstrated by ATP-dependent relaxation of supercoiled DNA in an agarose gel based assay. An 8-fold DNA-dependent increase in ATPase activity of this target compared to its intrinsic activity was also demonstrated in a high-throughput ATPase fluorescence based assay. Human topoisomerase IIα inhibitors etoposide, quercetin and suramin were tested in the fluorescence assay. IC(50) values obtained were in good agreement with published data. These inhibitors also demonstrated ≥ 30-fold potency over the anti-bacterial topoisomerase II inhibitor ciprofloxacin in the assay. Collectively these data validated the enzyme and the high-throughput fluorescence assay as tools for inhibitor identification and selectivity studies.
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Affiliation(s)
- Praveen K Singh
- Biological Reagents & Assay Development, GlaxoSmithKline R&D, New Frontiers Science Park, Harlow, Essex, UK.
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McClendon AK, Gentry AC, Dickey JS, Brinch M, Bendsen S, Andersen AH, Osheroff N. Bimodal recognition of DNA geometry by human topoisomerase II alpha: preferential relaxation of positively supercoiled DNA requires elements in the C-terminal domain. Biochemistry 2008; 47:13169-78. [PMID: 19053267 PMCID: PMC2629653 DOI: 10.1021/bi800453h] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human topoisomerase IIalpha, but not topoisomerase IIbeta, can sense the geometry of DNA during relaxation and removes positive supercoils >10-fold faster than it does negative superhelical twists. In contrast, both isoforms maintain lower levels of DNA cleavage intermediates with positively supercoiled substrates. Since topoisomerase IIalpha and IIbeta differ primarily in their C-terminal domains (CTD), this portion of the protein may play a role in sensing DNA geometry. Therefore, to more fully assess the importance of the topoisomerase IIalpha CTD in the recognition of DNA topology, hTop2alphaDelta1175, a mutant human enzyme that lacks its CTD, was examined. The mutant enzyme relaxed negative and positive supercoils at similar rates but still maintained lower levels of cleavage complexes with positively supercoiled DNA. Furthermore, when the CTD of topoisomerase IIbeta was replaced with that of the alpha isoform, the resulting enzyme preferentially relaxed positively supercoiled substrates. In contrast, a chimeric topoisomerase IIalpha that carried the CTD of the beta isoform lost its ability to recognize the geometry of DNA supercoils during relaxation. These findings demonstrate that human topoisomerase IIalpha recognizes DNA geometry in a bimodal fashion, with the ability to preferentially relax positive DNA supercoils residing in the CTD. Finally, results with a series of human topoisomerase IIalpha mutants suggest that clusters of positively charged amino acid residues in the CTD are required for the enzyme to distinguish supercoil geometry during DNA relaxation and that deletion of even the most C-terminal cluster abrogates this recognition.
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MESH Headings
- Amino Acid Sequence
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Binding Sites/genetics
- DNA Cleavage
- DNA Topoisomerases, Type II/chemistry
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA-Binding Proteins/antagonists & inhibitors
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Humans
- Molecular Sequence Data
- Protein Structure, Tertiary/genetics
- Sequence Deletion
- Topoisomerase II Inhibitors
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Affiliation(s)
- A Kathleen McClendon
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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11
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Rao SS, Savithri HS, Raghunathan M. Down regulation of gyrase A gene expression in E. coli by antisense ribozymes using RT-PCR. Mol Biol Rep 2007; 35:575-8. [PMID: 17701288 DOI: 10.1007/s11033-007-9126-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 07/26/2007] [Indexed: 11/28/2022]
Abstract
Nucleic acid-based gene interference technologies represent promising strategies for specific inhibition of mRNA sequences of choice. Recently, small interfering RNAs have been implicated in inducing endogenous RNase of the RNA-induced silencing complex in the RNA interference pathway to inhibit gene expression and growth of several human viruses. We report down regulation of gene expression of E. coli gyrase A, an essential gene for DNA supercoiling and antibiotic susceptibility in BL21 (DE3) strain of E. coli, using Ribonuclease P based external guide sequence (EGS) technique. EGS directed against gyrase A gene that was cloned into pUC vector, which contains the ampicillin (Amp) resistance gene. The recombinant plasmid pT7EGyrA was transformed into BL21 (DE3) and inductions were performed using IPTG. RT-PCR experiment was done to investigate the down regulation of gyrase A gene. RT-PCR results demonstrated a significant decrease of gyrase A gene after 18 h of induction of the transformants. These experiments showed that the down regulation of the gene was seen after 18 h of induction than earlier hours of induction with IPTG suggesting inhibition of gyrase A gene with profound effect on cell viability. These results demonstrate the utility of EGS RNAs in gene therapy applications, by inhibiting the expression of essential proteins.
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Affiliation(s)
- Shilpakala Sainath Rao
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600 113, India
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12
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McClendon AK, Dickey JS, Osheroff N. Ability of viral topoisomerase II to discern the handedness of supercoiled DNA: bimodal recognition of DNA geometry by type II enzymes. Biochemistry 2006; 45:11674-80. [PMID: 16981727 PMCID: PMC2517260 DOI: 10.1021/bi0520838] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previous studies with human and bacterial topoisomerases suggest that the type II enzyme utilizes two distinct mechanisms to recognize the handedness of DNA supercoils. It has been proposed that the ability of some type II enzymes, such as human topoisomerase IIalpha and Escherichia coli topoisomerase IV, to distinguish supercoil geometry during DNA relaxation is mediated by elements in the variable C-terminal domain of the protein. In contrast, the ability of human topoisomerase IIalpha and topoisomerase IIbeta to discern the handedness of supercoils during DNA cleavage suggests that residues in the conserved N-terminal or central domain of the protein are involved in this process. To test this hypothesis, the ability of Paramecium bursaria chlorella virus-1 (PBCV-1) and chlorella virus Marburg-1 (CVM-1) topoisomerase II to relax and cleave negatively and positively supercoiled plasmids was assessed. These enzymes display a high degree of sequence identity with the N-terminal and central domains of eukaryotic topoisomerase II but naturally lack the C-terminal domain. While PBCV-1 and CVM-1 topoisomerase II relaxed under- and overwound substrates at similar rates, they were able to discern the handedness of supercoils during the cleavage reaction and preferentially cut negatively supercoiled DNA. Preferential cleavage was not due to a change in site specificity, DNA binding, or religation. These findings are consistent with a bimodal recognition of DNA geometry in which topoisomerase II uses elements in the C-terminal domain to sense the handedness of supercoils during DNA relaxation and elements in the conserved N-terminal or central domain during DNA cleavage.
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Affiliation(s)
| | | | - Neil Osheroff
- To whom correspondence should be addressed. Tel: 615−322−4338. Fax: 615−343−1166. E-mail:
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Dickey JS, Choi TJ, Van Etten JL, Osheroff N. Chlorella virus Marburg topoisomerase II: high DNA cleavage activity as a characteristic of Chlorella virus type II enzymes. Biochemistry 2005; 44:3899-908. [PMID: 15751965 DOI: 10.1021/bi047777f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the formation of a covalent enzyme-cleaved DNA complex is a prerequisite for the essential functions of topoisomerase II, this reaction intermediate has the potential to destabilize the genome. Consequently, all known eukaryotic type II enzymes maintain this complex at a low steady-state level. Recently, however, a novel topoisomerase II was discovered in Paramecium bursaria chlorella virus-1 (PBCV-1) that has an exceptionally high DNA cleavage activity [Fortune et al. (2001) J. Biol. Chem. 276, 24401-24408]. If robust DNA cleavage is critical to the physiological functions of chlorella virus topoisomerase II, then this remarkable characteristic should be conserved throughout the viral family. Therefore, topoisomerase II from Chlorella virus Marburg-1 (CVM-1), a distant family member, was expressed in yeast, isolated, and characterized. CVM-1 topoisomerase II is 1058 amino acids in length, making it the smallest known type II enzyme. The viral topoisomerase II displayed a high DNA strand passage activity and a DNA cleavage activity that was approximately 50-fold greater than that of human topoisomerase IIalpha. High DNA cleavage appeared to result from a greater rate of scission rather than promiscuous DNA site utilization, inordinately tight DNA binding, or diminished religation rates. Despite the fact that CVM-1 and PBCV-1 topoisomerase II share approximately 67% amino acid sequence identity, the two enzymes displayed clear differences in their DNA cleavage specificity/site utilization. These findings suggest that robust DNA cleavage is intrinsic to the viral enzyme and imply that chlorella virus topoisomerase II plays a physiological role beyond the control of DNA topology.
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Affiliation(s)
- Jennifer S Dickey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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14
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Sengupta T, Mukherjee M, Das R, Das A, Majumder HK. Characterization of the DNA-binding domain and identification of the active site residue in the 'Gyr A' half of Leishmania donovani topoisomerase II. Nucleic Acids Res 2005; 33:2364-73. [PMID: 15860773 PMCID: PMC1087781 DOI: 10.1093/nar/gki527] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
DNA topoisomerase II is a multidomain homodimeric enzyme that changes DNA topology by coupling ATP hydrolysis to the transport of one DNA helix through a transient double-stranded break in another. To investigate the biochemical properties of the individual domains of Leishmania donovani topoisomerase II, four truncation mutants were generated. Deletion of 178 aminoacids from the C-terminus (core and LdΔC1058) had no apparent effect on the DNA-binding or cleavage activities of the enzymes. However, when 429 aminoacids from the N-terminus and 451 aminoacids from the C-terminus were removed (LdΔNΔC), the enzyme was no longer active. Moreover, the removal of 429 aminoacids from the N-terminus (LdΔNΔC, core and LdΔN429) render the mutant proteins incapable of performing ATP hydrolysis. The mutant proteins show cleavage activities at wide range of KCl concentrations (25–350 mM). In addition, the mutant proteins, excepting LdΔNΔC, can also act on kDNA and linearize the minicircles. Surprisingly, the mutant proteins fail to show the formation of the enhanced cleavable complex in the presence of etoposide. Our findings suggest that the conformation required for interaction with the drug is absent in the mutant proteins. Here, we have also identified Tyr775 through direct sequencing of the DNA linked peptide as the catalytic residue implicated in DNA-breakage and rejoining. Taken together, our results demonstrate that topoisomerase II are functionally and mechanistically conserved enzymes and the variations in activity seem to reflect functional optimization for its physiological role during parasite genome replication.
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Affiliation(s)
| | | | | | - Aditi Das
- Sealy Center for Molecular Sciences, University of TexasMedical Branch, Galveston, USA
| | - Hemanta K. Majumder
- To whom correspondence should be addressed. Tel: +91 33 2412 3207; Fax: +91 33 2473 5197;
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15
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Baldwin EL, Byl JAW, Osheroff N. Cobalt Enhances DNA Cleavage Mediated by Human Topoisomerase IIαin Vitroand in Cultured Cells†. Biochemistry 2004; 43:728-35. [PMID: 14730977 DOI: 10.1021/bi035472f] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although cobalt is an essential trace element for humans, the metal is genotoxic and mutagenic at higher concentrations. Treatment of cells with cobalt generates DNA strand breaks and covalent protein-DNA complexes. However, the basis for these effects is not well understood. Since the toxic events induced by cobalt resemble those of topoisomerase II poisons, the effect of the metal on human topoisomerase IIalpha was examined. The level of enzyme-mediated DNA scission increased 6-13-fold when cobalt(II) replaced magnesium(II) in cleavage reactions. Cobalt(II) stimulated cleavage at all DNA sites observed in the presence of magnesium(II), and the enzyme cut DNA at several "cobalt-specific" sites. The increased level of DNA cleavage in the presence of cobalt(II) was partially due to a decrease in the rate of enzyme-mediated religation. Topoisomerase IIalpha retained many of its catalytic properties in reactions that included cobalt(II), including sensitivity to the anticancer drug etoposide and the ability to relax and decatenate DNA. Finally, cobalt(II) stimulated topoisomerase IIalpha-mediated DNA cleavage in the presence of magnesium(II) in purified systems and in human MCF-7 cells. These findings demonstrate that cobalt(II) is a topoisomerase II poison in vitro and in cultured cells and suggest that at least some of the genotoxic effects of the metal are mediated through topoisomerase IIalpha.
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Affiliation(s)
- Erin L Baldwin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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16
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Hettiarachchi GHCM, Yadav V, Reddy MK, Chattopadhyay S, Sopory SK. Light-mediated regulation defines a minimal promoter region of TOP2. Nucleic Acids Res 2003; 31:5256-65. [PMID: 12954761 PMCID: PMC203327 DOI: 10.1093/nar/gkg744] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Revised: 07/30/2003] [Accepted: 07/30/2003] [Indexed: 11/12/2022] Open
Abstract
Light signaling has been demonstrated to be an important factor for plant growth and development; however, its role in the regulation of DNA replication and cell cycle has just started to be unraveled. In this work, we have demonstrated that the TOP2 promoter of Pisum sativum (pea) is activated by a broad spectrum of light including far-red light (FR), red light (RL) and blue light (BL). Deletion analyses of the TOP2 promoter in transformed plants, Arabidopsis thaliana and Nicotiana tobaccum (tobacco), define a minimal promoter region that is induced by RL, FR and BL, and is essential and sufficient for light-mediated activation. The minimal promoter of TOP2 follows the phytochrome- mediated low-fluence response similar to complex light regulated promoters. DNA-protein interaction studies reveal the presence of a DNA binding activity specific to a 106 bp region of the minimal promoter that is crucial for light-mediated activation. These results altogether indicate a direct involvement of light signaling in the regulation of expression of TOP2, one of the components of the DNA replication/cell cycle machinery.
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MESH Headings
- Arabidopsis/enzymology
- Arabidopsis/genetics
- Arabidopsis/radiation effects
- Base Sequence
- Binding Sites/genetics
- Cells, Cultured
- Cotyledon/enzymology
- Cotyledon/genetics
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Electrophoretic Mobility Shift Assay
- Gene Expression Regulation, Enzymologic/radiation effects
- Gene Expression Regulation, Plant/radiation effects
- Glucuronidase/genetics
- Glucuronidase/metabolism
- Hypocotyl/enzymology
- Hypocotyl/genetics
- Light
- Molecular Sequence Data
- Oligonucleotides/genetics
- Oligonucleotides/metabolism
- Pisum sativum/enzymology
- Pisum sativum/genetics
- Pisum sativum/radiation effects
- Phytochrome/metabolism
- Plants, Genetically Modified
- Promoter Regions, Genetic/genetics
- Protein Binding
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Regulatory Sequences, Nucleic Acid/genetics
- Nicotiana/cytology
- Nicotiana/enzymology
- Nicotiana/genetics
- Nicotiana/radiation effects
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Affiliation(s)
- G H C M Hettiarachchi
- National Center for Plant Genome Research, PO Box 10531, JNU Campus, New Delhi 110067, India
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17
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Cortés F, Pastor N. Induction of endoreduplication by topoisomerase II catalytic inhibitors. Mutagenesis 2003; 18:105-12. [PMID: 12621064 DOI: 10.1093/mutage/18.2.105] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The striking phenomenon of endoreduplication has long attracted attention from cytogeneticists and researchers into cell cycle enzymology and dynamics alike. Because of the variety of agents able to induce endoreduplication and the various cell types where it has been described, until now no clear or unique mechanism of induction of this phenomenon, rare in animals but otherwise quite common in plants, has been proposed. Recent years, however, have witnessed the unfolding of a number of essential physiological roles for DNA topoisomerase II, with special emphasis on its major role in mitotic chromosome segregation after DNA replication. In spite of the lack of mammalian mutants defective in topoisomerase II as compared with yeast, experiments with inhibitors of the enzyme have supported the hypothesis that this crucial untangling of daughter DNA molecules by passing an intact helix through a transient double-stranded break carried out by the enzyme, when it fails, leads to aberrant mitosis that results in endoreduplication, polyploidy and eventually cell death. Anticancer drugs that interfere with topoisomerase II can be classified into two groups. The classical poisons act by stabilizing the enzyme in the so-called cleavable complex and result in DNA damage, which represents a problem in the study of endoreduplication. The true catalytic inhibitors, which are not cleavable complex stabilizers, allow us to use doses efficient in the induction of endoreduplication while eliminating high levels of DNA and chromosome damage. This review will discuss the basic and applied aspects of this as yet scarcely explored field.
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Affiliation(s)
- Felipe Cortés
- Department of Cell Biology, Faculty of Biology, University of Seville, Av Reina Mercedes, 6, E-41012 Seville, Spain.
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18
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Campbell S, Maxwell A. The ATP-operated clamp of human DNA topoisomerase IIalpha: hyperstimulation of ATPase by "piggy-back" binding. J Mol Biol 2002; 320:171-88. [PMID: 12079377 DOI: 10.1016/s0022-2836(02)00461-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have constructed a series of clones encoding N-terminal fragments of human DNA topoisomerase IIalpha. All fragments exhibit DNA-dependent ATPase activity. Fragment 1-420 shows hyperbolic dependence of ATPase on DNA concentration, whereas fragment 1-453 shows hyperstimulation at low ratios of DNA to enzyme, a phenomenon found previously with the full-length enzyme. The minimum length of DNA found to stimulate the ATPase activity was approximately 10 bp; fragments >or=32 bp manifest the hyperstimulation phenomenon. Molecular mass studies show that fragment 1-453 is a monomer in the absence of nucleotides and a dimer in the presence of nucleotide triphosphate. The results are consistent with the role of the N-terminal domain of topoisomerase II as an ATP-operated clamp that dimerises in the presence of ATP. The hyperstimulation effect can be interpreted in terms of a "piggy-back binding" model for protein-DNA interaction.
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Affiliation(s)
- Spencer Campbell
- Department of Biochemistry, University of Leicester, Leicester LE1 7RH, UK
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19
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Abstract
The fluoroquinolone ciprofloxacin is widely used in antimicrobial therapy. It inhibits the bacterial gyrase and in high concentrations in vitro also the functionally related eukaryotic topoisomerase-II, which resulted in genotoxic effects in several in vitro tests. In order to evaluate the relevance of these findings, ciprofloxacin was tested in vivo for genotoxic activity using the following test systems: micronucleus test in bone marrow of mice, cytogenetic chromosome analysis in Chinese hamster, dominant lethal assay in male mice and UDS tests in primary rat and mouse hepatocytes in vivo. These results are compared with already published in vitro and in vivo studies with ciprofloxacin. All in vivo genotoxicity revealed no genotoxic effect for ciprofloxacin. In addition, ciprofloxacin was found to be non-carcinogenic in two rodent long-term bioassays. Therefore, ciprofloxacin is considered to be safe for therapeutic use.
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Affiliation(s)
- B A Herbold
- Bayer AG, PH-PD Toxikologie, Gentoxikologie, Gebäude 514, Postfach 101709, D-42096 Wuppertal, Germany.
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20
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McKinney J, Guerrier-Takada C, Wesolowski D, Altman S. Inhibition of Escherichia coli viability by external guide sequences complementary to two essential genes. Proc Natl Acad Sci U S A 2001; 98:6605-10. [PMID: 11381134 PMCID: PMC34400 DOI: 10.1073/pnas.121180398] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Narrow spectrum antimicrobial activity has been designed to reduce the expression of two essential genes, one coding for the protein subunit of RNase P (C5 protein) and one for gyrase (gyrase A). In both cases, external guide sequences (EGS) have been designed to complex with either mRNA. Using the EGS technology, the level of microbial viability is reduced to less than 10% of the wild-type strain. The EGSs are additive when used together and depend on the number of nucleotides paired when attacking gyrase A mRNA. In the case of gyrase A, three nucleotides unpaired out of a 15-mer EGS still favor complete inhibition by the EGS but five unpaired nucleotides do not.
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Affiliation(s)
- J McKinney
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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21
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Brevini-Gandolfi TA, Cillo F, Favetta LA, Montagna A, Motta M. Somatostatin up-regulates topoisomerase II alpha expression and affects LNCaP cell cycle. Mol Cell Endocrinol 2001; 176:103-10. [PMID: 11369449 DOI: 10.1016/s0303-7207(01)00448-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
mRNA differential display-PCR analysis was used to perform a systematic screening of Somatostatin (SS)-regulated genes in the human prostatic carcinoma cell line LNCaP (Lymph Node Carcinoma of the Prostate). A 170 bp fragment was shown to be up-regulated by SS. Sequence analysis of this fragment revealed its homology with the human Topoisomerase II Alpha gene. Up-regulation of Topoisomerase II Alpha was confirmed by Northern blot hybridisation and was induced by the same dose of SS (1 nM) earlier demonstrated to inhibit LNCaP cell growth. Furthermore, SS possible effects on timing, as well as concentration of Topoisomerase II Alpha along the different phases of the cell cycle were investigated. To this purpose changes in the enzyme protein concentration in response to SS were assessed in synchronised LNCaP cells. The hormone was shown to exert a perturbing effect on both parameters considered, possibly related to its inhibitory action on LNCaP cell replication.
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MESH Headings
- Antigens, Neoplasm
- Base Sequence
- Blotting, Northern
- Blotting, Western
- Cell Cycle/drug effects
- Cell Division/drug effects
- Cloning, Molecular
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA-Binding Proteins
- Enzyme-Linked Immunosorbent Assay
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Male
- Molecular Sequence Data
- Polymerase Chain Reaction
- Prostatic Neoplasms/enzymology
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/pathology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Homology, Amino Acid
- Somatostatin/pharmacology
- Tumor Cells, Cultured
- Up-Regulation/drug effects
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Affiliation(s)
- T A Brevini-Gandolfi
- Centre for Endocrinological Oncology, Department of Endocrinology, University of Milan, Milan, Italy.
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22
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Gemkow MJ, Dichter J, Arndt-Jovin DJ. Developmental regulation of DNA-topoisomerases during Drosophila embryogenesis. Exp Cell Res 2001; 262:114-21. [PMID: 11139335 DOI: 10.1006/excr.2000.5084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Type I and type II DNA-topoisomerases are essential enzymes that mediate replication, transcription, recombination, and mitosis in multicellular eukaryotes but the extent of their interchange for specific reactions in vivo is controversial. Expression patterns for topoisomerase I and topoisomerase II during the embryogenesis of Drosophila melanogaster were compared with patterns of DNA replication and expression of the histone genes. In late oogenesis the maternally supplied top2 mRNA was evenly distributed throughout the egg with elevated levels at the posterior tip, a pattern that is maintained in syncytial blastoderm embryos. During gastrulation, top2 mRNA became differentially localized only to regions of DNA replication, including new expression in the gonads preceding mitosis/meiosis. Significantly higher levels of top2 mRNA were found in mitotic compared to endoreplicating tissues. The total histone mRNA was exclusively associated with DNA replication but, in contrast to top2 mRNA, mitotic and endoreplicating cells contained similar expression levels with no expression in the gonads. Striking differences exist between the distribution of the top2 mRNA and topoisomerase II protein. The protein localizes to all evolving nuclei where it persists throughout embryogenesis. A high level of top1 mRNA transcript was present without differential tissue distribution throughout embryogenesis.
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Affiliation(s)
- M J Gemkow
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, 37070, Germany
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23
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Petruti-Mot AS, Earnshaw WC. Two differentially spliced forms of topoisomerase IIalpha and beta mRNAs are conserved between birds and humans. Gene 2000; 258:183-92. [PMID: 11111056 DOI: 10.1016/s0378-1119(00)00465-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Screening of chicken cDNA libraries has identified four distinct forms of topoisomerase IIalpha and beta cDNAs. Two of these, designated topo IIalpha-1 and topo IIbeta-1, were previously deposited in the database. The other two, topo IIalpha-2 and topo IIbeta-2, are novel variants that appear to be conserved between chicken and human. Topo IIalpha-2 encodes a protein with an additional 35 amino acids inserted after K321 of the chicken topo IIalpha-1 protein sequence. Topo IIbeta-2 encodes a protein missing 86 amino acids following V27 in the topo IIbeta-1 protein sequence. We have also detected several alternatively spliced forms of human topo IIalpha. One of these, topo IIalpha-3, appears to correspond to chicken topo IIalpha-2. The other two are novel. The existence of these alternatively spliced forms in mature cytoplasmic RNA was confirmed by RT-PCR in several cell lines. Interestingly, these alternatively spliced forms carry sites for post-translational modification, suggesting that they may be subject to differential regulation from the canonical forms. These results suggest that cells express a more complex repertoire of topo II isoforms than previously thought, raising the possibility that different forms of topo II may fulfil specialized functions in chromosome dynamics.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Antigens, Neoplasm
- Base Sequence
- Chickens/genetics
- Conserved Sequence
- DNA/chemistry
- DNA/genetics
- DNA Topoisomerases, Type II/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA-Binding Proteins
- Genetic Variation
- HeLa Cells
- Humans
- Isoenzymes/genetics
- Molecular Sequence Data
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tumor Cells, Cultured
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Affiliation(s)
- A S Petruti-Mot
- Wellcome Centre for Cell Biology, Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
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24
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Robertson JD, Gogvadze V, Zhivotovsky B, Orrenius S. Distinct pathways for stimulation of cytochrome c release by etoposide. J Biol Chem 2000; 275:32438-43. [PMID: 10961984 DOI: 10.1074/jbc.c000518200] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Induction of apoptosis by DNA-damaging agents, such as etoposide, is known to involve the release of mitochondrial cytochrome c, although the mechanism responsible for this event is unclear. In the present study, using Jurkat T-lymphocytes, a reconstituted cell-free system, or isolated liver mitochondria, we demonstrate the ability of etoposide to induce cytochrome c release via two distinct pathways. Caspase inhibition by either benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl ketone (z-VAD-fmk) or benzyloxycarbonyl-Val-Asp-Val-Ala-Asp-fluoromethyl ketone (z-VDVAD-fmk) attenuates cytochrome c release triggered by a low dose of etoposide via an apparent inhibition of nuclear events involving the release of protein factor(s) that is (are) able to interact with mitochondria. In contrast, caspase inhibition has no effect on cytochrome c release induced by a higher dose of etoposide. Moreover, the higher dose of etoposide heightens the sensitivity of Ca(2+)-loaded isolated mitochondria to mitochondrial permeability transition, an effect that is completely abolished by cyclosporin A. Interestingly, cyclosporin A is ineffective at preventing similar mitochondrial damage in Jurkat cells treated with etoposide. We propose that lower doses of etoposide predominantly target the nucleus and stimulate the release of caspase-sensitive protein factor(s) that interact with mitochondria to trigger cytochrome c release, whereas higher doses of the drug impart a more direct effect on mitochondria and thus are not mitigated by caspase inhibition.
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Affiliation(s)
- J D Robertson
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden.
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25
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Bjergbaek L, Kingma P, Nielsen IS, Wang Y, Westergaard O, Osheroff N, Andersen AH. Communication between the ATPase and cleavage/religation domains of human topoisomerase IIalpha. J Biol Chem 2000; 275:13041-8. [PMID: 10777608 DOI: 10.1074/jbc.275.17.13041] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA strand passage activity of eukaryotic topoisomerase II relies on a cascade of conformational changes triggered by ATP binding to the N-terminal domain of the enzyme. To investigate the interdomain communication between the ATPase and cleavage/religation domains of human topoisomerase IIalpha, we characterized a mutant enzyme that contains a deletion at the interface between the two domains, covering amino acids 350-407. The ATPase domain retained full activity with a rate of ATP hydrolysis that was severalfold higher than normal, but the ATPase activity was unaffected by DNA. The cleavage and religation activities of the enzyme were comparable with those of the wild-type enzyme both in the absence and presence of cancer chemotherapeutic agents. However, neither ATP nor a nonhydrolyzable ATP analog stimulated cleavage complex formation. Although both conserved domains retained full activity, the mutant enzyme was unable to coordinate these activities into strand passage. Our findings suggest that the normal conformational transitions occurring in the enzyme upon ATP binding are hampered or lacking in the mutant enzyme. Consistent with this hypothesis, the enzyme displayed an abnormal clamp closing activity. In summary, the region covering amino acids 350-407 in human topoisomerase IIalpha seems to be essential for correct interdomain communication and probably is involved in signaling ATP binding to the rest of the enzyme.
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Affiliation(s)
- L Bjergbaek
- Department of Molecular and Structural Biology, University of Aarhus, C. F. Mollers Allé, Building 130, 8000 Arhus C, Denmark
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26
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Fortune JM, Osheroff N. Topoisomerase II as a target for anticancer drugs: when enzymes stop being nice. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2000; 64:221-53. [PMID: 10697411 DOI: 10.1016/s0079-6603(00)64006-0] [Citation(s) in RCA: 259] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Topoisomerase II is an essential enzyme that plays a role in virtually every cellular DNA process. This enzyme interconverts different topological forms of DNA by passing one nucleic acid segment through a transient double-stranded break generated in a second segment. By virtue of its double-stranded DNA passage reaction, topoisomerase II is able to regulate DNA over- and underwinding, and can resolve knots and tangles in the genetic material. Beyond the critical physiological functions of the eukaryotic enzyme, topoisomerase II is the target for some of the most successful anticancer drugs used to treat human malignancies. These agents are referred to as topoisomerase II poisons, because they transform the enzyme into a potent cellular toxin. Topoisomerase II poisons act by increasing the concentration of covalent enzyme-cleaved DNA complexes that normally are fleeting intermediates in the catalytic cycle of topoisomerase II. As a result of their action, these drugs generate high levels of enzyme-mediated breaks in the genetic material of treated cells and ultimately trigger cell death pathways. Topoisomerase II is also the target for a second category of drugs referred to as catalytic inhibitors. Compounds in this category prevent topoisomerase II from carrying out its required physiological functions. Drugs from both categories vary widely in their mechanisms of actions. This review focuses on topoisomerase II function and how drugs alter the catalytic cycle of this important enzyme.
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Affiliation(s)
- J M Fortune
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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27
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Gaasterland T, Ragan MA. Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. MICROBIAL & COMPARATIVE GENOMICS 1999; 3:199-217. [PMID: 10027190 DOI: 10.1089/omi.1.1998.3.199] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have implemented a statistically based approach to comparative genomics that allows us to define and characterize distributional patterns of conceptually translated open reading frames (ORFs) at different confidence levels based on pairwise FASTA matches. In this report, we apply this methodology to nine microbial genomes, focusing particularly on phyletic and functional patterns of ORF distribution within and between the two prokaryotic domains of life, Bacteria and Archaea. We examine patterns of presence and absence of matches, determine the universal ORF set, analyze features of genome specialization between closely related organisms, and present genomic evidence for the monophyly of Archaea. These analyses illustrate how a quantitative approach to comparative genomics can illuminate questions of fundamental biological significance.
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Affiliation(s)
- T Gaasterland
- Mathematics and Computer Science Division, Argonne National Laboratory, Illinois, USA.
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28
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Gardiner LP, Roper DI, Hammonds TR, Maxwell A. The N-terminal domain of human topoisomerase IIalpha is a DNA-dependent ATPase. Biochemistry 1998; 37:16997-7004. [PMID: 9836594 DOI: 10.1021/bi9818321] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have constructed clones encoding N-terminal fragments of human DNA topoisomerase IIalpha. We show that the N-terminal domain (approximately 50 kDa) has an intrinsic ATPase activity that can be stimulated by DNA. The enzyme obeys Michaelis-Menten kinetics showing a approximately 6-fold increase in kcat in the presence of DNA. Cross-linking studies indicate that the N-terminal domain is a dimer in the absence and presence of nucleotides. Using site-directed mutagenesis, we have identified the catalytic residue for ATP hydrolysis as Glu86. Phosphorylation of the N-terminal domain with protein kinase C does not affect the ATPase activity. The ATPase domain of human topoisomerase IIalpha shows significant differences from its counterpart in DNA gyrase and we discuss the mechanistic implications of these data.
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Affiliation(s)
- L P Gardiner
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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29
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Burden DA, Osheroff N. Mechanism of action of eukaryotic topoisomerase II and drugs targeted to the enzyme. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1400:139-54. [PMID: 9748545 DOI: 10.1016/s0167-4781(98)00132-8] [Citation(s) in RCA: 378] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Topoisomerase II is a ubiquitous enzyme that is essential for the survival of all eukaryotic organisms and plays critical roles in virtually every aspect of DNA metabolism. The enzyme unknots and untangles DNA by passing an intact helix through a transient double-stranded break that it generates in a separate helix. Beyond its physiological functions, topoisomerase II is the target for some of the most active and widely prescribed anticancer drugs currently utilized for the treatment of human cancers. These drugs act in an insidious fashion and kill cells by increasing levels of covalent topoisomerase II-cleaved DNA complexes that are normally fleeting intermediates in the catalytic cycle of the enzyme. Over the past several years, we have made considerable strides in our understanding of the catalytic mechanism of topoisomerase II and the mechanism of action of drugs targeted to this enzyme. These advances have provided novel insights into the physiological functions of topoisomerase II and have led to the development of more efficacious chemotherapeutic regimens and novel anticancer drugs. Considering the importance of topoisomerase II to the eukaryotic cell and to cancer chemotherapy, it is essential to understand its enzymatic function and pharmacological properties. Therefore, this review will discuss the mechanism of action of eukaryotic topoisomerase II and topoisomerase II-targeted drugs.
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Affiliation(s)
- D A Burden
- Department of Biochemistry, 654 Medical Research Building I, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
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30
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Levine C, Hiasa H, Marians KJ. DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1400:29-43. [PMID: 9748489 DOI: 10.1016/s0167-4781(98)00126-2] [Citation(s) in RCA: 261] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA gyrase and topoisomerase IV are the two type II topoisomerases present in bacteria. Though clearly related, based on amino acid sequence similarity, they each play crucial, but distinct, roles in the cell. Gyrase is involved primarily in supporting nascent chain elongation during replication of the chromosome, whereas topoisomerase IV separates the topologically linked daughter chromosomes during the terminal stage of DNA replication. These different roles can be attributed to differences in the biochemical properties of the two enzymes. The biochemical activities, physiological roles, and drug sensitivities of the enzymes are reviewed.
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Affiliation(s)
- C Levine
- Graduate Program in Molecular Biology, Cornell University Graduate School of Medical Sciences, New York, NY, USA
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31
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Kreuzer KN. Bacteriophage T4, a model system for understanding the mechanism of type II topoisomerase inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1400:339-47. [PMID: 9748648 DOI: 10.1016/s0167-4781(98)00145-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteriophage T4 provides a simple model system for analyzing the mechanism of action of antitumor agents that inhibit DNA topoisomerases. The phage-encoded type II topoisomerase is sensitive to many of the same antitumor agents that inhibit mammalian type II topoisomerase, including m-AMSA, ellipticines, mitoxantrone and epipodophyllotoxins. Results from the T4 model system provided a convincing demonstration that topoisomerase is the physiological drug target and strong evidence that the drug-induced cleavage complex is important for cytotoxicity. The detailed molecular steps involved in cytotoxicity, and the mechanism of recombinational repair of inhibitor-induced DNA damage, are currently being analyzed using this model system. Studies with the T4 topoisomerase have also provided compelling evidence that topoisomerase inhibitors interact with DNA at the active site of the enzyme, with each class of inhibitor favoring a different subset of cleavage sites based on DNA sequence. Finally, analysis of drug-resistance mutations in the T4 topoisomerase have implicated certain regions of the protein in drug interaction and provided a strong link between the mechanism of action of the antibacterial quinolones, which inhibit DNA gyrase, and the various antitumor agents, which inhibit mammalian type II topoisomerase.
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Affiliation(s)
- K N Kreuzer
- Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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Nakayama H, Izuta M, Nagahashi S, Sihta EY, Sato Y, Yamazaki T, Arisawa M, Kitada K. A controllable gene-expression system for the pathogenic fungus Candida glabrata. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 9):2407-2415. [PMID: 9782488 DOI: 10.1099/00221287-144-9-2407] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A system for controlling gene expression was established in the pathogenic fungus Candida glabrata to elucidate the physiological functions of genes. To control the expression of the gene of interest, the C. glabrata cells were first transformed with the plasmid carrying the tetracycline repressor-transactivator fusion tetR::GAL4, then with the DNA fragment containing the controllable cassette, the tetracycline operator chimeric promoter (tetO::ScHOP1). The peptide elongation factor 3 (CgTEF3) and DNA topoisomerase II (CgTOP2) genes from C. glabrata were cloned and their expression assessed using this system. When the promoter of CgTEF3 or CgTOP2 was replaced with tetO::ScHOP1, doxycycline almost completely repressed the expression of both mRNAs, and impaired growth. Repression of the TOP2 or TEF3 gene by doxycycline also hampered the survival of C. glabrata cells in mice; in mouse kidneys the number of C. glabrata cells, in which the TOP2 or TEF3 promoter was replaced with the tetO::ScHOP1 controllable cassette, did not increase when the mice were given doxycycline. Thus, it appears that the gene repression mediated by doxycycline occurred not only in culture media but also in animals; therefore, this system can be used to elucidate the function of the gene in fungal infections and pathogenesis.
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Affiliation(s)
- Hironobu Nakayama
- Department of Mycology, Nippon Roche Research Center,200 Kajiwara, Kamakura, Kanagawa 247,Japan
| | - Miho Izuta
- Department of Mycology, Nippon Roche Research Center,200 Kajiwara, Kamakura, Kanagawa 247,Japan
| | - Shigehisa Nagahashi
- Department of Mycology, Nippon Roche Research Center,200 Kajiwara, Kamakura, Kanagawa 247,Japan
| | - Emi Y Sihta
- Department of Mycology, Nippon Roche Research Center,200 Kajiwara, Kamakura, Kanagawa 247,Japan
| | - Yasuko Sato
- Department of Mycology, Nippon Roche Research Center,200 Kajiwara, Kamakura, Kanagawa 247,Japan
| | - Toshikazu Yamazaki
- Department of Mycology, Nippon Roche Research Center,200 Kajiwara, Kamakura, Kanagawa 247,Japan
| | - Mikio Arisawa
- Department of Mycology, Nippon Roche Research Center,200 Kajiwara, Kamakura, Kanagawa 247,Japan
| | - Kunio Kitada
- Department of Mycology, Nippon Roche Research Center,200 Kajiwara, Kamakura, Kanagawa 247,Japan
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Hammonds TR, Maxwell A. The DNA dependence of the ATPase activity of human DNA topoisomerase IIalpha. J Biol Chem 1997; 272:32696-703. [PMID: 9405488 DOI: 10.1074/jbc.272.51.32696] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have purified human topoisomerase IIalpha from HeLa cells and studied its ATPase reaction. The ATPase activity is stimulated by DNA and shows apparent Michaelis-Menten kinetics. Although the ATPase activity of human topoisomerase IIalpha is lower than that of Saccharomyces cerevisiae, it is more active in decatenation, implying more efficient coupling of the ATPase to DNA strand passage under these conditions. Using plasmid pBR322 as the DNA cofactor, the reaction shows hyperstimulation by DNA at a base pair to enzyme dimer ratio of 100-200:1. When DNA fragments are used as the cofactor, the reaction requires > approximately 100 base pairs to stimulate the activity and fragments of approximately 300 base pairs show hyperstimulation. This behavior can be rationalized in terms of the enzyme requiring fragments that can bind to both the DNA gate and the ATP-operated clamp in order for the ATPase reaction to be stimulated. Hyperstimulation is a consequence of the saturation of DNA with enzyme. The mechanistic implications of these results are discussed.
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Affiliation(s)
- T R Hammonds
- Department of Biochemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
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Kroll DJ. Homologous and heterologous protein-protein interactions of human DNA topoisomerase IIalpha. Arch Biochem Biophys 1997; 345:175-84. [PMID: 9308887 DOI: 10.1006/abbi.1997.0267] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA topoisomerase II (topo II; EC 5.99.1.3) is a nuclear enzyme whose DNA decatenating activity on newly replicated DNA is essential to successful cell division. Topo II catalytic activity proceeds by a concerted DNA breakage-reunion reaction coordinated between two interacting, homologous subunits. Human and yeast topo II have recently been shown to enter into heterologous protein-protein interactions and some of these interactions appear necessary for successful chromosomal segregation. In the present study, the sequences mediating homologous and heterologous protein-protein interactions have been investigated biochemically using various truncated peptides from the major alpha form of human topo II. From nonreducing gel electrophoresis and solid-phase protein-protein binding (Far Western) assays, topo II homodimerization appeared to be minimally governed by the region between amino acids 951 and 1042. However, maximal homodimerization and multimerization required sequences C-terminal to position 1042. Topo II peptides were also able to interact with 10-12 nuclear proteins from HeLa cells, termed topo II-interactive proteins or TIPs. Interestingly, small topo II peptides between residues 808 and 951 that did not homodimerize with topo II (857-1447) were nonetheless capable of binding to HeLa TIPs. These interactions were confirmed by use of topo II affinity chromatography for isolation of specific TIPs from HeLa nuclear extracts. Taken together, these data confirm that human topo II is also capable of heterologous interactions with nuclear proteins and that the region governing these interactions is distinct from, but has some overlap with, sequences directing topo II homodimerization.
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Affiliation(s)
- D J Kroll
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center and University of Colorado Cancer Center, Denver 80262, USA.
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Sato M, Ishida R, Narita T, Kato J, Ikeda H, Fukazawa H, Andoh T. Interaction of the DNA topoisomerase II catalytic inhibitor meso-2,3-bis(3,5-dioxopiperazine-1-yl)butane (ICRF-193), a bisdioxopiperazine derivative, with the conserved region(s) of eukaryotic but not prokaryotic enzyme. Biochem Pharmacol 1997; 54:545-50. [PMID: 9337070 DOI: 10.1016/s0006-2952(97)00201-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
ICRF-193 [meso-2,3-bis(3,5-dioxopiperazine-1-yl)butane], a bisdioxopiperazine compound, has been shown to be a catalytic inhibitor of DNA topoisomerase II by stabilizing the enzyme in the form of a closed "protein clamp," an intermediate form in the catalytic cycle (Roca et al., Proc Natl Acad Sci USA 91: 1781-1785, 1994). In view of its usefulness as a probe in the functional analysis of the enzyme, we tried further to define the domain(s) of the enzyme interacting with the drug by examining its inhibitory activity on type II topoisomerases from various species of eukaryotes and prokaryotes. ICRF-193 inhibited the enzyme from yeast, fly, frog, plant, and mammals at IC50 values in the range of 1-13 microM. Experiments using fission yeast truncated mutant type II enzyme lacking both amino-terminal 74 amino acids and carboxy-terminal 265 amino acids revealed that ICRF-193 interacts with the 125 kDa "core" polypeptide of the enzyme. In contrast, prokaryotic type II enzymes, Escherichia coli DNA gyrase, topo IV, and phage T4 topo, were not affected by the drug. From these results, the domain(s) common to eukaryotic but not to prokaryotic type II enzymes interacting with ICRF-193 was speculated.
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Affiliation(s)
- M Sato
- Research Laboratory, Zenyaku Kogyo Co., Ltd., Tokyo, Japan
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Adachi N, Miyaike M, Kato S, Kanamaru R, Koyama H, Kikuchi A. Cellular distribution of mammalian DNA topoisomerase II is determined by its catalytically dispensable C-terminal domain. Nucleic Acids Res 1997; 25:3135-42. [PMID: 9224616 PMCID: PMC146861 DOI: 10.1093/nar/25.15.3135] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian cells express two genetically distinct isoforms of DNA topoisomerase II, designated topoisomerase IIalphaand topoisomerase IIbeta. We have recently shown that mouse topoisomerase IIalpha can substitute for the yeast topoisomerase II enzyme and complement yeast top2 mutations. This functional complementation allowed functional analysis of the C-terminal domain (CTD) of mammalian topoisomerase II, where the amino acid sequences are divergent and species-specific, in contrast to the highly conserved N-terminal and central domains. Several C-terminal deletion mutants of mouse topoisomerase IIalpha were constructed and expressed in yeast top2 cells. We found that the CTD of topoisomerase IIalphais dispensable for enzymatic activity in vitro but is required for nuclear localization in vivo. Interestingly, the CTD of topoisomerase IIbetawas also able to function as a signal for nuclear targeting. We therefore examined whether the CTD alone is sufficient for nuclear localization in vivo . The C-terminal region was fused to GFP (green fluorescent protein) and expressed under the GAL1 promoter in yeast cells. As expected, GFP signal was exclusively detected in the nucleus, irrespective of the CTD derived from either topoisomerase IIalphaor IIbeta. Surprisingly, when the upstream sequence of each CTD was added nuclear localization of the GFP signal was found to be cell cycle dependent: topoisomerase IIalpha-GFP was seen in the mitotic nucleus but was absent from the interphase nucleus, while topoisomerase IIbeta-GFP was detected predominantly in the interphase nucleus and less in the mitotic nucleus. Our results suggest that the catalytically dispensable CTD of topoisomerase II is sufficient as a signal for nuclear localization and that yeast cells can distinguish between the two isoforms of mammalian topoisomerase II, localizing each protein properly.
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Affiliation(s)
- N Adachi
- Mitsubishi Kasei Institute of Life Sciences, 11 Minamiooya, Machida-shi, Tokyo 194, Japan
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Kingma PS, Greider CA, Osheroff N. Spontaneous DNA lesions poison human topoisomerase IIalpha and stimulate cleavage proximal to leukemic 11q23 chromosomal breakpoints. Biochemistry 1997; 36:5934-9. [PMID: 9166762 DOI: 10.1021/bi970507v] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Topoisomerase II-targeted drugs, such as etoposide, "poison" this enzyme and kill cells by increasing levels of covalent topoisomerase II-cleaved DNA complexes. In spite of the success of this drug in the treatment of human cancers, a significant proportion of patients treated with etoposide eventually develop secondary leukemias that are characterized by translocations at chromosome band 11q23. Since similar translocations are associated with primary leukemias in previously untreated infants, we questioned whether they could also be triggered by the actions of "endogenous topoisomerase II poisons". Recent studies, which demonstrated that several forms of spontaneous DNA damage stimulate cleavage mediated by Drosophila topoisomerase II, suggest that DNA lesions may act as these endogenous poisons. Therefore, to determine whether the ability to recognize spontaneous DNA damage has been conserved from this lower eukaryote to mammalian species, the effects of apurinic sites, apyrimidinic sites, and deaminated cytosine residues on human topoisomerase IIalpha were assessed. All three lesions were potent poisons of the human enzyme and stimulated cleavage when located within the four-base overhang generated by enzyme-mediated DNA scission. Furthermore, these lesions increased levels of cleavage at five sites proximal to 11q23 translocation breakpoints and did so with an efficacy that was comparable to or greater than that of therapeutic concentrations of etoposide. Although the physiological relevance of these findings has yet to be established, they suggest a potential role for endogenous topoisomerase II poisons in the initiation of leukemic chromosomal breakpoints.
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Affiliation(s)
- P S Kingma
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Funatsuki K, Tanaka R, Inagaki S, Konno H, Katoh K, Nakamura H. acrB mutation located at carboxyl-terminal region of gyrase B subunit reduces DNA binding of DNA gyrase. J Biol Chem 1997; 272:13302-8. [PMID: 9148951 DOI: 10.1074/jbc.272.20.13302] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mutations that exhibit susceptibility to acriflavine have been isolated and classified as acr mutations in Escherichia coli. We cloned the acrB gene, which has been identified as a mutation of the gyrB gene, and found a double point mutation altering two consecutive amino acids (S759R/R760C) in the COOH-terminal region of the gyrase B subunit. The mutant B subunit was found to associate with the A subunit to make the quaternary structure, and the reconstituted gyrase showed an 80-fold reduction of specific activity in DNA supercoiling assay; the sensitivity to acriflavine was not different in the same unit of wild-type and mutant gyrases. The mutant enzyme retained intrinsic ATPase activity, but DNA-dependent stimulation was observed infrequently. A gel shift assay showed that acriflavine inhibited the DNA binding of gyrase. The acrB mutation also reduced significantly the DNA binding of gyrase but did not change the sensitivity to acriflavine. These results revealed that the acrB mutation is related to the inhibitory mechanism of acriflavine; and the acriflavine sensitivity of the mutant, at least in vitro, is caused mainly by reduction of the enzyme activity. Further, our findings suggest that the COOH-terminal region of the B subunit is essential for the initial binding of gyrase to the substrate DNA.
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Affiliation(s)
- K Funatsuki
- Aburahi Laboratories, Shionogi and Company, Ltd., Koka, Shiga 520-34, Japan
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Komori K, Kuroe K, Yanagisawa K, Tanaka Y. Cloning and characterization of the gene encoding a mitochondrially localized DNA topoisomerase II in Dictyostelium discoideum. Western blot analysis. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1352:63-72. [PMID: 9177484 DOI: 10.1016/s0167-4781(96)00229-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We cloned a gene (topA) encoding DNA topoisomerase II from Dictyostelium discoideum nuclear DNA using oligo probes corresponding to the consensus amino acid sequences found in the gene in other eukaryotes. The gene encoding a predicted polypeptide of 1282 amino acids with M(r) of about 146 kDa, is a single copy that is expressed as a polyadenylated 4.5 kb RNA. The predicted amino acid sequence shares similarity with those of other eukaryotes with identity between 32 and 46%. The protein is 260-300 amino acids shorter in the C-terminal region and 50-80 longer in the N-terminal region than those of other eukaryotes. In TopA of D. discoideum, the N-terminal region with stretches of charged and hydrophilic amino acids is predicted to fold into an amphiphilic alpha-helix which is characteristic of a mitochondrial targeting signal presequence. Four independent polyclonal antibodies against bacterially expressed GST fusion proteins containing four portions of the polypeptide detected a single band on Western blots at about 135 kDa. Western blots analysis of subcellular fractions revealed that this protein is localized in mitochondria. The protein and the mRNA are present in growth phase and during development, although levels of both declined as development proceeded.
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Affiliation(s)
- K Komori
- Institute of Biological Sciences, University of Tsukuba, Ibaraki, Japan
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40
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41
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Jensen S, Andersen AH, Kjeldsen E, Biersack H, Olsen EH, Andersen TB, Westergaard O, Jakobsen BK. Analysis of functional domain organization in DNA topoisomerase II from humans and Saccharomyces cerevisiae. Mol Cell Biol 1996; 16:3866-77. [PMID: 8668204 PMCID: PMC231383 DOI: 10.1128/mcb.16.7.3866] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The functional domain structure of human DNA topoisomerase IIalpha and Saccharomyces cerevisiae DNA topoisomerase II was studied by investigating the abilities of insertion and deletion mutant enzymes to support mitotic growth and catalyze transitions in DNA topology in vitro. Alignment of the human topoisomerase IIalpha and S. cerevisiae topoisomerase II sequences defined 13 conserved regions separated by less conserved or differently spaced sequences. The spatial tolerance of the spacer regions was addressed by insertion of linkers. The importance of the conserved regions was assessed through deletion of individual domains. We found that the exact spacing between most of the conserved domains is noncritical, as insertions in the spacer regions were tolerated with no influence on complementation ability. All conserved domains, however, are essential for sustained mitotic growth of S. cerevisiae and for enzymatic activity in vitro. A series of topoisomerase II carboxy-terminal truncations were investigated with respect to the ability to support viability, cellular localization, and enzymatic properties. The analysis showed that the divergent carboxy-terminal region of human topoisomerase IIalpha is dispensable for catalytic activity but contains elements that specifically locate the protein to the nucleus.
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Affiliation(s)
- S Jensen
- Department of Molecular Biology, University of Aarhus, Denmark
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42
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Roca J, Berger JM, Harrison SC, Wang JC. DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proc Natl Acad Sci U S A 1996; 93:4057-62. [PMID: 8633016 PMCID: PMC39486 DOI: 10.1073/pnas.93.9.4057] [Citation(s) in RCA: 152] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Recent biochemical and crystallographic results suggest that a type II DNA topoisomerase acts as an ATP-modulated clamp with two sets of jaws at opposite ends: a DNA-bound enzyme can admit a second DNA through one set of jaws; upon binding ATP, this DNA is passed through an enzyme-mediated opening in the first DNA and expelled from the enzyme through the other set of jaws. Experiments based on the introduction of reversible disulfide links across one dimer interface of yeast DNA topoisomerase II have confirmed this mechanism. The second DNA is found to enter the enzyme through the gate formed by the N-terminal parts of the enzyme and leave it through the gate close to the C termini.
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Affiliation(s)
- J Roca
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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Heisig P. Genetic evidence for a role of parC mutations in development of high-level fluoroquinolone resistance in Escherichia coli. Antimicrob Agents Chemother 1996; 40:879-85. [PMID: 8849244 PMCID: PMC163223 DOI: 10.1128/aac.40.4.879] [Citation(s) in RCA: 209] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fifteen strains of Escherichia coli with MICs of ciprofloxacin (CIP) between 0.015 and 256 micrograms/ml were examined for the presence of mutations in the quinolone resistance-determining region of the gyrA gene and in an analogous region of the parC gene. No mutation was found in a susceptible isolate (MIC of CIP, 0.015 microgram/ml). Four moderately resistant strains (MIC of CIP 0.06 to 4 micrograms/ml) carried one gyrA mutation affecting serine 83, but in only one strain was an additional parC mutation (Gly-78 to Asp) detected. All ten highly resistant strains examined (MIC of CIP, > 4 micrograms/ml) carried two gyrA mutations affecting residues serine 83 and aspartate 87, and at least one parC mutation. These parC mutations included alterations of serine 80 to arginine or isoleucine and glutamate 84 to glycine or lysine. The parC+ and two mutant alleles (parCI-80 and parCI-80,G-84) were inserted into the mobilizable vector pBP507. Transfer of a plasmid-coded parC+ allele into parC+ strains did not alter the susceptibilities towards ciprofloxacin or nalidixic acid, while a significant increase in susceptibility was detectable for parC mutants. This increase, however, did not restore wild-type susceptibility, whereas transfer of a plasmid-coded gyrA+ allele alone or in combination with parC+ did. These data are in agreement with the view that topoisomerase IV is a secondary, less sensitive target for quinolone action in Escherichia coli and that the development of high-level fluoroquinolone resistance in E. coli requires at least one parC mutation in addition to the gyrA mutation(s).
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Affiliation(s)
- P Heisig
- Pharmazeutische Mikrobiologie, Universität Bonn, Germany
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44
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Abstract
Type II DNA topoisomerases are enzymes that are capable of transporting one duplex DNA through another. Recent experimental results, including the structure of a fragment of yeast topoisomerase II, have provided new insights into the mechanism of the strand passage reaction. Other results have begun to define the role of ATP in the catalytic cycle and illuminate how DNA breaks mediated by topoisomerase II can occur.
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Affiliation(s)
- J M Berger
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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45
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Abstract
The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an ATP-modulated clamp with two sets of jaws at opposite ends, connected by multiple joints. An enzyme with bound DNA can admit a second DNA duplex through one set of jaws, transport it through the cleaved first duplex, and expel it through the other set of jaws.
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Affiliation(s)
- J M Berger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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46
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Simon H, Roth M, Zimmer C. Biochemical complementation studies in vitro of gyrase subunits from different species. FEBS Lett 1995; 373:88-92. [PMID: 7589441 DOI: 10.1016/0014-5793(95)01007-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To investigate the functional equivalence of DNA gyrase subunits from different bacterial sources hybrid enzymes were formed using purified A and B subunits from three species of Streptomycetes, E. coli and B. subtilis. The activity of gyrase hybrids composed of heterologous gyr A and gyr B proteins and of the gyrases containing homologous subunits was characterized by binding studies and a cleavage assay with two different DNA fragments. Likewise the enzyme activity was monitored by the super-coiling and relaxation assay with pBR322 DNA. We found that cleavage reactions are largely determined by the source of the gyr B subunits whereas DNA supercoiling and relaxation reactions of pBR322 catalyzed by DNA gyrase are limited to a combination of homologous A and B subunits or of heterologous A and B subunits from the taxonomically related bacteria Streptomycetes.
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Affiliation(s)
- H Simon
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Germany
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47
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Kingma PS, Corbett AH, Burcham PC, Marnett LJ, Osheroff N. Abasic sites stimulate double-stranded DNA cleavage mediated by topoisomerase II. DNA lesions as endogenous topoisomerase II poisons. J Biol Chem 1995; 270:21441-4. [PMID: 7665552 DOI: 10.1074/jbc.270.37.21441] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Several clinically relevant anticancer drugs induce genomic mutations and cell death by increasing topoisomerase II-mediated DNA breakage. To determine whether endogenous DNA damage also affects this cleavage event, the effects of abasic sites (the most commonly formed spontaneous DNA lesion) on topoisomerase II activity were investigated. The presence of 3 abasic sites/plasmid stimulated enzyme-mediated DNA breakage > 6-fold, primarily by enhancing the forward rate of cleavage. This corresponds to a potency that is > 2000-fold higher than that of the anticancer drug, etoposide. These findings suggest that abasic sites represent endogenous topoisomerase II poisons and imply that anticancer drugs mimic the cleavage-enhancing actions of naturally occurring DNA lesions.
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Affiliation(s)
- P S Kingma
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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48
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Froelich-Ammon SJ, Osheroff N. Topoisomerase poisons: harnessing the dark side of enzyme mechanism. J Biol Chem 1995; 270:21429-32. [PMID: 7665550 DOI: 10.1074/jbc.270.37.21429] [Citation(s) in RCA: 466] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- S J Froelich-Ammon
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Austin CA, Marsh KL, Wasserman RA, Willmore E, Sayer PJ, Wang JC, Fisher LM. Expression, domain structure, and enzymatic properties of an active recombinant human DNA topoisomerase II beta. J Biol Chem 1995; 270:15739-46. [PMID: 7797575 DOI: 10.1074/jbc.270.26.15739] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Human cells express two genetically distinct isoforms of DNA topoisomerase II, alpha and beta, which catalyze ATP-dependent DNA strand passage and are an important antitumor drug target. Here we report for the first time the successful overexpression of human topoisomerase II beta in yeast by cloning a topoisomerase II beta cDNA in a yeast shuttle vector under the control of a galactose-inducible promoter. Recombinant human topoisomerase II beta (residues 46-1621 fused to the first 5 residues of yeast topoisomerase II) was purified to homogeneity, yielding an enzymatically active polypeptide in sufficient quantity to allow analysis of its domain structure and comparison with that of recombinant human topoisomerase II alpha. Partial digestion of beta with either trypsin or protease SV8 generated fragments of approximately 130, 90, 62, and 45-50 kDa, arising from cleavage at three limited and discrete regions of the protein (A, B, and C) indicating the presence of at least four structural domains. Recombinant human topoisomerase II alpha and beta induced DNA breakage which was promoted by a variety of agents. Isoform differences in drug-induced DNA breakage were observed. These studies of human topoisomerase II beta in concert with alpha should aid the determination of their individual roles in cancer chemotherapy and should facilitate the design, targeting, and testing of cytotoxic antitumor agents.
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Affiliation(s)
- C A Austin
- Department of Biochemistry and Genetics, Medical School, University, Newcastle-upon-Tyne, United Kingdom
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Hughes AL, Hughes MK. Self peptides bound by HLA class I molecules are derived from highly conserved regions of a set of evolutionarily conserved proteins. Immunogenetics 1995; 41:257-62. [PMID: 7536709 DOI: 10.1007/bf00172149] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An evolutionary analysis of self peptides reported to be bound by HLA class I molecules showed that these peptides are largely derived from proteins that have been highly conserved in the history of mammals. These proteins also often have universal tissue expression and have a higher than average frequency of highly hydrophilic residues. The peptides themselves are generally still more highly conserved than the source proteins and have a higher frequency of highly hydrophobic residues, evidently often being derived from conserved hydrophobic cores of the source proteins. These results suggest that the mechanism by which peptides are derived for MHC presentation may preferentially select peptides from conserved protein regions. In the case of parasite-derived peptides, such a mechanism would be adaptive in that it would reduce the likelihood of escape mutants.
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Affiliation(s)
- A L Hughes
- Department of Biology, Pennsylvania State University, University Park 16802, USA
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