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Botta L, Filippi S, Zippilli C, Cesarini S, Bizzarri BM, Cirigliano A, Rinaldi T, Paiardini A, Fiorucci D, Saladino R, Negri R, Benedetti P. Artemisinin Derivatives with Antimelanoma Activity Show Inhibitory Effect against Human DNA Topoisomerase 1. ACS Med Chem Lett 2020; 11:1035-1040. [PMID: 32435422 DOI: 10.1021/acsmedchemlett.0c00131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/10/2020] [Indexed: 02/07/2023] Open
Abstract
Artesunic acid and artemisinin are natural substances with promiscuous anticancer activity against different types of cancer cell lines. The mechanism of action of these compounds is associated with the formation of reactive radical species by cleavage of the sesquiterpene pharmacophore endoperoxide bridge. Here we suggested topoisomerase 1 as a possible molecular target for the improvement of the anticancer activity of these compounds. In this context, we report that novel hybrid and dimer derivatives of artesunic acid and artemisinin, bearing camptothecin and SN38 as side-chain biological effectors, can inhibit growth of yeast cells overexpressing human topoisomerase 1 and its enzymatic activity in vitro. These derivatives showed also anticancer activity in melanoma cell lines higher than camptothecin and paclitaxel. In silico molecular docking calculations highlighted a common binding mode for the novel derivatives, with the sesquiterpene lactone scaffold being located near the traditional recognition site for camptothecin, while the bioactive side-chain effector laid in the camptothecin cleft.
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Affiliation(s)
- Lorenzo Botta
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Silvia Filippi
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Claudio Zippilli
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Silvia Cesarini
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Bruno Mattia Bizzarri
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Angela Cirigliano
- Istituto di Biologia e Patologia Molecolari, CNR Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Teresa Rinaldi
- Sapienza University of Rome, Department of Biology and Biotechnology, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Diego Fiorucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Rodolfo Negri
- Sapienza University of Rome, Department of Biology and Biotechnology, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Pietro Benedetti
- Dipartimento di Biologia, Università di Padova Distaccato presso il “Centro Linceo Beniamino Segre” Accademia Nazionale dei Lincei, Palazzo Corsini, Via della Lungara 10, 00165 Rome, Italy
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2
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Soren BC, Dasari JB, Ottaviani A, Iacovelli F, Fiorani P. Topoisomerase IB: a relaxing enzyme for stressed DNA. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:18-25. [PMID: 35582040 PMCID: PMC9094055 DOI: 10.20517/cdr.2019.106] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 11/12/2022]
Abstract
DNA topoisomerase I enzymes relieve the torsional strain in DNA; they are essential for fundamental molecular processes such as DNA replication, transcription, recombination, and chromosome condensation; and act by cleaving and then religating DNA strands. Over the past few decades, scientists have focused on the DNA topoisomerases biological functions and established a unique role of Type I DNA topoisomerases in regulating gene expression and DNA chromosome condensation. Moreover, the human enzyme is being investigated as a target for cancer chemotherapy. The active site tyrosine is responsible for initiating two transesterification reactions to cleave and then religate the DNA backbone, allowing the release of superhelical tension. The different steps of the catalytic mechanism are affected by various inhibitors; some of them prevent the interaction between the enzyme and the DNA while others act as poisons, leading to TopI-DNA lesions, breakage of DNA, and eventually cellular death. In this review, our goal is to provide an overview of mechanism of human topoisomerase IB action together with the different types of inhibitors and their effect on the enzyme functionality.
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Affiliation(s)
- Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy.,Present address: Department of Research and Application Development, Biogenex Life Sciences, Telangana 501510, India
| | - Alessio Ottaviani
- Institute of Translational Pharmacology, National Research Council, Rome 00133, Italy
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy.,Institute of Translational Pharmacology, National Research Council, Rome 00133, Italy
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3
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Weidlich D, Klostermeier D. Functional interactions between gyrase subunits are optimized in a species-specific manner. J Biol Chem 2020; 295:2299-2312. [PMID: 31953321 DOI: 10.1074/jbc.ra119.010245] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/03/2020] [Indexed: 11/06/2022] Open
Abstract
DNA gyrase is a bacterial DNA topoisomerase that catalyzes ATP-dependent negative DNA supercoiling and DNA decatenation. The enzyme is a heterotetramer comprising two GyrA and two GyrB subunits. Its overall architecture is conserved, but species-specific elements in the two subunits are thought to optimize subunit interaction and enzyme function. Toward understanding the roles of these different elements, we compared the activities of Bacillus subtilis, Escherichia coli, and Mycobacterium tuberculosis gyrases and of heterologous enzymes reconstituted from subunits of two different species. We show that B. subtilis and E. coli gyrases are proficient DNA-stimulated ATPases and efficiently supercoil and decatenate DNA. In contrast, M. tuberculosis gyrase hydrolyzes ATP only slowly and is a poor supercoiling enzyme and decatenase. The heterologous enzymes are generally less active than their homologous counterparts. The only exception is a gyrase reconstituted from mycobacterial GyrA and B. subtilis GyrB, which exceeds the activity of M. tuberculosis gyrase and reaches the activity of the B. subtilis gyrase, indicating that the activities of enzymes containing mycobacterial GyrB are limited by ATP hydrolysis. The activity pattern of heterologous gyrases is in agreement with structural features present: B. subtilis gyrase is a minimal enzyme, and its subunits can functionally interact with subunits from other bacteria. In contrast, the specific insertions in E. coli and mycobacterial gyrase subunits appear to prevent efficient functional interactions with heterologous subunits. Understanding the molecular details of gyrase adaptations to the specific physiological requirements of the respective organism might aid in the development of species-specific gyrase inhibitors.
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Affiliation(s)
- Daniela Weidlich
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany.
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4
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Andersen MB, Tesauro C, Gonzalez M, Kristoffersen EL, Alonso C, Rubiales G, Coletta A, Frøhlich R, Stougaard M, Ho YP, Palacios F, Knudsen BR. Advantages of an optical nanosensor system for the mechanistic analysis of a novel topoisomerase I targeting drug: a case study. NANOSCALE 2017; 9:1886-1895. [PMID: 28094391 DOI: 10.1039/c6nr06848k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The continuous need for the development of new small molecule anti-cancer drugs calls for easily accessible sensor systems for measuring the effect of vast numbers of new drugs on their potential cellular targets. Here we demonstrate the use of an optical DNA biosensor to unravel the inhibitory mechanism of a member of a new family of small molecule human topoisomerase I inhibitors, the so-called indeno-1,5-naphthyridines. By analysing human topoisomerase I catalysis on the biosensor in the absence or presence of added drug complemented with a few traditional assays, we demonstrate that the investigated member of the indeno-1,5-naphthyridine family inhibited human topoisomerase I activity by blocking enzyme-DNA dissociation. To our knowledge, this represents the first characterized example of a small molecule drug that inhibits a post-ligation step of catalysis. The elucidation of a completely new and rather surprising drug mechanism-of-action using an optical real time sensor highlights the value of this assay system in the search for new topoisomerase I targeting small molecule drugs.
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Affiliation(s)
- Marie B Andersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - María Gonzalez
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Emil L Kristoffersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Andrea Coletta
- Department of Chemistry, Langelandsgade 140, Aarhus University, 8000 Aarhus C, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Nørrebrogade 44 building 18B, Aarhus University, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark. and Interdisciplinary Nanoscience Center, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark and Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
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5
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Molecular Mechanism of DNA Topoisomerase I-Dependent rDNA Silencing: Sir2p Recruitment at Ribosomal Genes. J Mol Biol 2016; 428:4905-4916. [PMID: 27825925 DOI: 10.1016/j.jmb.2016.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/25/2016] [Accepted: 10/30/2016] [Indexed: 11/24/2022]
Abstract
Saccharomyces cerevisiae sir2Δ or top1Δ mutants exhibit similar phenotypes involving ribosomal DNA, including (i) loss of transcriptional silencing, resulting in non-coding RNA hyperproduction from cryptic RNA polymerase II promoters; (ii) alterations in recombination; and (iii) a general increase in histone acetylation. Given the distinct enzymatic activities of Sir2 and Top1 proteins, a histone deacetylase and a DNA topoisomerase, respectively, we investigated whether genetic and/or physical interactions between the two proteins could explain the shared ribosomal RNA genes (rDNA) phenotypes. We employed an approach of complementing top1Δ cells with yeast, human, truncated, and chimeric yeast/human TOP1 constructs and of assessing the extent of non-coding RNA silencing and histone H4K16 deacetylation. Our findings demonstrate that residues 115-125 within the yeast Top1p N-terminal domain are required for the complementation of the top1∆ rDNA phenotypes. In chromatin immunoprecipitation and co-immunoprecipitation experiments, we further demonstrate the physical interaction between Top1p and Sir2p. Our genetic and biochemical studies support a model whereby Top1p recruits Sir2p to the rDNA and clarifies a structural role of DNA topoisomerase I in the epigenetic regulation of rDNA, independent of its known catalytic activity.
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6
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Guyader CPE, Lamarre B, De Santis E, Noble JE, Slater NK, Ryadnov MG. Autonomously folded α-helical lockers promote RNAi. Sci Rep 2016; 6:35012. [PMID: 27721465 PMCID: PMC5056365 DOI: 10.1038/srep35012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/22/2016] [Indexed: 12/23/2022] Open
Abstract
RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi.
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Affiliation(s)
- Christian P. E. Guyader
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB2 3RA, UK
- National Physical Laboratory, Teddington, Middlesex, TW11 0WL, UK
| | - Baptiste Lamarre
- National Physical Laboratory, Teddington, Middlesex, TW11 0WL, UK
| | | | - James E. Noble
- National Physical Laboratory, Teddington, Middlesex, TW11 0WL, UK
| | - Nigel K. Slater
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB2 3RA, UK
| | - Maxim G. Ryadnov
- National Physical Laboratory, Teddington, Middlesex, TW11 0WL, UK
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7
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Vieira S, Castelli S, Desideri A. Importance of a stable topoisomerase IB clamping for an efficient DNA processing: Effect of the Lys 369 Glu mutation. Int J Biol Macromol 2015; 81:76-82. [DOI: 10.1016/j.ijbiomac.2015.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/24/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
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8
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Wright CM, van der Merwe M, DeBrot AH, Bjornsti MA. DNA topoisomerase I domain interactions impact enzyme activity and sensitivity to camptothecin. J Biol Chem 2015; 290:12068-78. [PMID: 25795777 DOI: 10.1074/jbc.m114.635078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 11/06/2022] Open
Abstract
During processes such as DNA replication and transcription, DNA topoisomerase I (Top1) catalyzes the relaxation of DNA supercoils. The nuclear enzyme is also the cellular target of camptothecin (CPT) chemotherapeutics. Top1 contains four domains: the highly conserved core and C-terminal domains involved in catalysis, a coiled-coil linker domain of variable length, and a poorly conserved N-terminal domain. Yeast and human Top1 share a common reaction mechanism and domain structure. However, the human Top1 is ∼100-fold more sensitive to CPT. Moreover, substitutions of a conserved Gly(717) residue, which alter intrinsic enzyme sensitivity to CPT, induce distinct phenotypes in yeast. To address the structural basis for these differences, reciprocal swaps of yeast and human Top1 domains were engineered in chimeric enzymes. Here we report that intrinsic Top1 sensitivity to CPT is dictated by the composition of the conserved core and C-terminal domains. However, independent of CPT, biochemically similar chimeric enzymes produced strikingly distinct phenotypes in yeast. Expression of a human Top1 chimera containing the yeast linker domain proved toxic, even in the context of a catalytically inactive Y723F enzyme. Lethality was suppressed either by splicing the yeast N-terminal domain into the chimera, deleting the human N-terminal residues, or in enzymes reconstituted by polypeptide complementation. These data demonstrate a functional interaction between the N-terminal and linker domains, which, when mispaired between yeast and human enzymes, induces cell lethality. Because toxicity was independent of enzyme catalysis, the inappropriate coordination of N-terminal and linker domains may induce aberrant Top1-protein interactions to impair cell growth.
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Affiliation(s)
- Christine M Wright
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
| | - Marié van der Merwe
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Amanda H DeBrot
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
| | - Mary-Ann Bjornsti
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
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9
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Ucuncuoglu N, Andricioaei I, Sari L. Insights from simulations into the mechanism of human topoisomerase I: Explanation for a seeming controversy in experiments. J Mol Graph Model 2013; 44:286-96. [DOI: 10.1016/j.jmgm.2013.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 11/27/2022]
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10
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11
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Wereszczynski J, Andricioaei I. Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition. Biophys J 2010; 99:869-78. [PMID: 20682265 DOI: 10.1016/j.bpj.2010.04.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 04/06/2010] [Accepted: 04/21/2010] [Indexed: 11/16/2022] Open
Abstract
Topoisomerases maintain the proper topological state of DNA. Human topoisomerase I removes DNA supercoils by clamping a duplex DNA segment, nicking one strand at a phosphodiester bond, covalently attaching to the 3' end of the nick, and allowing the DNA downstream of the cut to rotate around the intact strand. Using molecular dynamics simulations and umbrella sampling free energy calculations, we show that the rotation of downstream DNA in the grip of the enzyme that brings about release of positive or negative supercoils occurs by thermally assisted diffusion on ratchet energy profiles. The ratchetlike free-energy-versus-rotation profile that we compute provides a model for the function of topoisomerase in which the periodic maxima along the profile modulate the rate of supercoil relaxation, while the minima provide metastable conformational states for DNA religation. The results confirm previous experimental and computational work, and suggest that relaxation of the two types of supercoils involves distinct protein pathways. Additionally, simulations performed with the ternary complex of topoisomerase, DNA, and the chemotherapeutic drug topotecan show important differences in the mechanisms for supercoil relaxation when the drug is present, accounting for the relative values of relaxation rates measured in single-molecule experiments. Good agreement is found between rate constants from tweezer experiments and those calculated from simulations. Evidence is presented for the existence of semiopen states of the protein, which facilitate rotations after the initial one, as a result of biasing the protein into a conformation more favorable to strand rotation than the closed state required for nicking of the DNA.
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Affiliation(s)
- Jeff Wereszczynski
- Department of Chemistry, University of California, Irvine, California, USA
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12
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Koster DA, Crut A, Shuman S, Bjornsti MA, Dekker NH. Cellular strategies for regulating DNA supercoiling: a single-molecule perspective. Cell 2010; 142:519-30. [PMID: 20723754 PMCID: PMC2997354 DOI: 10.1016/j.cell.2010.08.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Entangling and twisting of cellular DNA (i.e., supercoiling) are problems inherent to the helical structure of double-stranded DNA. Supercoiling affects transcription, DNA replication, and chromosomal segregation. Consequently the cell must fine-tune supercoiling to optimize these key processes. Here, we summarize how supercoiling is generated and review experimental and theoretical insights into supercoil relaxation. We distinguish between the passive dissipation of supercoils by diffusion and the active removal of supercoils by topoisomerase enzymes. We also review single-molecule studies that elucidate the timescales and mechanisms of supercoil removal.
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Affiliation(s)
- Daniel A. Koster
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Aurélien Crut
- LASIM, Université Lyon 1-CNRS, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
| | - Stewart Shuman
- Molecular Biology Program, Sloan–Kettering Institute, New York, NY 10065, USA
| | - Mary-Ann Bjornsti
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 1670 University Blvd, Birmingham, AL 35294, USA
| | - Nynke H. Dekker
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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13
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Szklarczyk O, Staroń K, Cieplak M. Native state dynamics and mechanical properties of human topoisomerase I within a structure-based coarse-grained model. Proteins 2009; 77:420-31. [DOI: 10.1002/prot.22450] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Abstract
DNA topoisomerases are a diverse set of essential enzymes responsible for maintaining chromosomes in an appropriate topological state. Although they vary considerably in structure and mechanism, the partnership between topoisomerases and DNA has engendered commonalities in how these enzymes engage nucleic acid substrates and control DNA strand manipulations. All topoisomerases can harness the free energy stored in supercoiled DNA to drive their reactions; some further use the energy of ATP to alter the topology of DNA away from an enzyme-free equilibrium ground state. In the cell, topoisomerases regulate DNA supercoiling and unlink tangled nucleic acid strands to actively maintain chromosomes in a topological state commensurate with particular replicative and transcriptional needs. To carry out these reactions, topoisomerases rely on dynamic macromolecular contacts that alternate between associated and dissociated states throughout the catalytic cycle. In this review, we describe how structural and biochemical studies have furthered our understanding of DNA topoisomerases, with an emphasis on how these complex molecular machines use interfacial interactions to harness and constrain the energy required to manage DNA topology.
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15
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Palle K, Pattarello L, van der Merwe M, Losasso C, Benedetti P, Bjornsti MA. Disulfide cross-links reveal conserved features of DNA topoisomerase I architecture and a role for the N terminus in clamp closure. J Biol Chem 2008; 283:27767-27775. [PMID: 18693244 DOI: 10.1074/jbc.m804826200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, DNA topoisomerase I (Top1) catalyzes the relaxation of supercoiled DNA by a conserved mechanism of transient DNA strand breakage, rotation, and religation. The unusual architecture of the monomeric human enzyme comprises a conserved protein clamp, which is tightly wrapped about duplex DNA, and an extended coiled-coil linker domain that appropriately positions the C-terminal active site tyrosine domain against the Top1 core to form the catalytic pocket. A structurally undefined N-terminal domain, dispensable for enzyme activity, mediates protein-protein interactions. Previously, reversible disulfide bonds were designed to assess whether locking the Top1 clamp around duplex DNA would restrict DNA strand rotation within the covalent Top1-DNA intermediate. The active site proximal disulfide bond in full-length Top1-clamp(534) restricted DNA rotation (Woo, M. H., Losasso, C., Guo, H., Pattarello, L., Benedetti, P., and Bjornsti, M. A. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 13767-13772), whereas the more distal disulfide bond of the N-terminally truncated Topo70-clamp(499) did not (Carey, J. F., Schultz, S. J., Sisson, L., Fazzio, T. G., and Champoux, J. J. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 5640-5645). To assess the contribution of the N-terminal domain to the dynamics of Top1 clamping of DNA, the same disulfide bonds were engineered into full-length Top1 and truncated Topo70, and the activities of these proteins were assessed in vitro and in yeast. Here we report that the N terminus impacts the opening and closing of the Top1 protein clamp. We also show that the architecture of yeast and human Top1 is conserved in so far as cysteine substitutions of the corresponding residues suffice to lock the Top1-clamp. However, the composition of the divergent N-terminal/linker domains impacts Top1-clamp activity and stability in vivo.
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Affiliation(s)
- Komaraiah Palle
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38015
| | - Luca Pattarello
- Department of Biology, University of Padua, Via U. Bassi 58/B, Padova, PD 35131, Italy
| | - Marié van der Merwe
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38015
| | - Carmen Losasso
- Department of Biology, University of Padua, Via U. Bassi 58/B, Padova, PD 35131, Italy
| | - Piero Benedetti
- Department of Biology, University of Padua, Via U. Bassi 58/B, Padova, PD 35131, Italy.
| | - Mary-Ann Bjornsti
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38015.
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16
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van der Merwe M, Bjornsti MA. Mutation of Gly721 alters DNA topoisomerase I active site architecture and sensitivity to camptothecin. J Biol Chem 2007; 283:3305-3315. [PMID: 18056711 DOI: 10.1074/jbc.m705781200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA topoisomerase I (Top1p) catalyzes the relaxation of supercoiled DNA via a concerted mechanism of DNA strand cleavage and religation. Top1p is the cellular target of the anti-cancer drug camptothecin (CPT), which reversibly stabilizes a covalent enzyme-DNA intermediate. Top1p clamps around duplex DNA, wherein the core and C-terminal domains are connected by extended alpha-helices (linker domain), which position the active site Tyr of the C-terminal domain within the catalytic pocket. The physical connection of the linker with the Top1p clamp as well as linker flexibility affect enzyme sensitivity to CPT. Crystallographic data reveal that a conserved Gly residue (located at the juncture between the linker and C-terminal domains) is at one end of a short alpha-helix, which extends to the active site Tyr covalently linked to the DNA. In the presence of drug, the linker is rigid and this alpha-helix extends to include Gly and the preceding Leu. We report that mutation of this conserved Gly in yeast Top1p alters enzyme sensitivity to CPT. Mutating Gly to Asp, Glu, Asn, Gln, Leu, or Ala enhanced enzyme CPT sensitivity, with the acidic residues inducing the greatest increase in drug sensitivity in vivo and in vitro. By contrast, Val or Phe substituents rendered the enzyme CPT-resistant. Mutation-induced alterations in enzyme architecture preceding the active site Tyr suggest these structural transitions modulate enzyme sensitivity to CPT, while enhancing the rate of DNA cleavage. We postulate that this conserved Gly residue provides a flexible hinge within the Top1p catalytic pocket to facilitate linker dynamics and the structural alterations that accompany drug binding of the covalent enzyme-DNA intermediate.
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Affiliation(s)
- Marié van der Merwe
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Mary-Ann Bjornsti
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.
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17
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Frøhlich RF, Veigaard C, Andersen FF, McClendon AK, Gentry AC, Andersen AH, Osheroff N, Stevnsner T, Knudsen BR. Tryptophane-205 of human topoisomerase I is essential for camptothecin inhibition of negative but not positive supercoil removal. Nucleic Acids Res 2007; 35:6170-80. [PMID: 17827209 PMCID: PMC2094083 DOI: 10.1093/nar/gkm669] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Positive supercoils are introduced in cellular DNA in front of and negative supercoils behind tracking polymerases. Since DNA purified from cells is normally under-wound, most studies addressing the relaxation activity of topoisomerase I have utilized negatively supercoiled plasmids. The present report compares the relaxation activity of human topoisomerase I variants on plasmids containing equal numbers of superhelical twists with opposite handedness. We demonstrate that the wild-type enzyme and mutants lacking amino acids 1–206 or 191–206, or having tryptophane-205 replaced with a glycine relax positive supercoils faster than negative supercoils under both processive and distributive conditions. In contrast to wild-type topoisomerase I, which exhibited camptothecin sensitivity during relaxation of both negative and positive supercoils, the investigated N-terminally mutated variants were sensitive to camptothecin only during removal of positive supercoils. These data suggest different mechanisms of action during removal of supercoils of opposite handedness and are consistent with a recently published simulation study [Sari and Andricioaei (2005) Nucleic Acids Res., 33, 6621–6634] suggesting flexibility in distinct parts of the enzyme during clockwise or counterclockwise strand rotation.
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Affiliation(s)
- Rikke From Frøhlich
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Christopher Veigaard
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Félicie Faucon Andersen
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - A. Kathleen McClendon
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Amanda C. Gentry
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Anni Hangaard Andersen
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Neil Osheroff
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Tinna Stevnsner
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Birgitta Ruth Knudsen
- Department of Molecular Biology, Aarhus University, C. F. Møllers Allé Bldg. 130, 8000 Århus C, Denmark and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- *To whom correspondence should be addressed. +4589422703+4589422612
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18
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Koster DA, Palle K, Bot ESM, Bjornsti MA, Dekker NH. Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature 2007; 448:213-7. [PMID: 17589503 DOI: 10.1038/nature05938] [Citation(s) in RCA: 213] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2007] [Accepted: 05/15/2007] [Indexed: 11/09/2022]
Abstract
Increasing the ability of chemotherapeutic drugs to kill cancer cells is often hampered by a limited understanding of their mechanism of action. Camptothecins, such as topotecan, induce cell death by poisoning DNA topoisomerase I, an enzyme capable of removing DNA supercoils. Topotecan is thought to stabilize a covalent topoisomerase-DNA complex, rendering it an obstacle to DNA replication forks. Here we use single-molecule nanomanipulation to monitor the dynamics of human topoisomerase I in the presence of topotecan. This allowed us to detect the binding and unbinding of an individual topotecan molecule in real time and to quantify the drug-induced trapping of topoisomerase on DNA. Unexpectedly, our findings also show that topotecan significantly hinders topoisomerase-mediated DNA uncoiling, with a more pronounced effect on the removal of positive (overwound) versus negative supercoils. In vivo experiments in the budding yeast verified the resulting prediction that positive supercoils would accumulate during transcription and replication as a consequence of camptothecin poisoning of topoisomerase I. Positive supercoils, however, were not induced by drug treatment of cells expressing a catalytically active, camptothecin-resistant topoisomerase I mutant. This combination of single-molecule and in vivo data suggests a cytotoxic mechanism for camptothecins, in which the accumulation of positive supercoils ahead of the replication machinery induces potentially lethal DNA lesions.
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Affiliation(s)
- Daniel A Koster
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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19
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Chillemi G, Bruselles A, Fiorani P, Bueno S, Desideri A. The open state of human topoisomerase I as probed by molecular dynamics simulation. Nucleic Acids Res 2007; 35:3032-8. [PMID: 17439970 PMCID: PMC1888835 DOI: 10.1093/nar/gkm199] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The open state of human topoisomerase I has been probed by molecular dynamics simulation, starting from the coordinates of the closed structure of the protein complexed with DNA, after elimination of the 22-bp DNA duplex oligonucleotide. A repulsion force between the two lips of the protein has been introduced for a short time to induce destabilization of the local minimum, after which an unperturbed simulation has been carried out for 10 ns. The simulation shows that the protein undergoes a large conformational change due to rearrangements in the orientation of the protein domains, which however move as a coherent unit, fully maintaining their secondary and tertiary structures. Despite movements between the domains as large as 80-90 A, the catalytic pentad remains preassembled, the largest deviation of the active site backbone atoms from the starting crystallographic structure being only 1.7 A. Electrostatic calculation of the open protein structure shows that the protein displays a vast positive region with the active site residues located nearly at its center, in a conformation perfectly suited to interact with the negatively charged supercoiled DNA substrate.
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Affiliation(s)
- Giovanni Chillemi
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Alessandro Bruselles
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Paola Fiorani
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Susana Bueno
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Alessandro Desideri
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
- *To whom correspondence should be addressed. +39 0672594376+39 062022798
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20
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Christmann-Franck S, Fermandjian S, Mirambeau G, Der Garabedian PA. Molecular modelling studies on the interactions of human DNA topoisomerase IB with pyridoxal-compounds. Biochimie 2007; 89:468-73. [PMID: 17116355 DOI: 10.1016/j.biochi.2006.10.007] [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: 08/11/2006] [Accepted: 10/10/2006] [Indexed: 11/27/2022]
Abstract
Candida guilliermondii and human DNA topoisomerases I are inhibited by PL (pyridoxal), PLP (pyridoxal 5'-phosphate) and PLP-AMP (pyridoxal 5'-diphospho-5'-adenosine) (PL<PLP<PLP-AMP). We have recently shown that PLP acted as a competitive inhibitor of C. guilliermondii topoisomerase I, impeding the formation of the cleavable complex from a selective binding to an active site lysine. The targeted lysine in C. guilliermondii topoisomerase I occupies a position equivalent to that of lysine 532 (K(532)) in human topoisomerase I. K(532) acts as a general acid catalyst and is essential for the enzyme activity. This observation has suggested that, in the cell, PLP could down-regulate topoisomerases IB. We have proposed that PLP could be used as a new lead for anticancer drugs trapping the active site lysine (K(532)) and also as a tool to explore the enzyme dynamics required for catalysis. Now we explore the effects of PL, PLP and PLP-AMP on topoisomerases by a molecular modelling approach using the crystal structure of the human topoisomerase I active site and the conformation of K(39)-PLP moiety in Bacillus subtilis alanine racemase as templates. In the modified topoisomerase I several reactive atoms of the K(532)-PLP moiety are at close distance of the catalytic residues R(488), R(590), H(632) and Y(723,) suggesting that PLP develops disturbing interactions with these important residues. These interactions and the corresponding induced fit in the active site conformation are compared with the ones occurring with PL and PLP-AMP. The results could be useful in the search of topoisomerase I inhibitors related to the pyridoxal family.
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Affiliation(s)
- Serge Christmann-Franck
- Département de Biologie et Pharmacologie Structurales, CNRS UMR 8113, Institut Gustave Roussy et ENS Cachan, 61 Avenue du Président Wilson, 94235 Cachan Cedex, France
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21
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Montaudon D, Palle K, Rivory LP, Robert J, Douat-Casassus C, Quideau S, Bjornsti MA, Pourquier P. Inhibition of topoisomerase I cleavage activity by thiol-reactive compounds: importance of vicinal cysteines 504 and 505. J Biol Chem 2007; 282:14403-12. [PMID: 17355975 DOI: 10.1074/jbc.m611673200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA topoisomerase I (Top1) is a nuclear enzyme that plays a crucial role in the removal of DNA supercoiling associated with replication and transcription. It is also the target of the anticancer agent, camptothecin (CPT). Top1 contains eight cysteines, including two vicinal residues (504 and 505), which are highly conserved across species. In this study, we show that thiol-reactive compounds such as N-ethylmaleimide and phenylarsine oxide can impair Top1 catalytic activity. We demonstrate that in contrast to CPT, which inhibits Top1-catalyzed religation, thiolation of Top1 inhibited the DNA cleavage step of the reaction. This inhibition was more pronounced when Top1 was preincubated with the thiol-reactive compound and could be reversed in the presence of dithiothreitol. We also established that phenylarsine oxide-mediated inhibition of Top1 cleavage involved the two vicinal cysteines 504 and 505, as this effect was suppressed when cysteines were mutated to alanines. Interestingly, mutation of Cys-505 also altered Top1 sensitivity to CPT, even in the context of the double Cys-504 to Cys-505 mutant, which relaxed supercoiled DNA with a comparable efficiency to that of wild-type Top1. This indicates that cysteine 505, which is located in the lower Lip domain of human Top1, is critical for optimal poisoning of the enzyme by CPT and its analogs. Altogether, our results suggest that conserved vicinal cysteines 504 and 505 of human Top1 play a critical role in enzyme catalytic activity and are the target of thiol-reactive compounds, which may be developed as efficient Top1 catalytic inhibitors.
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Affiliation(s)
- Danièle Montaudon
- Groupe de Pharmacologie Moléculaire INSERM E347 and Institut Bergonié, 229 Cours de l'Argonne, Université Victor Segalen Bordeaux II, 146 Rue Léo Saignat, 33076 Bordeaux Cedex, France
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22
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Losasso C, Cretaio E, Palle K, Pattarello L, Bjornsti MA, Benedetti P. Alterations in linker flexibility suppress DNA topoisomerase I mutant-induced cell lethality. J Biol Chem 2007; 282:9855-9864. [PMID: 17276985 DOI: 10.1074/jbc.m608200200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic DNA topoisomerase I (Top1p) catalyzes changes in DNA topology via the formation of a covalent enzyme-DNA intermediate, which is reversibly stabilized by the anticancer agent camptothecin (CPT). Crystallographic studies of the 70-kDa C terminus of human Top1p bound to duplex DNA describe a monomeric protein clamp circumscribing the DNA helix. The structures, which lack the N-terminal domain, comprise the conserved clamp, an extended linker domain, and the conserved C-terminal active site Tyr domain. CPT bound to the covalent Top1p-DNA complex limits linker flexibility, allowing structural determination of this domain. We previously reported that mutation of Ala(653) to Pro in the linker increases the rate of enzyme-catalyzed DNA religation, thereby rendering Top1A653Pp resistant to CPT (Fiorani, P., Bruselles, A., Falconi, M., Chillemi, G., Desideri, A., and Benedetti P. (2003) J. Biol. Chem. 278, 43268-43275). Molecular dynamics studies suggested mutation-induced increases in linker flexibility alter Top1p catalyzed DNA religation. To address the functional consequences of linker flexibility on enzyme catalysis and drug sensitivity, we investigated the interactions of the A653P linker mutation with a self-poisoning T718A mutation within the active site of Top1p. The A653P mutation suppressed the lethal phenotype of Top1T718Ap in yeast, yet did not restore enzyme sensitivity to CPT. However, the specific activity of the double mutant was decreased in vivo and in vitro, consistent with a decrease in DNA binding. These findings support a model where changes in the flexibility or orientation of the linker alter the geometry of the active site and thereby the kinetics of DNA cleavage/religation catalyzed by Top1p.
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Affiliation(s)
- Carmen Losasso
- Department of Biology, University of Padua, Padua 35131, Italy
| | - Erica Cretaio
- Department of Biology, University of Padua, Padua 35131, Italy
| | - Komaraiah Palle
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38104
| | - Luca Pattarello
- Department of Biology, University of Padua, Padua 35131, Italy
| | - Mary-Ann Bjornsti
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38104
| | - Piero Benedetti
- Department of Biology, University of Padua, Padua 35131, Italy.
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23
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Hede MS, Petersen RL, Frøhlich RF, Krüger D, Andersen FF, Andersen AH, Knudsen BR. Resolution of Holliday junction substrates by human topoisomerase I. J Mol Biol 2006; 365:1076-92. [PMID: 17101150 DOI: 10.1016/j.jmb.2006.10.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 09/15/2006] [Accepted: 10/15/2006] [Indexed: 11/23/2022]
Abstract
Prompted by the close relationship between tyrosine recombinases and type IB topoisomerases we have investigated the ability of human topoisomerase I to resolve the typical intermediate of recombinase catalysis, the Holliday junction. We demonstrate that human topoisomerase I catalyzes unidirectional resolution of a synthetic Holliday junction substrate containing two preferred cleavage sites surrounded by DNA sequences supporting branch migration. Deleting part of the N-terminal domain (amino acid residues 1-202) did not affect topoisomerase I resolution activity, whereas a topoisomerase I variant lacking both the N-terminal domain and amino acid residues 660-688 of the linker domain was unable to resolve the Holliday junction substrate. The inability of the double deleted variant to mediate resolution correlated with the inability of this enzyme to introduce concomitant cleavage at the two preferred cleavage sites in a single Holliday junction substrate, which is a prerequisite for resolution. As determined by the gel electrophoretic mobility of native enzyme or enzyme crosslinked by disulfide bridging, the double deleted mutant existed almost entirely in a dimeric form. The impairment of this enzyme in performing double cleavages on the Holliday junction substrate may be explained by only one cleavage competent active site being formed at a time within the dimer. The assembly of only one active site within dimers is a well-known characteristic of the tyrosine recombinases. Hence, the obtained results may suggest a recombinase-like active site assembly of the double deleted topoisomerase I variant. Taken together the presented results consolidate the relationship between type IB topoisomerases and tyrosine recombinases.
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Affiliation(s)
- Marianne S Hede
- Department of Molecular Biology, University of Aarhus, C.F. Møllers Allé, Building 130, DK-8000, Aarhus C, Denmark
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24
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Marchand C, Antony S, Kohn KW, Cushman M, Ioanoviciu A, Staker BL, Burgin AB, Stewart L, Pommier Y. A novel norindenoisoquinoline structure reveals a common interfacial inhibitor paradigm for ternary trapping of the topoisomerase I-DNA covalent complex. Mol Cancer Ther 2006; 5:287-95. [PMID: 16505102 PMCID: PMC2860177 DOI: 10.1158/1535-7163.mct-05-0456] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We show that five topoisomerase I inhibitors (two indenoisoquinolines, two camptothecins, and one indolocarbazole) each intercalate between the base pairs flanking the cleavage site generated during the topoisomerase I catalytic cycle and are further stabilized by a network of hydrogen bonds with topoisomerase I. The interfacial inhibition paradigm described for topoisomerase I inhibitors can be generalized to a variety of natural products that trap macromolecular complexes as they undergo catalytic conformational changes that create hotspots for drug binding. Stabilization of such conformational states results in uncompetitive inhibition and exemplifies the relevance of screening for ligands and drugs that stabilize ("trap") these macromolecular complexes.
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Affiliation(s)
- Christophe Marchand
- Laboratory of Molecular Pharmacology, Bldg. 37, Rm. 5068, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4255
| | - Smitha Antony
- Laboratory of Molecular Pharmacology, Bldg. 37, Rm. 5068, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4255
| | - Kurt W. Kohn
- Laboratory of Molecular Pharmacology, Bldg. 37, Rm. 5068, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4255
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, IN 47907
| | - Alexandra Ioanoviciu
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, School of Pharmacy and Pharmaceutical Sciences, Purdue University, West Lafayette, IN 47907
| | - Bart L. Staker
- deCODE biostructures, Inc., 7869 Northeast Day Road West, Bainbridge Island, WA 98110
| | - Alex B. Burgin
- deCODE biostructures, Inc., 7869 Northeast Day Road West, Bainbridge Island, WA 98110
| | - Lance Stewart
- deCODE biostructures, Inc., 7869 Northeast Day Road West, Bainbridge Island, WA 98110
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Bldg. 37, Rm. 5068, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4255
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25
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Alfadhli A, Dhenub TC, Still A, Barklis E. Analysis of human immunodeficiency virus type 1 Gag dimerization-induced assembly. J Virol 2006; 79:14498-506. [PMID: 16282449 PMCID: PMC1287545 DOI: 10.1128/jvi.79.23.14498-14506.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleocapsid (NC) domains of retrovirus precursor Gag (PrGag) proteins play an essential role in virus assembly. Evidence suggests that NC binding to viral RNA promotes dimerization of PrGag capsid (CA) domains, which triggers assembly of CA N-terminal domains (NTDs) into hexamer rings that are interconnected by CA C-terminal domains. To examine the influence of dimerization on human immunodeficiency virus type 1 (HIV-1) Gag protein assembly in vitro, we analyzed the assembly properties of Gag proteins in which NC domains were replaced with cysteine residues that could be linked via chemical treatment. In accordance with the model that Gag protein pairing triggers assembly, we found that cysteine cross-linking or oxidation reagents induced the assembly of virus-like particles. However, efficient assembly also was observed to be temperature dependent or required the tethering of NTDs. Our results suggest a multistep pathway for HIV-1 Gag protein assembly. In the first step, Gag protein pairing through NC-RNA interactions or C-terminal cysteine linkage fosters dimerization. Next, a conformational change converts assembly-restricted dimers or small oligomers into assembly-competent ones. At the final stage, final particle assembly occurs, possibly through a set of larger intermediates.
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Affiliation(s)
- Ayna Alfadhli
- Vollum Institute and Department of Microbiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97201, USA
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26
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Pommier Y, Barcelo J, Rao VA, Sordet O, Jobson AG, Thibaut L, Miao Z, Seiler J, Zhang H, Marchand C, Agama K, Redon C. Repair of topoisomerase I-mediated DNA damage. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2006; 81:179-229. [PMID: 16891172 PMCID: PMC2576451 DOI: 10.1016/s0079-6603(06)81005-6] [Citation(s) in RCA: 234] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Topoisomerase I (Top1) is an abundant and essential enzyme. Top1 is the selective target of camptothecins, which are effective anticancer agents. Top1-DNA cleavage complexes can also be trapped by various endogenous and exogenous DNA lesions including mismatches, abasic sites and carcinogenic adducts. Tyrosyl-DNA phosphodiesterase (Tdp1) is one of the repair enzymes for Top1-DNA covalent complexes. Tdp1 forms a multiprotein complex that includes poly(ADP) ribose polymerase (PARP). PARP-deficient cells are hypersensitive to camptothecins and functionally deficient for Tdp1. We will review recent developments in several pathways involved in the repair of Top1 cleavage complexes and the role of Chk1 and Chk2 checkpoint kinases in the cellular responses to Top1 inhibitors. The genes conferring camptothecin hypersensitivity are compiled for humans, budding yeast and fission yeast.
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Affiliation(s)
- Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Juana Barcelo
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - V. Ashutosh Rao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Olivier Sordet
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Andrew G. Jobson
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Laurent Thibaut
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Zheyong Miao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Jennifer Seiler
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Christophe Redon
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
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27
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Patel A, Shuman S, Mondragón A. Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA. J Biol Chem 2005; 281:6030-7. [PMID: 16368685 DOI: 10.1074/jbc.m512332200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type IB DNA topoisomerases are found in all eukarya, two families of eukaryotic viruses (poxviruses and mimivirus), and many genera of bacteria. They alter DNA topology by cleaving and resealing one strand of duplex DNA via a covalent DNA-(3-phosphotyrosyl)-enzyme intermediate. Bacterial type IB enzymes were discovered recently and are described as poxvirus-like with respect to their small size, primary structures, and bipartite domain organization. Here we report the 1.75-A crystal structure of Deinococcus radiodurans topoisomerase IB (DraTopIB), a prototype of the bacterial clade. DraTopIB consists of an amino-terminal (N) beta-sheet domain (amino acids 1-90) and a predominantly alpha-helical carboxyl-terminal (C) domain (amino acids 91-346) that closely resemble the corresponding domains of vaccinia virus topoisomerase IB. The five amino acids of DraTopIB that comprise the catalytic pentad (Arg-137, Lys-174, Arg-239, Asn-280, and Tyr-289) are preassembled into the active site in the absence of DNA in a manner nearly identical to the pentad configuration in human topoisomerase I bound to DNA. This contrasts with the apoenzyme of vaccinia topoisomerase, in which three of the active site constituents are either displaced or disordered. The N and C domains of DraTopIB are splayed apart in an "open" conformation, in which the surface of the catalytic domain containing the active site is exposed for DNA binding. A comparison with the human topoisomerase I-DNA cocrystal structure suggests how viral and bacterial topoisomerase IB enzymes might bind DNA circumferentially via movement of the N domain into the major groove and clamping of a disordered loop of the C domain around the helix.
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Affiliation(s)
- Asmita Patel
- Department of Biochemistry, Molecular and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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28
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Sari L, Andricioaei I. Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation. Nucleic Acids Res 2005; 33:6621-34. [PMID: 16314322 PMCID: PMC1298917 DOI: 10.1093/nar/gki935] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Topoisomerases are enzymes of quintessence to the upkeep of superhelical DNA, and are vital for replication, transcription and recombination. An atomic-resolution model for human topoisomerase I in covalent complex with DNA is simulated using molecular dynamics with external potentials that mimic torque and bias the DNA duplex downstream of a single-strand cut to rotate around the intact strand, according to the prevailing enzymatic mechanism. The simulations reveal the first dynamical picture of how topoisomerase accommodates large-scale motion of DNA as it changes its supercoiling state, and indicate that relaxation of positive and negative supercoils are fundamentally different. To relax positive supercoils, two separate domains (the 'lips') of the protein open up by about 10-14 A, whereas to relax negative supercoils, a continuous loop connecting the upper and lower parts (and which was a hinge for opening the lips) stretches about 12 A while the lips remain unseparated. Normal mode analysis is additionally used to characterize the functional flexibility of the protein. Remarkably, the same combination of low-frequency eigenvectors exhibit the dominant contribution for both rotation mechanisms through a see-saw motion. The simulated mechanisms suggest mutations to control the relaxation of either type of supercoiling selectively and advance a hypothesis for the debated role of the N-terminal domain in supercoil relaxation.
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Affiliation(s)
| | - Ioan Andricioaei
- To whom correspondence should be addressed. Tel: +1 734 763 8013; Fax: +1 734 615 6553;
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29
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Li J, Spletter ML, Johnson DA, Wright LS, Svendsen CN, Johnson JA. Rotenone-induced caspase 9/3-independent and -dependent cell death in undifferentiated and differentiated human neural stem cells. J Neurochem 2005; 92:462-76. [PMID: 15659217 DOI: 10.1111/j.1471-4159.2004.02872.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We used human neural stem cells (hNSCs) and their differentiated cultures as a model system to evaluate the mechanism(s) involved in rotenone (RO)- and camptothecin (CA)-induced cytotoxicity. Results from ultrastructural damage and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining indicated that RO-induced cytotoxicity resembled CA-induced apoptosis more than H(2)O(2)-induced necrosis. However, unlike CA-induced, caspase 9/3-dependent apoptosis, there was no increased activity in caspase 9, caspase 3 or poly (ADP-ribose) polymerase (PARP) cleavage in RO-induced cytotoxicity, in spite of time-dependent release of cytochrome c and apoptosis-inducing factor (AIF) following mitochondrial membrane depolarization and a significant increase in reactive oxygen species generation. Equal doses of RO and CA used in hNSCs induced caspase 9/3-dependent apoptosis in differentiated cultures. Time-dependent ATP depletion occurred earlier and to a greater extent in RO-treated hNSCs than in CA-treated hNSCs, or differentiated cultures treated with RO or CA. In conclusion, these results represent a unique ultrastructural and molecular characterization of RO- and CA-induced cytotoxicity in hNSCs and their differentiated cultures. Intracellular ATP levels may play an important role in determining whether neural progenitors or their differentiated cells follow a caspase 9/3-dependent or -independent pathway in response to acute insults from neuronal toxicants.
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Affiliation(s)
- Jiang Li
- School of Pharmacy, University of Wisconsin at Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA
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30
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Chillemi G, Fiorani P, Castelli S, Bruselles A, Benedetti P, Desideri A. Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study. Nucleic Acids Res 2005; 33:3339-50. [PMID: 15944452 PMCID: PMC1145191 DOI: 10.1093/nar/gki642] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The functional and dynamical properties of the human topoisomerase I Thr718Ala mutant have been compared to that of the wild-type enzyme using functional assays and molecular dynamics (MD) simulations. At physiological ionic strength, the cleavage and religation rates, evaluated on oligonucleotides containing the preferred topoisomerase I DNA sequence, are almost identical for the wild-type and the mutated enzymes, as is the cleavage/religation equilibrium. On the other hand, the Thr718Ala mutant shows a decreased efficiency in a DNA plasmid relaxation assay. The MD simulation, carried out on the enzyme complexed with its preferred DNA substrate, indicates that the mutant has a different dynamic behavior compared to the wild-type enzyme. Interestingly, no changes are observed in the proximity of the mutation site, whilst a different flexibility is detected in regions contacting the DNA scissile strand, such as the linker and the V-shaped α helices. Taken together, the functional and simulation results indicate a direct communication between the mutation site and regions located relatively far away, such as the linker domain, that with their altered flexibility confer a reduced DNA relaxation efficiency. These results provide evidence that the comprehension of the topoisomerase I dynamical properties are an important element in the understanding of its complex catalytic cycle.
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Affiliation(s)
- Giovanni Chillemi
- CASPUR Interuniversities Consortium for Supercomputing ApplicationsVia dei Tizii 6b, Rome 00185, Italy
| | - Paola Fiorani
- Department of Biology, National Institute for the Physics of Matter, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
| | - Silvia Castelli
- Department of Biology, National Institute for the Physics of Matter, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
| | - Alessandro Bruselles
- CASPUR Interuniversities Consortium for Supercomputing ApplicationsVia dei Tizii 6b, Rome 00185, Italy
- Department of Biology, National Institute for the Physics of Matter, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
| | - Piero Benedetti
- Department of Biology, University of PaduaVia Ugo Bassi 58/B, Padua 35131, Italy
| | - Alessandro Desideri
- Department of Biology, National Institute for the Physics of Matter, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
- To whom correspondence should be addressed. Tel: +39 06 72594376; Fax: +39 06 2022798;
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31
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Leppard JB, Champoux JJ. Human DNA topoisomerase I: relaxation, roles, and damage control. Chromosoma 2005; 114:75-85. [PMID: 15830206 DOI: 10.1007/s00412-005-0345-5] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Revised: 03/29/2005] [Accepted: 03/30/2005] [Indexed: 11/28/2022]
Abstract
Human DNA topoisomerase I is an essential enzyme involved in resolving the torsional stress associated with DNA replication, transcription, and chromatin condensation. The catalytic cycle of the enzyme consists of DNA cleavage to form a covalent enzyme-DNA intermediate, DNA relaxation, and finally, re-ligation of the phosphate backbone to restore the continuity of the DNA. Structure/function studies have elucidated a flexible enzyme that relaxes DNA through coordinated, controlled movements of distinct enzyme domains. The cellular roles of topoisomerase I are apparent throughout the nucleus, but the concentration of processes acting on ribosomal DNA results in topoisomerase I accumulation in the nucleolus. Although the activity of topoisomerase I is required in these processes, the enzyme can also have a deleterious effect on cells. In the event that the final re-ligation step of the reaction cycle is prevented, the covalent topoisomerase I-DNA intermediate becomes a toxic DNA lesion that must be repaired. The complexities of the relaxation reaction, the cellular roles, and the pathways that must exist to repair topoisomerase I-mediated DNA damage highlight the importance of continued study of this essential enzyme.
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Affiliation(s)
- John B Leppard
- Department of Microbiology, School of Medicine, University of Washington, P.O. Box 357242, 1959 N.E. Pacific St., Seattle, WA 98195-7242, USA
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32
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Koster DA, Croquette V, Dekker C, Shuman S, Dekker NH. Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature 2005; 434:671-4. [PMID: 15800630 DOI: 10.1038/nature03395] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Accepted: 01/25/2005] [Indexed: 11/09/2022]
Abstract
Topoisomerases relieve the torsional strain in DNA that is built up during replication and transcription. They are vital for cell proliferation and are a target for poisoning by anti-cancer drugs. Type IB topoisomerase (TopIB) forms a protein clamp around the DNA duplex and creates a transient nick that permits removal of supercoils. Using real-time single-molecule observation, we show that TopIB releases supercoils by a swivel mechanism that involves friction between the rotating DNA and the enzyme cavity: that is, the DNA does not freely rotate. Unlike a nicking enzyme, TopIB does not release all the supercoils at once, but it typically does so in multiple steps. The number of supercoils removed per step follows an exponential distribution. The enzyme is found to be torque-sensitive, as the mean number of supercoils per step increases with the torque stored in the DNA. We propose a model for topoisomerization in which the torque drives the DNA rotation over a rugged periodic energy landscape in which the topoisomerase has a small but quantifiable probability to religate the DNA once per turn.
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Affiliation(s)
- Daniel A Koster
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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33
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Colley WC, van der Merwe M, Vance JR, Burgin AB, Bjornsti MA. Substitution of Conserved Residues within the Active Site Alters the Cleavage Religation Equilibrium of DNA Topoisomerase I. J Biol Chem 2004; 279:54069-78. [PMID: 15489506 DOI: 10.1074/jbc.m409764200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic DNA topoisomerase I (Top1p) catalyzes the relaxation of supercoiled DNA and constitutes the cellular target of camptothecin (CPT). Mutation of conserved residues in close proximity to the active site tyrosine (Tyr(727) of yeast Top1p) alters the DNA cleavage religation equilibrium, inducing drug-independent cell lethality. Previous studies indicates that yeast Top1T722Ap and Top1N726Hp cytotoxicity results from elevated levels of covalent enzyme-DNA intermediates. Here we show that Top1T722Ap acts as a CPT mimetic by exhibiting reduced rates of DNA religation, whereas increased Top1N726Hp.DNA complexes result from elevated DNA binding and cleavage. We also report that the combination of the T722A and N726H mutations in a single protein potentiates the cytotoxic action of the enzyme beyond that induced by co-expression of the single mutants. Moreover, the addition of CPT to cells expressing the double top1T722A/N726H mutant did not enhance cell lethality. Thus, independent alterations in DNA cleavage and religation contribute to the lethal phenotype. The formation of distinct cytotoxic lesions was also evidenced by the different responses induced by low levels of these self-poisoning enzymes in isogenic strains defective for the Rad9 DNA damage checkpoint, processive DNA replication, or ubiquitin-mediated proteolysis. Substitution of Asn(726) with Phe or Tyr also produces self-poisoning enzymes, implicating stacking interactions in the increased kinetics of DNA cleavage by Top1N726Hp and Top1N726Fp. In contrast, replacing the amide side chain of Asn(726) with Gln renders Top1N726Qp resistant to CPT, suggesting that the orientation of the amide within the active site is critical for effective CPT binding.
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Affiliation(s)
- William C Colley
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Vermeersch JJ, Christmann-Franck S, Karabashyan LV, Fermandjian S, Mirambeau G, Der Garabedian PA. Pyridoxal 5'-phosphate inactivates DNA topoisomerase IB by modifying the lysine general acid. Nucleic Acids Res 2004; 32:5649-57. [PMID: 15494452 PMCID: PMC524305 DOI: 10.1093/nar/gkh897] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 07/16/2004] [Accepted: 09/30/2004] [Indexed: 11/14/2022] Open
Abstract
The present results demonstrate that pyridoxal, pyridoxal 5'-phosphate (PLP) and pyridoxal 5'-diphospho-5'-adenosine (PLP-AMP) inhibit Candida guilliermondii and human DNA topoisomerases I in forming an aldimine with the epsilon-amino group of an active site lysine. PLP acts as a competitive inhibitor of C.guilliermondii topoisomerase I (K(i) = 40 microM) that blocks the cleavable complex formation. Chemical reduction of PLP-treated enzyme reveals incorporation of 1 mol of PLP per mol of protein. The limited trypsic proteolysis releases a 17 residue peptide bearing a lysine-bound PLP (KPPNTVIFDFLGK*DSIR). Targeted lysine (K*) in C.guilliermondii topoisomerase I corresponds to that found in topoisomerase I of Homo sapiens (K532), Candida albicans (K468), Saccharomyces cerevisiae (K458) and Schizosaccharomyces pombe (K505). In the human enzyme, K532, belonging to the active site acts as a general acid catalyst and is therefore essential for activity. The spatial orientation of K532-PLP within the active site was approached by molecular modeling using available crystallographic data. The PLP moiety was found at close proximity of several active residues. PLP could be involved in the cellular control of topoisomerases IB. It constitutes an efficient tool to explore topoisomerase IB dynamics during catalysis and is also a lead for new drugs that trap the lysine general acid.
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Affiliation(s)
- Jacqueline J Vermeersch
- Biochimie des Signaux Régulateurs Cellulaires et Moléculaires, Université Pierre et Marie Curie, CNRS FRE 2621, 96 Boulevard Raspail, 75006 Paris, France
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35
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Chillemi G, Redinbo M, Bruselles A, Desideri A. Role of the linker domain and the 203-214 N-terminal residues in the human topoisomerase I DNA complex dynamics. Biophys J 2004; 87:4087-97. [PMID: 15347588 PMCID: PMC1304917 DOI: 10.1529/biophysj.104.044925] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The influence of the N-terminal residues 203-214 and the linker domain on motions in the human topoisomerase I-DNA complex has been investigated by comparing the molecular dynamics simulations of the system with (topo70) or without (topo58/6.3) these regions. Topo58/6.3 is found to fluctuate more than topo70, indicating that the presence of the N-terminal residues and the linker domain dampen the core and C-terminal fluctuations. The simulations also show that residues 203-207 and the linker domain participate in a network of correlated movements with key regions of the enzyme, involved in the human topoisomerase I catalytic cycle, providing a structural-dynamical explanation for the better DNA relaxation activity of topo70 when compared to topo58/6.3. The data have been examined in relation to a wealth of biochemical, site-directed mutagenesis and crystallographic data on human topoisomerase I. The simulations finally show the occurrence of a network of direct and water mediated hydrogen bonds in the proximity of the active site, and the presence of a water molecule in the appropriate position to accept a proton from the catalytic Tyr-723 residue, suggesting that water molecules have an important role in the stabilization and function of this enzyme.
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Affiliation(s)
- G Chillemi
- CASPUR, Consortium for Supercomputing in Research, Via dei Tizii 6b, Rome, Italy
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36
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Chrencik JE, Staker BL, Burgin AB, Pourquier P, Pommier Y, Stewart L, Redinbo MR. Mechanisms of camptothecin resistance by human topoisomerase I mutations. J Mol Biol 2004; 339:773-84. [PMID: 15165849 DOI: 10.1016/j.jmb.2004.03.077] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 03/30/2004] [Accepted: 03/31/2004] [Indexed: 11/28/2022]
Abstract
Human topoisomerase I relaxes superhelical tension associated with DNA replication, transcription and recombination by reversibly nicking one strand of duplex DNA and forming a covalent 3'-phosphotyrosine linkage. This enzyme is the sole target of the camptothecin family of anticancer compounds, which acts by stabilizing the covalent protein-DNA complex and enhancing apoptosis through blocking the advancement of replication forks. Mutations that impart resistance to camptothecin have been identified in several regions of human topoisomerase I. We present the crystal structures of two camptothecin-resistant forms of human topoisomerase I (Phe361Ser at 2.6A resolution and Asn722Ser at 2.3A resolution) in ternary complexes with DNA and topotecan (Hycamtin), a camptothecin analogue currently in widespread clinical use. While the alteration of Asn722 to Ser leads to the elimination of a water-mediated contact between the enzyme and topotecan, we were surprised to find that a well-ordered water molecule replaces the hydrophobic phenylalanine side-chain in the Phe361Ser structure. We further consider camptothecin-resistant mutations at seven additional sites in human topoisomerase I and present structural evidence explaining their possible impact on drug binding. These results advance our understanding of the mechanism of cell poisoning by camptothecin and suggest specific modifications to the drug that may improve efficacy.
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Affiliation(s)
- Jill E Chrencik
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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