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Tan T, Tan Y, Wang Y, Yang X, Zhai B, Zhang S, Yang X, Nie H, Gao J, Zhou J, Zhang L, Wang S. Negative supercoils regulate meiotic crossover patterns in budding yeast. Nucleic Acids Res 2022; 50:10418-10435. [PMID: 36107772 PMCID: PMC9561271 DOI: 10.1093/nar/gkac786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/21/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
Interference exists ubiquitously in many biological processes. Crossover interference patterns meiotic crossovers, which are required for faithful chromosome segregation and evolutionary adaption. However, what the interference signal is and how it is generated and regulated is unknown. We show that yeast top2 alleles which cannot bind or cleave DNA accumulate a higher level of negative supercoils and show weaker interference. However, top2 alleles which cannot religate the cleaved DNA or release the religated DNA accumulate less negative supercoils and show stronger interference. Moreover, the level of negative supercoils is negatively correlated with crossover interference strength. Furthermore, negative supercoils preferentially enrich at crossover-associated Zip3 regions before the formation of meiotic DNA double-strand breaks, and regions with more negative supercoils tend to have more Zip3. Additionally, the strength of crossover interference and homeostasis change coordinately in mutants. These findings suggest that the accumulation and relief of negative supercoils pattern meiotic crossovers.
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Affiliation(s)
- Taicong Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Yingjin Tan
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Ying Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Xiao Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University , Jinan, Shandong 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education , Jinan, Shandong 250001, China
- Shandong Provincial Clinical Research Center for Reproductive Health , Jinan, Shandong 250012, China
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
| | - Binyuan Zhai
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University , Jinan, Shandong 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education , Jinan, Shandong 250001, China
- Shandong Provincial Clinical Research Center for Reproductive Health , Jinan, Shandong 250012, China
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
| | - Shuxian Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- Advanced Medical Research Institute, Shandong University , Jinan, Shandong 250012, China
| | - Xuan Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
| | - Hui Nie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Jinmin Gao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Liangran Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- Advanced Medical Research Institute, Shandong University , Jinan, Shandong 250012, China
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University , Jinan 250014, Shandong, China
| | - Shunxin Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, State Key Laboratory of Microbial Technology, Shandong University , China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University , Jinan, Shandong 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education , Jinan, Shandong 250001, China
- Shandong Provincial Clinical Research Center for Reproductive Health , Jinan, Shandong 250012, China
- Shandong Key Laboratory of Reproductive Medicine , Jinan, Shandong 250012, China
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2
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Topoisomerase IIIβ Deficiency Induces Neuro-Behavioral Changes and Brain Connectivity Alterations in Mice. Int J Mol Sci 2021; 22:ijms222312806. [PMID: 34884616 PMCID: PMC8657541 DOI: 10.3390/ijms222312806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
Topoisomerase IIIβ (Top3β), the only dual-activity topoisomerase in mammals that can change topology of both DNA and RNA, is known to be associated with neurodevelopment and mental dysfunction in humans. However, there is no report showing clear associations of Top3β with neuropsychiatric phenotypes in mice. Here, we investigated the effect of Top3β on neuro-behavior using newly generated Top3β deficient (Top3β-/-) mice. We found that Top3β-/- mice showed decreased anxiety and depression-like behaviors. The lack of Top3β was also associated with changes in circadian rhythm. In addition, a clear expression of Top3β was demonstrated in the central nervous system of mice. Positron emission tomography/computed tomography (PET/CT) analysis revealed significantly altered connectivity between many brain regions in Top3β-/- mice, including the connectivity between the olfactory bulb and the cerebellum, the connectivity between the amygdala and the olfactory bulb, and the connectivity between the globus pallidus and the optic nerve. These connectivity alterations in brain regions are known to be linked to neurodevelopmental as well as psychiatric and behavioral disorders in humans. Therefore, we conclude that Top3β is essential for normal brain function and behavior in mice and that Top3β could be an interesting target to study neuropsychiatric disorders in humans.
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3
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Spakman D, Bakx JAM, Biebricher AS, Peterman EJG, Wuite GJL, King GA. Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches. Nucleic Acids Res 2021; 49:5470-5492. [PMID: 33963870 PMCID: PMC8191776 DOI: 10.1093/nar/gkab239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
Topoisomerases are essential enzymes that regulate DNA topology. Type 1A family topoisomerases are found in nearly all living organisms and are unique in that they require single-stranded (ss)DNA for activity. These enzymes are vital for maintaining supercoiling homeostasis and resolving DNA entanglements generated during DNA replication and repair. While the catalytic cycle of Type 1A topoisomerases has been long-known to involve an enzyme-bridged ssDNA gate that allows strand passage, a deeper mechanistic understanding of these enzymes has only recently begun to emerge. This knowledge has been greatly enhanced through the combination of biochemical studies and increasingly sophisticated single-molecule assays based on magnetic tweezers, optical tweezers, atomic force microscopy and Förster resonance energy transfer. In this review, we discuss how single-molecule assays have advanced our understanding of the gate opening dynamics and strand-passage mechanisms of Type 1A topoisomerases, as well as the interplay of Type 1A topoisomerases with partner proteins, such as RecQ-family helicases. We also highlight how these assays have shed new light on the likely functional roles of Type 1A topoisomerases in vivo and discuss recent developments in single-molecule technologies that could be applied to further enhance our understanding of these essential enzymes.
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Affiliation(s)
- Dian Spakman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Julia A M Bakx
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Andreas S Biebricher
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Graeme A King
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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4
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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: 8] [Impact Index Per Article: 2.0] [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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5
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Reguera RM, Elmahallawy EK, García-Estrada C, Carbajo-Andrés R, Balaña-Fouce R. DNA Topoisomerases of Leishmania Parasites; Druggable Targets for Drug Discovery. Curr Med Chem 2019; 26:5900-5923. [DOI: 10.2174/0929867325666180518074959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/15/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
DNA topoisomerases (Top) are a group of isomerase enzymes responsible for controlling the topological problems caused by DNA double helix in the cell during the processes of replication, transcription and recombination. Interestingly, these enzymes have been known since long to be key molecular machines in several cellular processes through overwinding or underwinding of DNA in all living organisms. Leishmania, a trypanosomatid parasite responsible for causing fatal diseases mostly in impoverished populations of low-income countries, has a set of six classes of Top enzymes. These are placed in the nucleus and the single mitochondrion and can be deadly targets of suitable drugs. Given the fact that there are clear differences in structure and expression between parasite and host enzymes, numerous studies have reported the therapeutic potential of Top inhibitors as antileishmanial drugs. In this regard, numerous compounds have been described as Top type IB and Top type II inhibitors in Leishmania parasites, such as camptothecin derivatives, indenoisoquinolines, indeno-1,5- naphthyridines, fluoroquinolones, anthracyclines and podophyllotoxins. The aim of this review is to highlight several facts about Top and Top inhibitors as potential antileishmanial drugs, which may represent a promising strategy for the control of this disease of public health importance.
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Affiliation(s)
- Rosa M. Reguera
- Department of Biomedical Sciences, University of Leon (ULE), Leon, Spain
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6
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Bizard AH, Yang X, Débat H, Fogg JM, Zechiedrich L, Strick TR, Garnier F, Nadal M. TopA, the Sulfolobus solfataricus topoisomerase III, is a decatenase. Nucleic Acids Res 2019; 46:861-872. [PMID: 29253195 PMCID: PMC5778498 DOI: 10.1093/nar/gkx1247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/12/2017] [Indexed: 12/03/2022] Open
Abstract
DNA topoisomerases are essential enzymes involved in all the DNA processes and among them, type IA topoisomerases emerged as a key actor in the maintenance of genome stability. The hyperthermophilic archaeon, Sulfolobus solfataricus, contains three topoisomerases IA including one classical named TopA. SsoTopA is very efficient at unlinking DNA catenanes, grouping SsoTopA into the topoisomerase III family. SsoTopA is active over a wide range of temperatures and at temperatures of up to 85°C it produces highly unwound DNA. At higher temperatures, SsoTopA unlinks the two DNA strands. Thus depending on the temperature, SsoTopA is able to either prevent or favor DNA melting. While canonical topoisomerases III require a single-stranded DNA region or a nick in one of the circles to decatenate them, we show for the first time that a type I topoisomerase, SsoTopA, is able to efficiently unlink covalently closed catenanes, with no additional partners. By using single molecule experiments we demonstrate that SsoTopA requires the presence of a short single-stranded DNA region to be efficient. The unexpected decatenation property of SsoTopA probably comes from its high ability to capture this unwound region. This points out a possible role of TopA in S. solfataricus as a decatenase in Sulfolobus.
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Affiliation(s)
- Anna H Bizard
- Université Versailles St-Quentin, Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, 91405 Orsay Cedex, France
| | - Xi Yang
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592 CNRS, 75013 Paris, France.,Programme Equipes Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| | - Hélène Débat
- Programme Equipes Labellisées, Ligue Contre le Cancer, 75013 Paris, France.,Université Versailles St-Quentin, Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, 75013 Paris, France
| | - Jonathan M Fogg
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, MS: BCM-280, Houston, TX 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, MS: BCM-280, Houston, TX 77030, USA.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, MS: BCM-280, Houston, TX 77030, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, MS: BCM-280, Houston, TX 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, MS: BCM-280, Houston, TX 77030, USA.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, MS: BCM-280, Houston, TX 77030, USA
| | - Terence R Strick
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592 CNRS, 75013 Paris, France.,Programme Equipes Labellisées, Ligue Contre le Cancer, 75013 Paris, France.,Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Florence Garnier
- Programme Equipes Labellisées, Ligue Contre le Cancer, 75013 Paris, France.,Université Versailles St-Quentin, Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, 75013 Paris, France
| | - Marc Nadal
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Jacques Monod, UMR 7592 CNRS, 75013 Paris, France.,Programme Equipes Labellisées, Ligue Contre le Cancer, 75013 Paris, France
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7
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Abstract
Bacterial Topoisomerase I is a potential target for the identification of novel topoisomerase poison inhibitors that could provide leads for a new class of antibacterial compounds. Here we describe in detail a fluorescence-based cleavage assay that is successfully used in HTS for the discovery of bacterial topoisomerase Ι poisons.
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8
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DNA topoisomerase I and DNA gyrase as targets for TB therapy. Drug Discov Today 2017; 22:510-518. [DOI: 10.1016/j.drudis.2016.11.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/20/2022]
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9
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Pommier Y, Sun Y, Huang SYN, Nitiss JL. Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat Rev Mol Cell Biol 2016; 17:703-721. [DOI: 10.1038/nrm.2016.111] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Topoisomerase I (TopA) is recruited to ParB complexes and is required for proper chromosome organization during Streptomyces coelicolor sporulation. J Bacteriol 2013; 195:4445-55. [PMID: 23913317 DOI: 10.1128/jb.00798-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Streptomyces species are bacteria that resemble filamentous fungi in their hyphal mode of growth and sporulation. In Streptomyces coelicolor, the conversion of multigenomic aerial hyphae into chains of unigenomic spores requires synchronized septation accompanied by segregation of tens of chromosomes into prespore compartments. The chromosome segregation is dependent on ParB protein, which assembles into an array of nucleoprotein complexes in the aerial hyphae. Here, we report that nucleoprotein ParB complexes are bound in vitro and in vivo by topoisomerase I, TopA, which is the only topoisomerase I homolog found in S. coelicolor. TopA cannot be eliminated, and its depletion inhibits growth and blocks sporulation. Surprisingly, sporulation in the TopA-depleted strain could be partially restored by deletion of parB. Furthermore, the formation of regularly spaced ParB complexes, which is a prerequisite for proper chromosome segregation and septation during the development of aerial hyphae, has been found to depend on TopA. We hypothesize that TopA is recruited to ParB complexes during sporulation, and its activity is required to resolve segregating chromosomes.
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11
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Vanga BR, Butler RC, Toth IK, Ronson CW, Pitman AR. Inactivation of PbTopo IIIβ causes hyper-excision of the Pathogenicity Island HAI2 resulting in reduced virulence of Pectobacterium atrosepticum. Mol Microbiol 2012; 84:648-63. [PMID: 22524709 DOI: 10.1111/j.1365-2958.2012.08050.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Topoisomerase III enzymes are present only in a limited set of bacteria and their physiological role remains unclear. Here, we show that PbTopo IIIβ, a homologue of topoisomerase III encoded on the chromosome of Pectobacterium atrosepticum strain SCRI1043 (Pba SCRI1043), is involved in excision of HAI2, a discrete ~100 kb region, from the Pba SCRI1043 chromosome. HAI2 is a Pathogenicity Island (PAI) that encodes coronafacic acid (Cfa), a major virulence determinant required for infection of potato. PAIs are horizontally acquired genetic elements that in some instances are able to excise from the chromosome of their host cell to form a circular episome prior to transfer to a recipient bacterium. We demonstrate excision of HAI2 from the chromosome, a process that is independent of growth phase and that results in the production of a circular intermediate. Inactivation of PbTopo IIIβ causes a 10(3) - to 10(4) -fold increase in excision, leading to reduced fitness in vitro and a decrease in the virulence of Pba SCRI1043 on potato. These results suggest that PbTopo IIIβ is required for stable maintenance of HAI2 in the chromosome of Pba SCRI1043 and may control as yet unidentified genes involved in viability and virulence of Pba SCRI1043 on potato.
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Affiliation(s)
- Bhanupratap R Vanga
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
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12
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Narula G, Annamalai T, Aedo S, Cheng B, Sorokin E, Wong A, Tse-Dinh YC. The strictly conserved Arg-321 residue in the active site of Escherichia coli topoisomerase I plays a critical role in DNA rejoining. J Biol Chem 2011; 286:18673-80. [PMID: 21478161 DOI: 10.1074/jbc.m111.229450] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The strictly conserved arginine residue proximal to the active site tyrosine of type IA topoisomerases is required for the relaxation of supercoiled DNA and was hypothesized to be required for positioning of the scissile phosphate for DNA cleavage to take place. Mutants of recombinant Yersinia pestis topoisomerase I with hydrophobic substitutions at this position were found in genetic screening to exhibit a dominant lethal phenotype, resulting in drastic loss in Escherichia coli viability when overexpressed. In depth biochemical analysis of E. coli topoisomerase I with the corresponding Arg-321 mutation showed that DNA cleavage can still take place in the absence of this arginine function if Mg(2+) is present to enhance the interaction of the enzyme with the scissile phosphate. However, DNA rejoining is inhibited in the absence of this conserved arginine, resulting in accumulation of the cleaved covalent intermediate and loss of relaxation activity. These new experimental results demonstrate that catalysis of DNA rejoining by type IA topoisomerases has a more stringent requirement than DNA cleavage. In addition to the divalent metal ions, the side chain of this arginine residue is required for the precise positioning of the phosphotyrosine linkage for nucleophilic attack by the 3'-OH end to result in DNA rejoining. Small molecules that can interfere or distort the enzyme-DNA interactions required for DNA rejoining by bacterial type IA topoisomerases could be developed into novel antibacterial drugs.
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Affiliation(s)
- Gagandeep Narula
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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13
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Bizard A, Garnier F, Nadal M. TopR2, the second reverse gyrase of Sulfolobus solfataricus, exhibits unusual properties. J Mol Biol 2011; 408:839-49. [PMID: 21435345 DOI: 10.1016/j.jmb.2011.03.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 03/10/2011] [Accepted: 03/15/2011] [Indexed: 01/02/2023]
Abstract
Whereas reverse gyrase is considered as a strong marker of thermophily, the function of this peculiar type IA topoisomerase still remains to be elucidated. The archaeon Sulfolobus solfataricus encodes two reverse gyrases, TopR1 and TopR2. This duplication seems to be important because most of Crenarcheota exhibit two copies of reverse gyrase. However, to date, while TopR1 has been well characterized, no characterization of TopR2 has been reported. In this study, we describe for the first time the activity of S. solfataricus TopR2 that appears as a new reverse gyrase. Indeed, in spite of the sequence similarities between TopR1 and TopR2, we evidence unexpected great differences between the two enzymes. While TopR1 exhibits ATP-independent relaxation activity, TopR2 does not, and its activity is strictly dependent on the presence of ATP. Whereas TopR1 is a distributive topoisomerase, TopR2 exhibits an amazing high intrinsic processivity compared to all the topoisomerases studied so far. TopR2 is able to introduce a very high number of positive superturns in DNA, while TopR1 generates weakly positively supercoiled DNA. Finally, TopR2 behaves differently from TopR1 when incubated at different assay temperatures. All the results presented in this study indicate that TopR1 and TopR2 have, in vitro, different activities suggesting different functions in vivo.
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Affiliation(s)
- Anna Bizard
- Université Versailles Saint-Quentin, 45 Avenue des Etats-Unis, 78035 Versailles, Institut de Génétique et Microbiologie, UMR 8621 CNRS, Université Paris-Sud, Bât. 409, 91405 Orsay Cedex, France
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14
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Narula G, Becker J, Cheng B, Dani N, Abrenica MV, Tse-Dinh YC. The DNA relaxation activity and covalent complex accumulation of Mycobacterium tuberculosis topoisomerase I can be assayed in Escherichia coli: application for identification of potential FRET-dye labeling sites. BMC BIOCHEMISTRY 2010; 11:41. [PMID: 20920291 PMCID: PMC2958883 DOI: 10.1186/1471-2091-11-41] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 09/30/2010] [Indexed: 01/30/2023]
Abstract
Background Mycobacterium tuberculosis topoisomerase I (MtTOP1) and Escherichia coli topoisomerase I have highly homologous transesterification domains, but the two enzymes have distinctly different C-terminal domains. To investigate the structure-function of MtTOP1 and to target its activity for development of new TB therapy, it is desirable to have a rapid genetic assay for its catalytic activity, and potential bactericidal consequence from accumulation of its covalent complex. Results We show that plasmid-encoded recombinant MtTOP1 can complement the temperature sensitive topA function of E. coli strain AS17. Moreover, expression of MtTOP1-G116 S enzyme with the TOPRIM mutation that inhibits DNA religation results in SOS induction and loss of viability in E. coli. The absence of cysteine residues in the MtTOP1 enzyme makes it an attractive system for introduction of potentially informative chemical or spectroscopic probes at specific positions via cysteine mutagenesis. Such probes could be useful for development of high throughput screening (HTS) assays. We employed the AS17 complementation system to screen for sites in MtTOP1 that can tolerate cysteine substitution without loss of complementation function. These cysteine substitution mutants were confirmed to have retained the relaxation activity. One such mutant of MtTOP1 was utilized for fluorescence probe incorporation and fluorescence resonance energy transfer measurement with fluorophore-labeled oligonucleotide substrate. Conclusions The DNA relaxation and cleavage complex accumulation of M. tuberculosis topoisomerase I can be measured with genetic assays in E. coli, facilitating rapid analysis of its activities, and discovery of new TB therapy targeting this essential enzyme.
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Affiliation(s)
- Gagandeep Narula
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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15
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Bhat AG, Leelaram MN, Hegde SM, Nagaraja V. Deciphering the distinct role for the metal coordination motif in the catalytic activity of Mycobacterium smegmatis topoisomerase I. J Mol Biol 2009; 393:788-802. [PMID: 19733176 DOI: 10.1016/j.jmb.2009.08.064] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/27/2009] [Accepted: 08/27/2009] [Indexed: 11/17/2022]
Abstract
Mycobacterium smegmatis topoisomerase I (MstopoI) is distinct from typical type IA topoisomerases. The enzyme binds to both single- and double-stranded DNA with high affinity, making specific contacts. The enzyme comprises conserved regions similar to type IA topoisomerases from Escherichia coli and other eubacteria but lacks the typically found zinc fingers in the carboxy-terminal domain. The enzyme can perform DNA cleavage in the absence of Mg(2+), but religation needs exogenously added Mg(2+). One molecule of Mg(2+) tightly bound to the enzyme has no role in DNA cleavage but is needed only for the religation reaction. The toprim (topoisomerase-primase) domain in MstopoI comprising the Mg(2+) binding pocket, conserved in both type IA and type II topoisomerases, was subjected to mutagenesis to understand the role of Mg(2+) in different steps of the reaction. The residues D108, D110, and E112 of the enzyme, which form the acidic triad in the DXDXE motif, were changed to alanines. D108A mutation resulted in an enzyme that is Mg(2+) dependent for DNA cleavage unlike MstopoI and exhibited enhanced DNA cleavage property and reduced religation activity. The mutant was toxic for cell growth, most likely due to the imbalance in cleavage-religation equilibrium. In contrast, the E112A mutant behaved like wild-type enzyme, cleaving DNA in a Mg(2)(+)-independent fashion, albeit to a reduced extent. Intra- and intermolecular religation assays indicated specific roles for D108 and E112 residues during the reaction. Together, these results indicate that the D108 residue has a major role during cleavage and religation, while E112 is important for enhancing the efficiency of cleavage. Thus, although architecturally and mechanistically similar to topoisomerase I from E. coli, the metal coordination pattern of the mycobacterial enzyme is distinct, opening up avenues to exploit the enzyme to develop inhibitors.
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Affiliation(s)
- Anuradha Gopal Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, CV Raman Avenue, Bangalore 560 012, India
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16
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Hydroxyl radicals are involved in cell killing by the bacterial topoisomerase I cleavage complex. J Bacteriol 2009; 191:5315-9. [PMID: 19525344 DOI: 10.1128/jb.00559-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli expressing SOS-inducing mutant topoisomerase I was utilized to demonstrate that covalent protein-DNA complex accumulation results in oxidative damage. Hydroxyl radicals were detected following mutant topoisomerase induction. The presence of the Fe(2+) chelator 2,2'-dipyridyl and an iscS mutation affecting Fe-S cluster formation protect against topoisomerase I cleavage complex-mediated cell killing.
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17
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Annamalai T, Dani N, Cheng B, Tse-Dinh YC. Analysis of DNA relaxation and cleavage activities of recombinant Mycobacterium tuberculosis DNA topoisomerase I from a new expression and purification protocol. BMC BIOCHEMISTRY 2009; 10:18. [PMID: 19519900 PMCID: PMC2702276 DOI: 10.1186/1471-2091-10-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 06/11/2009] [Indexed: 11/29/2022]
Abstract
Background Mycobacterium tuberculosis DNA topoisomerase I is an attractive target for discovery of novel TB drugs that act by enhancing the accumulation of the topoisomerase-DNA cleavage product. It shares a common transesterification domain with other type IA DNA topoisomerases. There is, however, no homology between the C-terminal DNA binding domains of Escherichia coli and M. tuberculosis DNA topoisomerase I proteins. Results A new protocol for expression and purification of recombinant M. tuberculosis DNA topoisomerase I (MtTOP) has been developed to produce enzyme of much higher specific activity than previously characterized recombinant enzyme. MtTOP was found to be less efficient than E. coli DNA topoisomerase I (EcTOP) in removal of remaining negative supercoils from partially relaxed DNA. DNA cleavage by MtTOP was characterized for the first time. Comparison of DNA cleavage site selectivity with EcTOP showed differences in cleavage site preferences, but the preferred sites of both enzymes have a C nucleotide in the -4 position. Conclusion Recombinant M. tuberculosis DNA topoisomerase I can be expressed as a soluble protein and purified in high yield from E. coli host with a new protocol. Analysis of DNA cleavage with M. tuberculosis DNA substrate showed that the preferred DNA cleavage sites have a C nucleotide in the -4 position.
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18
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Sissi C, Palumbo M. Effects of magnesium and related divalent metal ions in topoisomerase structure and function. Nucleic Acids Res 2009; 37:702-11. [PMID: 19188255 PMCID: PMC2647314 DOI: 10.1093/nar/gkp024] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The catalytic steps through which DNA topoisomerases produce their biological effects and the interference of drug molecules with the enzyme–DNA cleavage complex have been thoroughly investigated both from the biophysical and the biochemical point of view. This provides the basic structural insight on how this family of essential enzymes works in living systems and how their functions can be impaired by natural and synthetic compounds. Besides other factors, the physiological environment is known to affect substantially the biological properties of topoisomerases, a key role being played by metal ion cofactors, especially divalent ions (Mg2+), that are crucial to bestow and modulate catalytic activity by exploiting distinctive chemical features such as ionic size, hardness and characteristics of the coordination sphere including coordination number and geometry. Indeed, metal ions mediate fundamental aspects of the topoisomerase-driven transphosphorylation process by affecting the kinetics of the forward and the reverse steps and by modifying the enzyme conformation and flexibility. Of particular interest in type IA and type II enzymes are ionic interactions involving the Toprim fold, a protein domain conserved through evolution that contains a number of acidic residues essential for catalysis. A general two-metal ion mechanism is widely accepted to account for the biophysical and biochemical data thus far available.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
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19
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Luijsterburg MS, White MF, van Driel R, Dame RT. The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 2009; 43:393-418. [PMID: 19037758 DOI: 10.1080/10409230802528488] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.
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Affiliation(s)
- Martijn S Luijsterburg
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan, Amsterdam, The Netherlands
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20
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Tse-Dinh YC. Bacterial topoisomerase I as a target for discovery of antibacterial compounds. Nucleic Acids Res 2008; 37:731-7. [PMID: 19042977 PMCID: PMC2647297 DOI: 10.1093/nar/gkn936] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacterial topoisomerase I is a potential target for discovery of new antibacterial compounds. Mutant topoisomerases identified by SOS induction screening demonstrated that accumulation of the DNA cleavage complex formed by type IA topoisomerases is bactericidal. Characterization of these mutants of Yersinia pestis and Escherichia coli topoisomerase I showed that DNA religation can be inhibited while maintaining DNA cleavage activity by decreasing the binding affinity of Mg(II) ions. This can be accomplished either by mutation of the TOPRIM motif involved directly in Mg(II) binding or by altering the charge distribution of the active site region. Besides being used to elucidate the key elements for the control of the cleavage-religation equilibrium, the SOS-inducing mutants of Y. pestis and E. coli topoisomerase I have also been utilized as models to study the cellular response following the accumulation of bacterial topoisomerase I cleavage complex. Bacterial topoisomerase I is required for preventing hypernegative supercoiling of DNA during transcription. It plays an important role in transcription of stress genes during bacterial stress response. Topoisomerase I targeting poisons may be particularly effective when the bacterial pathogen is responding to host defense, or in the presence of other antibiotics that induce the bacterial stress response.
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Affiliation(s)
- Yuk-Ching Tse-Dinh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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21
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22
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Garnier F, Nadal M. Transcriptional analysis of the two reverse gyrase encoding genes of Sulfolobus solfataricus P2 in relation to the growth phases and temperature conditions. Extremophiles 2008; 12:799-809. [PMID: 18777006 DOI: 10.1007/s00792-008-0186-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2008] [Accepted: 08/04/2008] [Indexed: 10/21/2022]
Abstract
Sulfolobus solfataricus, a hyperthermophilic crenarchaeon, contains two genes encoding reverse gyrases, topR1 and topR2. The steady-state level of their transcripts were quantified during the growth phases for cells maintained either at 72, or 80 degrees C, and after temperature changes from one to the other temperature. The transcripts of both genes are weakly expressed, but the highest level is observed in actively dividing cells, and is almost undetectable in cells in decline phase. During the temperature shift experiments, there is no significant topR2 variation. By contrast, there is a maximum 2.4-fold increase in topR1 transcripts within 30 min after the downshift. After 1 h, the transcript level reaches the level characteristic of cells adapted to the new temperature. After an upward shift, the topR1 expression pattern is inversely regulated with a transient decrease with the same time course. The topR1 expression profile is completely different from that of topR2 after temperature shift experiments; this suggests a different regulation process for the two reverse gyrase genes. The fine tuning of the topR1 transcript expression within a short interval of time after a temperature shift illustrates a rapid adaptation response to temperature change.
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Affiliation(s)
- Florence Garnier
- Laboratoire de Génétique et Biologie Cellulaire, Université de Versailles-Saint-Quentin-en-Yvelines, CNRS UMR 8159, Bâtiment Buffon, 45 Avenue des Etats-Unis, 78035, Versailles cedex, France
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23
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Deweese JE, Osheroff MA, Osheroff N. DNA Topology and Topoisomerases: Teaching a "Knotty" Subject. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2008; 37:2-10. [PMID: 19225573 PMCID: PMC2643378 DOI: 10.1002/bmb.20244] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DNA is essentially an extremely long double-stranded rope in which the two strands are wound about one another. As a result, topological properties of the genetic material, including DNA underwinding and overwinding, knotting, and tangling, profoundly influence virtually every major nucleic acid process. Despite the importance of DNA topology, it is a conceptionally difficult subject to teach, because it requires students to visualize three-dimensional relationships. This article will familiarize the reader with the concept of DNA topology and offer practical approaches and demonstrations to teaching this "knotty" subject in the classroom. Furthermore, it will discuss topoisomerases, the enzymes that regulate the topological state of DNA in the cell. These ubiquitous enzymes perform a number of critical cellular functions by generating transient breaks in the double helix. During this catalytic event, topoisomerases maintain genomic stability by forming covalent phosphotyrosyl bonds between active site residues and the newly generated DNA termini. Topoisomerases are essential for cell survival. However, because they cleave the genetic material, these enzymes also have the potential to fragment the genome. This latter feature of topoisomerases is exploited by some of the most widely prescribed anticancer and antibacterial drugs currently in clinical use. Finally, in addition to curing cancer, topoisomerase action also has been linked to the induction of specific types of leukemia.
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Affiliation(s)
- Joseph E. Deweese
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | | | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
- To whom correspondence should be addressed: Department of Biochemistry, 654 Robinson Research Building, Vanderbilt University School of Medicine, Nashville, TN 37232-0146. Tel: 1-615-322-4338; Fax: 1-615-343-1166; E-Mail:
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24
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Scocca JR, Shapiro TA. A mitochondrial topoisomerase IA essential for late theta structure resolution in African trypanosomes. Mol Microbiol 2007; 67:820-9. [PMID: 18179422 DOI: 10.1111/j.1365-2958.2007.06087.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Trypanosomes and Leishmania, protozoans that cause major human diseases, have a topologically intricate mitochondrial DNA (kinetoplast or kDNA) in the form of a network of thousands of interlocked circles. This unusual system provides a useful reporter for studying topoisomerase functions in vivo. We now find that these organisms have three type IA topoisomerases, one of which is phylogenetically distinctive and which we designate topoisomerase IA(mt). In Trypanosoma brucei topoisomerase IA(mt) immunolocalizes within the mitochondrion close to the kDNA disk in patterns that vary with the cell cycle. When expression of TOPIA(mt) is silenced by RNAi there is a striking accumulation of kDNA late theta structure replication intermediates, with subsequent loss of kDNA networks and halt in cell growth. This essential enzyme provides clear molecular evidence for the obligatory role of a type IA enzyme in the resolution of late theta structures in vivo. With no close orthologue in humans it also offers a target for the rational development of selectively toxic new antiprotozoal therapies.
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Affiliation(s)
- Jane R Scocca
- Division of Clinical Pharmacology, Department of Medicine and of Pharmacology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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25
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Nöllmann M, Crisona NJ, Arimondo PB. Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism. Biochimie 2007; 89:490-9. [PMID: 17397985 DOI: 10.1016/j.biochi.2007.02.012] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 02/20/2007] [Indexed: 11/27/2022]
Abstract
The level of negative DNA supercoiling of the Escherichia coli chromosome is tightly regulated in the cell and influences many DNA metabolic processes including DNA replication, transcription, repair and recombination. Gyrase is the only type II topoisomerase able to introduce negative supercoils into DNA, a unique ability that arises from the specialized C-terminal DNA wrapping domain of the GyrA subunit. Here, we review the biological roles of gyrase in vivo and its mechanism in vitro.
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Affiliation(s)
- Marcelo Nöllmann
- Department of Molecular and Cell Biology, University of California, 16 Barker Hall, Berkeley, CA 94720-3204, USA
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26
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Nadal M. Reverse gyrase: an insight into the role of DNA-topoisomerases. Biochimie 2007; 89:447-55. [PMID: 17316953 DOI: 10.1016/j.biochi.2006.12.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Accepted: 12/28/2006] [Indexed: 01/01/2023]
Abstract
Reverse gyrase was discovered more than twenty years ago. Recent biochemical and structural results have greatly enhanced our understanding of their positive supercoiling mechanism. In addition to new biochemical properties, a fine tuning of reverse gyrase regulation in response to DNA damaging agents has been recently described. These data give us a new insight in the cellular role of reverse gyrase. Moreover, it has been proposed that reverse gyrase has been implicated in genome stability.
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Affiliation(s)
- Marc Nadal
- Equipe Virologie Moléculaire et Microbiologie, Laboratoire de Génétique et de Biologie Cellulaire, CNRS UMR 8159, Université de Versailles St-Quentin-en-Yvelines, Bâtiment Buffon, 78 035 Versailles, France.
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27
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Viard T, de la Tour CB. Type IA topoisomerases: a simple puzzle? Biochimie 2006; 89:456-67. [PMID: 17141394 DOI: 10.1016/j.biochi.2006.10.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Accepted: 10/20/2006] [Indexed: 11/30/2022]
Abstract
Type IA topoisomerases are enzymes that can modify DNA topology. They form a distinct family of proteins present in all domains of life, from bacteria to archaea and higher eukaryotes. They are composed of two domains: a core domain containing all the conserved motifs involved in the trans-esterification reactions, and a carboxyl-terminal domain that is highly variable in size and sequence. The latter appears to interact with other proteins, defining the physiological use of the topoisomerase activity. The evolutionary relevance of this topoisomerase-cofactor complex, also known as the "toposome", as well as its enzymatic consequences are discussed in this review.
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Affiliation(s)
- Thierry Viard
- Nicholas Cozzarelli Laboratory, Molecular and Cell Biology Department, 16 Barker Hall, University of California, Berkeley, CA 94720-3204, USA.
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28
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Strahs D, Zhu CX, Cheng B, Chen J, Tse-Dinh YC. Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I. Nucleic Acids Res 2006; 34:1785-97. [PMID: 16582104 PMCID: PMC1421505 DOI: 10.1093/nar/gkl109] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 02/01/2006] [Accepted: 03/08/2006] [Indexed: 11/16/2022] Open
Abstract
Ser10 and Lys13 found near the active site tyrosine of Escherichia coli DNA topoisomerase I are conserved among the type IA topoisomerases. Site-directed mutagenesis of these two residues to Ala reduced the relaxation and DNA cleavage activity, with a more severe effect from the Lys13 mutation. Changing Ser10 to Thr or Lys13 to Arg also resulted in loss of DNA cleavage and relaxation activity of the enzyme. In simulations of the open form of the topoisomerase-DNA complex, Lys13 interacts directly with Glu9 (proposed to be important in the catalytic mechanism). This interaction is removed in the K13A mutant, suggesting the importance of lysine as either a proton donor or a stabilizing cation during strand cleavage, while the Lys to Arg mutation significantly distorts catalytic residues. Ser10 forms a direct hydrogen bond with a phosphate group near the active site and is involved in direct binding of the DNA substrate; this interaction is disturbed in the S10A and S10T mutants. This combination of a lysine and a serine residue conserved in the active site of type IA topoisomerases may be required for correct positioning of the scissile phosphate and coordination of catalytic residues relative to each other so that DNA cleavage and subsequent strand passage can take place.
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Affiliation(s)
- Daniel Strahs
- Department of Biology and Health Sciences, Pace UniversityNew York, NY 10038, USA
| | - Chang-Xi Zhu
- Department of Biochemistry and Molecular Biology, New York Medical College ValhallaNY 10595, USA
- Department of Biology and Health Sciences, Pace UniversityNew York, NY 10038, USA
| | - Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College ValhallaNY 10595, USA
- Department of Biology and Health Sciences, Pace UniversityNew York, NY 10038, USA
| | - Jason Chen
- Department of Biology and Health Sciences, Pace UniversityNew York, NY 10038, USA
| | - Yuk-Ching Tse-Dinh
- To whom correspondence should be addressed. Tel: +1 914 594 4061; Fax: +1 914 594 4058;
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Broccoli S, Rallu F, Sanscartier P, Cerritelli SM, Crouch RJ, Drolet M. Effects of RNA polymerase modifications on transcription-induced negative supercoiling and associated R-loop formation. Mol Microbiol 2005; 52:1769-79. [PMID: 15186424 DOI: 10.1111/j.1365-2958.2004.04092.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Transcription in the absence of topoisomerase I, but in the presence of DNA gyrase, can result in the formation of hypernegatively supercoiled DNA and associated R-loops. In this paper, we have used several strategies to study the effects of elongation/termination properties of RNA polymerase on such transcription-induced supercoiling. Effects on R-loop formation were exacerbated when cells were exposed to translation inhibitors, a condition that stimulated the accumulation of R-loop-dependent hypernegative supercoiling. Translation inhibitors were not acting by decreasing (p)ppGpp levels as the absence of (p)ppGpp in spoT relA mutant strains had little effect on hypernegative supercoiling. However, an rpoB mutation leading to the accumulation of truncated RNAs considerably reduced R-loop-dependent hypernegative supercoiling. Transcription of an rrnB fragment preceded by a mutated and inactive boxA sequence to abolish the rrnB antitermination system also considerably reduced R-loop-dependent supercoiling. Taken together, our results indicate that RNA polymerase elongation/termination properties can have a major impact on R-loop-dependent supercoiling. We discuss different possibilities by which RNA polymerase directly or indirectly participates in R-loop formation in Escherichia coli. Finally, our results also indicate that what determines the steady-state level of hypernegatively supercoiled DNA in topA null mutants is likely to be complex and involves a multitude of factors, including the status of RNA polymerase, transcription-translation coupling, the cellular level of RNase HI, the status of DNA gyrase and the rate of relaxation of supercoiled DNA.
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Affiliation(s)
- Sonia Broccoli
- Département de Microbiologie et Immunologie, Université de Montréal, CP 6128, Succursale Centre-ville, Montréal, P. Québec, Canada, H3C 3J7
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Abstract
The viability of the topA mutants lacking DNA topoisomerase I was thought to depend on the presence of compensatory mutations in Escherichia coli but not Salmonella typhimurium or Shigella flexneri. This apparent discrepancy in topA requirements in different bacteria prompted us to reexamine the topA requirements in E. coli. We find that E. coli strains bearing topA mutations, introduced into the strains by DNA-mediated gene replacement, are viable at 37 or 42 degrees C without any compensatory mutations. These topA(-) cells exhibit cold sensitivity in their growth, however, and this cold sensitivity phenotype appears to be caused by excessive negative supercoiling of intracellular DNA. In agreement with previous results (Zhu, Q., Pongpech, P., and DiGate, R. J. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 9766-9771), E. coli cells lacking both type IA DNA topoisomerases I and III are found to be nonviable, indicating that the two type IA enzymes share a critical cellular function.
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Affiliation(s)
- Vera A Stupina
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Cheng B, Feng J, Mulay V, Gadgil S, Tse-Dinh YC. Site-directed mutagenesis of residues involved in G Strand DNA binding by Escherichia coli DNA topoisomerase I. J Biol Chem 2004; 279:39207-13. [PMID: 15215234 DOI: 10.1074/jbc.m405891200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Crystal structures of complexes between type IA DNA topoisomerases and single-stranded DNA suggest that the residues Ser-192, Arg-195, and Gln-197 in a conserved region of Escherichia coli topoisomerase I may be important for direct interactions with phosphates on the G strand of DNA, which is the substrate for DNA cleavage and religation (Changela A., DiGate, R. J., and Mondragón, A. (2001) Nature 411, 1077-1081; Perry, K., and Mondragón, A. (2003) Structure 11, 1349-1358). Site-directed mutagenesis experiments altering these residues to alanines and other amino acids were carried out to probe the relevance of these interactions in the catalytic activities of the enzyme. The results show that the side chains of Arg-195 and Gln-197 are required for DNA cleavage by the enzyme and are likely to be important for positioning of the G strand of DNA at the active site prior to DNA cleavage. Mutation of Ser-192 did not affect DNA binding and cleavage but nevertheless decreased the overall rate of relaxation of supercoiled DNA probably because of its participation in a later step of the reaction pathway.
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Affiliation(s)
- Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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32
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Viard T, Cossard R, Duguet M, de La Tour CB. Thermotoga maritima-Escherichia coli chimeric topoisomerases. Answers about involvement of the carboxyl-terminal domain in DNA topoisomerase I-mediated catalysis. J Biol Chem 2004; 279:30073-80. [PMID: 15140883 DOI: 10.1074/jbc.m309692200] [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] [Indexed: 11/06/2022] Open
Abstract
Bacterial topoisomerases I are generally composed of two domains as follows: a core domain, which contains all the conserved motifs involved in the trans-esterification reactions, and a carboxyl-terminal domain, highly variable in size and sequence. In the present work, we have addressed the question of the respective roles of the two domains in the different steps of the topoisomerization cycle. For this purpose, we prepared various recombinant topoisomerases from two model enzymes: topoisomerase I from the hyperthermophilic bacterium Thermotoga maritima and topoisomerase I from Escherichia coli. We compared the properties of the two core domains to that of the topoisomerases formed by combining the core domain of one enzyme to the carboxyl-terminal domain of the other. We found that, contrary to E. coli (Lima, C. D., Wang, J. C., and Mondragon, A. (1993) J. Mol. Biol. 232, 1213-1216), the core domain from T. maritima (TmTop65) is able to sustain by itself a complete topoisomerization cycle, although with low efficiency. Fusion of TmTop65 to the entire carboxyl-terminal domain from E. coli considerably increases binding efficiency, thermal stability, and DNA relaxation activity. Moreover, the chimera predominantly acquires the cleavage specificity of E. coli full-length topoisomerase. For the chimera obtained by fusion of the T. maritima carboxyl-terminal domain to the core EcTop67, very low DNA relaxation activity and binding are recovered, but formation of a covalent DNA adduct is impaired. Taken together, our results show that the presence and the nature of the carboxyl-terminal domain of bacterial topoisomerases I strongly determine their DNA binding efficiency and cleavage specificity but is not strictly required for strand passage.
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Affiliation(s)
- Thierry Viard
- Laboratoire d'Enzymologie des Acides Nucléiques, Institut de Génétique et Microbiologie, UMR 8621 CNRS, Bātiment 400, Université Paris Sud, Centre d'Orsay, 91405 Orsay, France
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Cheng B, Feng J, Gadgil S, Tse-Dinh YC. Flexibility at Gly-194 is required for DNA cleavage and relaxation activity of Escherichia coli DNA topoisomerase I. J Biol Chem 2004; 279:8648-54. [PMID: 14711811 DOI: 10.1074/jbc.m312095200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proposed mechanism of type IA DNA topoisomerase I includes conformational changes by the single enzyme polypeptide to allow binding of the G strand of the DNA substrate at the active site, and the opening or closing of the "gate" created on the G strand of DNA to the passing single or double DNA strand(s) through the cleaved G strand DNA. The shifting of an alpha helix upon G strand DNA binding has been observed from the comparison of the type IA DNA topoisomerase crystal structures. Site-directed mutagenesis of the strictly conserved Gly-194 at the N terminus of this alpha helix in Escherichia coli DNA topoisomerase I showed that flexibility around this glycine residue is required for DNA cleavage and relaxation activity and supports a functional role for this hinge region in the enzyme conformational change.
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Affiliation(s)
- Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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Cheng B, Zhu CX, Ji C, Ahumada A, Tse-Dinh YC. Direct interaction between Escherichia coli RNA polymerase and the zinc ribbon domains of DNA topoisomerase I. J Biol Chem 2003; 278:30705-10. [PMID: 12788950 DOI: 10.1074/jbc.m303403200] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli DNA topoisomerase I (encoded by the topA gene) is important for maintaining steady-state DNA supercoiling and has been shown to influence vital cellular processes including transcription. Topoisomerase I activity is also needed to remove hypernegative supercoiling generated on the DNA template by the progressing RNA polymerase complex during transcription elongation. The accumulation of hypernegative supercoiling in the absence of topoisomerase I can lead to R-loop formation by the nascent transcript and template strand, leading to suppression of transcription elongation. Here we show by affinity chromatography and overlay blotting that E. coli DNA topoisomerase I interacts directly with the RNA polymerase complex. The protein-protein interaction involves the beta' subunit of RNA polymerase and the C-terminal domains of E. coli DNA topoisomerase I, which are homologous to the zinc ribbon domains in a number of transcription factors. This direct interaction can bring the topoisomerase I relaxing activity to the site of transcription where its activity is needed. The zinc ribbon C-terminal domains of other type IA topoisomerases, including mammalian topoisomerase III, may also help link the enzyme activities to their physiological functions, potentially including replication, transcription, recombination, and repair.
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Affiliation(s)
- Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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Nozawa N, Daikoku T, Yamauchi Y, Takakuwa H, Goshima F, Yoshikawa T, Nishiyama Y. Identification and characterization of the UL7 gene product of herpes simplex virus type 2. Virus Genes 2002; 24:257-66. [PMID: 12086147 DOI: 10.1023/a:1015332716927] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have raised a rabbit polyclonal antiserum against a recombinant 6x His-tagged herpes simplex virus type 2 (HSV-2) UL7 fusion protein expressed in Escherichia coli. The antiserum specifically reacted with a 33 kDa protein in HSV-1 and HSV-2-infected cell lysates, and was used to characterize the UL7 gene product of HSV-2. The UL7 protein was produced in the late phase of infection, and its synthesis was highly inhibited, but not abolished by the addition of acyclovir (ACV). The UL7 protein associated with extracellular virions and also with all types of capsids, including A, B, and C capsids, though the association seemed to be weak. Indirect immunofluorescence studies revealed that at 9 h postinfection, UL7 specific fluorescence was detected in part or all of the nucleus, and the specific fluorescence colocalized with the scaffold protein ICP35. However, at later times postinfection, the UL7 protein was mainly detected as a mass in a juxtanuclear cytoplasmic region. In addition, transmission immunoelectron microscopy (TIEM) confirmed the association of the UL7 protein with intracellular capsids and virions in HSV-2-infected cells. The HSV-2 UL7 protein contained a domain highly conserved in all herpesviruses, part of which exhibited a homology with domains in the fission yeast Schizosaccharomyces pombe DNA topoisomerase III. We discuss the possibility that the UL7 protein may play a supplementary role in the viral DNA cleavage/packaging process.
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Affiliation(s)
- Naoki Nozawa
- Laboratory of Virology, Research Institute for Disease Mechanism and Control, Nagoya University School of Medicine, Japan
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Ahumada A, Tse-Dinh YC. The role of the Zn(II) binding domain in the mechanism of E. coli DNA topoisomerase I. BMC BIOCHEMISTRY 2002; 3:13. [PMID: 12052259 PMCID: PMC115839 DOI: 10.1186/1471-2091-3-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2002] [Accepted: 05/29/2002] [Indexed: 11/10/2022]
Abstract
BACKGROUND Escherichia coli DNA topoisomerase I binds three Zn(II) with three tetracysteine motifs which, together with the 14 kDa C-terminal region, form a 30 kDa DNA binding domain (ZD domain). The 67 kDa N-terminal domain (Top67) has the active site tyrosine for DNA cleavage but cannot relax negatively supercoiled DNA. We analyzed the role of the ZD domain in the enzyme mechanism. RESULTS Addition of purified ZD domain to Top67 partially restored the relaxation activity, demonstrating that covalent linkage between the two domains is not necessary for removal of negative supercoils from DNA. The two domains had similar affinities to ssDNA. However, only Top67 could bind dsDNA with high affinity. DNA cleavage assays showed that the Top67 had the same sequence and structure selectivity for DNA cleavage as the intact enzyme. DNA rejoining also did not require the presence of the ZD domain. CONCLUSIONS We propose that during relaxation of negatively supercoiled DNA, Top67 by itself can position the active site tyrosine near the junction of double-stranded and single-stranded DNA for cleavage. However, the interaction of the ZD domain with the passing single-strand of DNA, coupled with enzyme conformational change, is needed for removal of negative supercoils.
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Affiliation(s)
- Adriana Ahumada
- Department of Biochemistry and Molecular Biology, New York Medical College Valhalla, NY USA
| | - Yuk-Ching Tse-Dinh
- Department of Biochemistry and Molecular Biology, New York Medical College Valhalla, NY USA
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37
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Abstract
DNA topoisomerases solve the topological problems associated with DNA replication, transcription, recombination, and chromatin remodeling by introducing temporary single- or double-strand breaks in the DNA. In addition, these enzymes fine-tune the steady-state level of DNA supercoiling both to facilitate protein interactions with the DNA and to prevent excessive supercoiling that is deleterious. In recent years, the crystal structures of a number of topoisomerase fragments, representing nearly all the known classes of enzymes, have been solved. These structures provide remarkable insights into the mechanisms of these enzymes and complement previous conclusions based on biochemical analyses. Surprisingly, despite little or no sequence homology, both type IA and type IIA topoisomerases from prokaryotes and the type IIA enzymes from eukaryotes share structural folds that appear to reflect functional motifs within critical regions of the enzymes. The type IB enzymes are structurally distinct from all other known topoisomerases but are similar to a class of enzymes referred to as tyrosine recombinases. The structural themes common to all topoisomerases include hinged clamps that open and close to bind DNA, the presence of DNA binding cavities for temporary storage of DNA segments, and the coupling of protein conformational changes to DNA rotation or DNA movement. For the type II topoisomerases, the binding and hydrolysis of ATP further modulate conformational changes in the enzymes to effect changes in DNA topology.
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Affiliation(s)
- J J Champoux
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington 98195-7242, USA.
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Wang Y, Lynch AS, Chen SJ, Wang JC. On the molecular basis of the thermal sensitivity of an Escherichia coli topA mutant. J Biol Chem 2002; 277:1203-9. [PMID: 11700321 DOI: 10.1074/jbc.m109436200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Studies of two temperature-sensitive Escherichia coli topA strains AS17 and BR83, both of which were supposed to carry a topA amber mutation and a temperature-sensitive supD43,74 amber-suppressor, led to conflicting results regarding the essentiality of DNA topoisomerase I in cells grown in media of low osmolarity. We have therefore reexamined the molecular basis of the temperature sensitivity of strain AS17. We find that the supD allele in this strain had lost its temperature sensitivity. The temperature sensitivity of the strain, in media of all osmolarity, results from the synthesis of a mutant DNA topoisomerase I that is itself temperature-sensitive. Nucleotide sequencing of the AS17 topA allele and studies of its expected cellular product show that the mutant enzyme is not as active as its wild-type parent even at 30 degrees C, a permissive temperature for the strain, and its activity relative to the wild-type enzyme is further reduced at 42 degrees C, a nonpermissive temperature. Our results thus implicate an indispensable role of DNA topoisomerase I in E. coli cells grown in media of any osmolarity.
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Affiliation(s)
- Yong Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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39
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Viard T, Lamour V, Duguet M, Bouthier de la Tour C. Hyperthermophilic topoisomerase I from Thermotoga maritima. A very efficient enzyme that functions independently of zinc binding. J Biol Chem 2001; 276:46495-503. [PMID: 11577108 DOI: 10.1074/jbc.m107714200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Topoisomerases, by controlling DNA supercoiling state, are key enzymes for adaptation to high temperatures in thermophilic organisms. We focus here on the topoisomerase I from the hyperthermophilic bacterium Thermotoga maritima (optimal growth temperature, 80 degrees C). To determine the properties of the enzyme compared with those of its mesophilic homologs, we overexpressed T. maritima topoisomerase I in Escherichia coli and purified it to near homogeneity. We show that T. maritima topoisomerase I exhibits a very high DNA relaxing activity. Mapping of the cleavage sites on a variety of single-stranded oligonucleotides indicates a strong preference for a cytosine at position -4 of the cleavage, a property shared by E. coli topoisomerase I and archaeal reverse gyrases. As expected, the mutation of the putative active site Tyr 288 to Phe led to a totally inactive protein. To investigate the role of the unique zinc motif (Cys-X-Cys-X(16)-Cys-X-Cys) present in T. maritima topoisomerase I, experiments have been performed with the protein mutated on the tetracysteine motif. Strikingly, the results show that zinc binding is not required for DNA relaxation activity, contrary to the E. coli enzyme. Furthermore, neither thermostability nor cleavage specificity is altered in this mutant. This finding opens the question of the role of the zinc-binding motif in T. maritima topoisomerase I and suggests that this hyperthermophilic topoisomerase possesses a different mechanism from its mesophilic homolog.
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Affiliation(s)
- T Viard
- Laboratoire d'Enzymologie des Acides Nucléiques, Institut de Génétique et Microbiologie, UMR 8621 CNRS, Bâtiment 400, Université de Paris Sud, Centre d'Orsay, 91405 Orsay Cedex, France
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40
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Roche CJ, Tse-Dinh YC. Effect of phosphorothioate substitutions on DNA cleavage by Escherichia coli DNA topoisomerase I. Int J Biol Macromol 2001; 29:175-80. [PMID: 11589970 DOI: 10.1016/s0141-8130(01)00165-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To evaluate the structural influence of the DNA phosphate backbone on the activity of Escherichia coli DNA topoisomerase I, modified forms of oligonucleotide dA(7) were synthesized with a chiral phosphorothioate replacing the non-bridging oxygens at each position along the backbone. A deoxy-iodo-uracil replaced the 5'-base to crosslink the oligonucleotides by ultraviolet (UV) and assess binding affinity. At the scissile phosphate there was little effect on the cleavage rate. At the +1 phosphate, the rectus phosphorus (Rp)-thio-substitution reduced the rate of cleavage by a factor of 10. At the +3 and -2 positions from the scissile bond, the Rp-isomer was cleaved at a faster rate than the sinister phosphorus (Sp)-isomer. The results demonstrate the importance of backbone contacts between DNA substrate and E. coli topoisomerase I.
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Affiliation(s)
- C J Roche
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
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41
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Kwan KY, Wang JC. Mice lacking DNA topoisomerase IIIbeta develop to maturity but show a reduced mean lifespan. Proc Natl Acad Sci U S A 2001; 98:5717-21. [PMID: 11331780 PMCID: PMC33279 DOI: 10.1073/pnas.101132498] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Targeted gene disruption in the murine TOP3beta gene-encoding DNA topoisomerase IIIbeta was carried out. In contrast to the embryonic lethality of mutant mice lacking DNA topoisomerase IIIalpha, top3beta(-/-) nulls are viable and grow to maturity with no apparent defects. Mice lacking DNA topoisomerase IIIbeta have a shorter life expectancy than their wild-type littermates, however. The mean lifespan of the top3beta(-/-) mice is about 15 months, whereas that of their wild-type littermates is longer than 2 years. Mortality of the top3beta(-/-) nulls appears to correlate with lesions in multiple organs, including hypertrophy of the spleen and submandibular lymph nodes, glomerulonephritis, and perivascular infiltrates in various organs. Because the DNA topoisomerase III isozymes are likely to interact with helicases of the RecQ family, enzymes that include the determinants of human Bloom, Werner, and Rothmund-Thomson syndromes, the shortened lifespan of top3beta(-/-) mice points to the possibility that the DNA topoisomerase III isozymes might be involved in the pathogenesis of progeroid syndromes caused by defective RecQ helicases.
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Affiliation(s)
- K Y Kwan
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
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42
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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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43
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Zhu CX, Tse-Dinh YC. The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change. J Biol Chem 2000; 275:5318-22. [PMID: 10681504 DOI: 10.1074/jbc.275.8.5318] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The acidic residues Asp-111, Asp-113, and Glu-115 of Escherichia coli DNA topoisomerase I are located near the active site Tyr-319 and are conserved in type IA topoisomerase sequences with counterparts in type IIA DNA topoisomerases. Their exact functional roles in catalysis have not been clearly defined. Mutant enzymes with two or more of these residues converted to alanines were found to have >90% loss of activity in the relaxation assay with 6 mM Mg(II) present. Mg(II) concentrations (15-20 mM) inhibitory for the wild type enzyme are needed by these double mutants for maximal relaxation activity. The triple mutant D111A/D113A/E115A had no detectable relaxation activity. Mg(II) binding to wild type enzyme resulted in an altered conformation detectable by Glu-C proteolytic digestion. This conformational change was not observed for the triple mutant or for the double mutant D111A/D113A. Direct measurement of Mg(II) bound showed the loss of 1-2 Mg(II) ions for each enzyme molecule due to the mutations. These results demonstrate a functional role for these acidic residues in the binding of Mg(II) to induce the conformational change required for the relaxation of supercoiled DNA by the enzyme.
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Affiliation(s)
- C X Zhu
- Department of Biochemistry, New York Medical College, Valhalla, New York 10595, USA
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44
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Qi H, Menzel R, Tse-Dinh YC. Increased thermosensitivity associated with topoisomerase I deletion and promoter mutations in Escherichia coli. FEMS Microbiol Lett 1999; 178:141-6. [PMID: 10483733 DOI: 10.1111/j.1574-6968.1999.tb13770.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
An Escherichia coli mutant with three of the promoters for the topoisomerase I gene (topA) deleted, such that only the sigma 32-dependent promoter (P1) remained, had a decreased level of topoisomerase I at 30 degrees C and showed increased thermosensitivity at 52 degrees C. However, it could still develop thermotolerance and had a wild-type level of resistance to 52 degrees C treatment if exposed first to 42 degrees C. This indicated that newly synthesized topoisomerase I from transcription initiated at P1 was important for development of thermotolerance. Two other E. coli mutants lacking topA were > 100 times more sensitive to high temperature than their wild-type isogenic strains.
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Affiliation(s)
- H Qi
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla 10595, USA
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