1
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Vidmar V, Vayssières M, Lamour V. What's on the Other Side of the Gate: A Structural Perspective on DNA Gate Opening of Type IA and IIA DNA Topoisomerases. Int J Mol Sci 2023; 24:ijms24043986. [PMID: 36835394 PMCID: PMC9960139 DOI: 10.3390/ijms24043986] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
DNA topoisomerases have an essential role in resolving topological problems that arise due to the double-helical structure of DNA. They can recognise DNA topology and catalyse diverse topological reactions by cutting and re-joining DNA ends. Type IA and IIA topoisomerases, which work by strand passage mechanisms, share catalytic domains for DNA binding and cleavage. Structural information has accumulated over the past decades, shedding light on the mechanisms of DNA cleavage and re-ligation. However, the structural rearrangements required for DNA-gate opening and strand transfer remain elusive, in particular for the type IA topoisomerases. In this review, we compare the structural similarities between the type IIA and type IA topoisomerases. The conformational changes that lead to the opening of the DNA-gate and strand passage, as well as allosteric regulation, are discussed, with a focus on the remaining questions about the mechanism of type IA topoisomerases.
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Affiliation(s)
- Vita Vidmar
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
| | - Marlène Vayssières
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
| | - Valérie Lamour
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
- Hôpitaux Universitaires de Strasbourg, 67098 Strasbourg, France
- Correspondence:
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2
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Moreira F, Arenas M, Videira A, Pereira F. Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa. J Mol Evol 2021; 89:384-395. [PMID: 33999213 DOI: 10.1007/s00239-021-10011-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/30/2021] [Indexed: 12/14/2022]
Abstract
DNA topoisomerase III beta (TOP3B) is unique by operating on both DNA and RNA substrates to regulate gene expression and genomic stability. Mutations in human TOP3B are linked to neurodevelopmental and cognitive disorders, highlighting its relevance for human health. Despite the emerging importance of TOP3B, its precise cellular functions and evolutionary history remain poorly understood. Here, we show that TOP3B is conserved across main metazoan groups and evolved under strong purifying selection. Subdomain IV was identified as the most conserved TOP3B region, in agreement with its role in providing the structural foundation of the protein. On the contrary, subdomain II is the less conserved, possibly because it is the most structurally flexible region of all TOP3B regions. Interestingly, TOP3B residue at position 472, previously associated with schizophrenia, is highly variable across animals, suggesting a more specific role in humans and related species. Finally, we show that all TOP3B CXXC zinc finger motifs previously identified at the protein C-terminal region are retained across metazoans. We also found that the two major methylation sites known to regulate TOP3B activity are located in the most conserved region of the C-terminal arginine-glycine-glycine (RGG) box, suggesting that a similar regulatory mechanism may operate throughout animals. Overall, our results provide a better understanding of the evolution and functional roles of TOP3B.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4450-208, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.,Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 36310, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4450-208, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal. .,Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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3
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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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4
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Garnier F, Debat H, Nadal M. Type IA DNA Topoisomerases: A Universal Core and Multiple Activities. Methods Mol Biol 2018; 1703:1-20. [PMID: 29177730 DOI: 10.1007/978-1-4939-7459-7_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
All the type IA topoisomerases display universal characteristics relying on a core region basically responsible for the transesterification and the strand passage reaction. First limited to the bacterial domain for a long time, these enzymes were further retrieved in Archaea and Eukarya as well. This is representative of an extremely ancient origin, probably due to an inheritance from the RNA world. As remaining evidence, some current topoisomerases IA have retained a RNA topoisomerase activity. Despite the presence of this core region in all of these TopoIAs, some differences exist and are originated from variable regions, located essentially within both extremities, conferring on them their specificities. During the last 2 decades the evidence of multiple activities and dedicated roles highlighted the importance of the topoisomerases IA. It is now obvious that topoisomerases IA are key enzymes involved in the maintenance of the genome stability. The discovery of these new activities was done thanks to the use of more accurate assays, based on new sophisticated DNA substrates.
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Affiliation(s)
- Florence Garnier
- Université Versailles St-Quentin, Institut Jacques Monod, UMR 7592 CNRS-Univ. Paris Diderot, 15, rue Hélène Brion, Paris, 75013, France
| | - Hélène Debat
- Université Versailles St-Quentin, Institut Jacques Monod, UMR 7592 CNRS-Univ. Paris Diderot, 15, rue Hélène Brion, Paris, 75013, France
| | - Marc Nadal
- Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, 15, rue Hélène Brion, Paris, 75013, France.
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5
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Balaña-Fouce R, Alvarez-Velilla R, Fernández-Prada C, García-Estrada C, Reguera RM. Trypanosomatids topoisomerase re-visited. New structural findings and role in drug discovery. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2014; 4:326-37. [PMID: 25516844 PMCID: PMC4266802 DOI: 10.1016/j.ijpddr.2014.07.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is an urgent need of new treatments against trypanosomatids-borne diseases. DNA topoisomerases are pointed as potential drug targets against unicellular parasites. Trypanosomatids have a full set of DNA topoisomerases in both nucleus and kinetoplast. TopII and TopIII are located in the kinetoplast and fully involved in kDNA replication. Tritryps TopIB differ in structure from mammalian’s pointing to an attractive target.
The Trypanosomatidae family, composed of unicellular parasites, causes severe vector-borne diseases that afflict human populations worldwide. Chagas disease, sleeping sickness, as well as different sorts of leishmaniases are amongst the most important infectious diseases produced by Trypanosoma cruzi, Trypanosoma brucei and Leishmania spp., respectively. All these infections are closely related to weak health care services in low-income populations of less developed and least economically developed countries. Search for new therapeutic targets in order to hit these pathogens is of paramount priority, as no effective vaccine is currently in use against any of these parasites. Furthermore, present-day chemotherapy comprises old-fashioned drugs full of important side effects. Besides, they are prone to produce tolerance and resistance as a consequence of their continuous use for decades. DNA topoisomerases (Top) are ubiquitous enzymes responsible for solving the torsional tensions caused during replication and transcription processes, as well as in maintaining genomic stability during DNA recombination. As the inhibition of these enzymes produces cell arrest and triggers cell death, Top inhibitors are among the most effective and most widely used drugs in both cancer and antibacterial therapies. Top relaxation and decatenation activities, which are based on a common nicking–closing cycle involving one or both DNA strands, have been pointed as a promising drug target. Specific inhibitors that bind to the interface of DNA-Top complexes can stabilize Top-mediated transient DNA breaks. In addition, important structural differences have been found between Tops from the Trypanosomatidae family members and Tops from the host. Such dissimilarities make these proteins very interesting for drug design and molecular intervention. The present review is a critical update of the last findings regarding trypanosomatid’s Tops, their new structural features, their involvement both in the physiology and virulence of these parasites, as well as their use as promising targets for drug discovery.
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Affiliation(s)
- Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Raquel Alvarez-Velilla
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | | | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Rosa M Reguera
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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6
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Bocquet N, Bizard AH, Abdulrahman W, Larsen NB, Faty M, Cavadini S, Bunker RD, Kowalczykowski SC, Cejka P, Hickson ID, Thomä NH. Structural and mechanistic insight into Holliday-junction dissolution by topoisomerase IIIα and RMI1. Nat Struct Mol Biol 2014; 21:261-8. [PMID: 24509834 PMCID: PMC4292918 DOI: 10.1038/nsmb.2775] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 01/17/2014] [Indexed: 12/19/2022]
Abstract
Repair of DNA double-strand breaks via homologous recombination can produce double Holliday junctions (dHJs) that require enzymatic separation. Topoisomerase IIIα (TopIIIα) together with RMI1 disentangles the final hemicatenane intermediate obtained once dHJs have converged. How binding of RMI1 to TopIIIα influences it to behave as a hemicatenane dissolvase, rather than as an enzyme that relaxes DNA topology, is unknown. Here, we present the crystal structure of human TopIIIα complexed to the first oligonucleotide-binding domain (OB fold) of RMI1. TopIII assumes a toroidal type 1A topoisomerase fold. RMI1 attaches to the edge of the gate in TopIIIα through which DNA passes. RMI1 projects a 23-residue loop into the TopIIIα gate, thereby influencing the dynamics of its opening and closing. Our results provide a mechanistic rationale for how RMI1 stabilizes TopIIIα-gate opening to enable dissolution and illustrate how binding partners modulate topoisomerase function.
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Affiliation(s)
- Nicolas Bocquet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Anna H Bizard
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Wassim Abdulrahman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Nicolai B Larsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mahamadou Faty
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Petr Cejka
- 1] Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA. [2]
| | - Ian D Hickson
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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7
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Forterre P. Introduction and Historical Perspective. CANCER DRUG DISCOVERY AND DEVELOPMENT 2012. [DOI: 10.1007/978-1-4614-0323-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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8
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Park JE, Kim HI, Park JW, Park JK, Lee JS. Cloning and biochemical characterization of Staphylococcus aureus type IA DNA topoisomerase comprised of distinct five domains. Arch Biochem Biophys 2011; 508:78-86. [PMID: 21281597 DOI: 10.1016/j.abb.2011.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 01/20/2011] [Accepted: 01/24/2011] [Indexed: 11/30/2022]
Abstract
DNA topoisomerases play critical roles in regulating DNA topology and are essential enzymes for cell survival. In this study, a gene encoding type IA DNA topoisomerase was cloned from Staphylococcus aureus (S. aureus) sp. strain C-66, and the biochemical properties of recombinant enzyme was characterized. The nucleotide sequence analysis showed that the cloned gene contained an open reading frame (2070 bp) that could encode a polypeptide of 689 amino acids. The cloned gene actually produced 79.1 kDa functional enzyme (named Sau-TopoI) in Escherichia coli (E. coli). Sau-TopoI enzyme purified from E. coli showed ATP-independent and Mg(2+)-dependent manners for relaxing negatively supercoiled DNA. The relaxation activity of Sau-TopoI was inhibited by camptothecin, but not by nalidixic acid and etoposide. Cleavage site mapping showed that the enzyme could preferentially bind to and cleave the sequence GGNN↓CAT (N and ↓ represent any nucleotide and cleavage site, respectively). All these results suggest that the purified enzyme is type IA DNA topoisomerase. In addition, domain mapping analysis showed that the enzyme was composed of conserved four domains (I through IV), together with a variable C-terminal region containing a unique domain V.
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Affiliation(s)
- Jung Eun Park
- Department of Biotechnology, Chosun University, Gwangju 501-759, Republic of Korea
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9
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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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10
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Xiong B, Burk DL, Shen J, Luo X, Liu H, Shen J, Berghuis AM. The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation. Proteins 2008; 71:1984-94. [DOI: 10.1002/prot.21876] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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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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12
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Rossignol JM, Jacquet M, Arimondo PB. «DNA, more than just a ladder» A tribute to Michel Duguet (1943–2005). Biochimie 2007; 89:423-6. [PMID: 17418930 DOI: 10.1016/j.biochi.2007.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 02/22/2007] [Indexed: 11/29/2022]
Affiliation(s)
- Jean-Michel Rossignol
- Laboratoire de Génétique et Biologie Cellulaire, UMR CNRS/UVSQ/EPHE 8159, Université de Versailles St Quentin, Versailles, France.
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13
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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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14
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Forterre P, Gribaldo S, Gadelle D, Serre MC. Origin and evolution of DNA topoisomerases. Biochimie 2007; 89:427-46. [PMID: 17293019 DOI: 10.1016/j.biochi.2006.12.009] [Citation(s) in RCA: 248] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 12/12/2006] [Indexed: 12/28/2022]
Abstract
The DNA topoisomerases are essential for DNA replication, transcription, recombination, as well as for chromosome compaction and segregation. They may have appeared early during the formation of the modern DNA world. Several families and subfamilies of the two types of DNA topoisomerases (I and II) have been described in the three cellular domains of life (Archaea, Bacteria and Eukarya), as well as in viruses infecting eukaryotes or bacteria. The main families of DNA topoisomerases, Topo IA, Topo IB, Topo IC (Topo V), Topo IIA and Topo IIB (Topo VI) are not homologous, indicating that they originated independently. However, some of them share homologous modules or subunits that were probably recruited independently to produce different topoisomerase activities. The puzzling phylogenetic distribution of the various DNA topoisomerase families and subfamilies cannot be easily reconciled with the classical models of early evolution describing the relationships between the three cellular domains. A possible scenario is based on a Last Universal Common Ancestor (LUCA) with a RNA genome (i.e. without the need for DNA topoisomerases). Different families of DNA topoisomerases (some of them possibly of viral origin) would then have been independently introduced in the different cellular domains. We review here the main characteristics of the different families and subfamilies of DNA topoisomerases in a historical and evolutionary perspective, with the hope to stimulate further works and discussions on the origin and evolution of these fascinating enzymes.
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Affiliation(s)
- Patrick Forterre
- Institut de Génétique et Microbiologie, UMR8621, Université Paris-Sud 11, Bat. 400-409, 91405 Orsay Cedex, France
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15
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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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