1
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Petersen M, Fang R, Majumdar A, Barrick D. Stability Islands and the Folding Cooperativity of a Seven-Repeat Array from Topoisomerase V. J Am Chem Soc 2023; 145:12641-12650. [PMID: 37262333 PMCID: PMC10416711 DOI: 10.1021/jacs.3c02193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cooperativity is a central feature of protein folding, but the thermodynamic and structural origins of cooperativity remain poorly understood. To quantify cooperativity, we measured guanidine-induced unfolding transitions of single helix-hairpin-helix (HhH)2 repeats and tandem pairs from a seven-repeat segment of Methanopyrus kandleri Topoisomerase V (Topo V) to determine intrinsic repeat stability and interfacial free energies between repeats. Most single-repeat constructs are folded and stable; moreover, several pairs have unfolding midpoints that exceed midpoints of the single repeats they comprise, demonstrating favorable coupling between repeats. Analyzing unfolding transitions with a modified Ising model, we find a broad range of intrinsic and interfacial free energies. Surprisingly, the G repeat, which lacks density in the crystal structure of Topo V without DNA, is the most stable repeat in the array. Using nuclear magnetic resonance spectroscopy, we demonstrate that the isolated G repeat adopts a canonical (HhH)2 fold and forms an ordered interface with the F-repeat but not with the H repeat. Using parameters from our paired Ising fit, we built a partition function for the seven-repeat array. The multistate unfolding transition predicted from this partition function is in excellent agreement with the experimental unfolding transition, providing strong justification for the nearest-neighbor model. The seven-repeat partition function predicts a native state in which three independent segments ("stability islands") of interacting repeats are separated by two unstable interfaces. We confirm this segmented architecture by measuring the unfolding transition of an equimolar mixture of these three separate polypeptides. This segmented structural organization may facilitate wrapping around DNA.
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Affiliation(s)
- Mark Petersen
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
| | - Rebecca Fang
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
| | - Ananya Majumdar
- The Johns Hopkins University Biomolecular NMR Center, Johns Hopkins University
| | - Doug Barrick
- The T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
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2
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Osterman A, Mondragón A. Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism. eLife 2022; 11:72702. [PMID: 35969036 PMCID: PMC9489208 DOI: 10.7554/elife.72702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 08/14/2022] [Indexed: 11/22/2022] Open
Abstract
Topoisomerase V is a unique topoisomerase that combines DNA repair and topoisomerase activities. The enzyme has an unusual arrangement, with a small topoisomerase domain followed by 12 tandem (HhH)2 domains, which include 3 AP lyase repair domains. The uncommon architecture of this enzyme bears no resemblance to any other known topoisomerase. Here, we present structures of topoisomerase V in complex with DNA. The structures show that the (HhH)2 domains wrap around the DNA and in this manner appear to act as a processivity factor. There is a conformational change in the protein to expose the topoisomerase active site. The DNA bends sharply to enter the active site, which melts the DNA and probably facilitates relaxation. The structures show a DNA-binding mode not observed before and provide information on the way this atypical topoisomerase relaxes DNA. In common with type IB enzymes, topoisomerase V relaxes DNA using a controlled rotation mechanism, but the structures show that topoisomerase V accomplishes this in different manner. Overall, the structures firmly establish that type IC topoisomerases form a distinct type of topoisomerases, with no similarities to other types at the sequence, structural, or mechanistic level. They represent a completely different solution to DNA relaxation.
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Affiliation(s)
- Amy Osterman
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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3
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A tale of topoisomerases and the knotty genetic material in the backdrop of Plasmodium biology. Biosci Rep 2022; 42:231351. [PMID: 35699968 PMCID: PMC9261774 DOI: 10.1042/bsr20212847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/05/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
The untangling or overwinding of genetic material is an inevitable part of DNA
replication, repair, recombination, and transcription. Topoisomerases belong to
a conserved enzyme family that amends DNA topology during various processes of
DNA metabolism. To relax the genetic material, topoisomerases transiently break
the phosphodiester bond on one or both DNA strands and remain associated with
the cleavage site by forming a covalent enzyme–DNA intermediate. This
releases torsional stress and allows the broken DNA to be re-ligated by the
enzyme. The biological function of topoisomerases ranges from the separation of
sister chromatids following DNA replication to the aiding of chromosome
condensation and segregation during mitosis. Topoisomerases are also actively
involved in meiotic recombination. The unicellular apicomplexan parasite,
Plasmodium falciparum, harbors different topoisomerase
subtypes, some of which have substantially different sequences and functions
from their human counterparts. This review highlights the biological function of
each identified Plasmodium topoisomerase along with a
comparative analysis of their orthologs in human or other model organisms. There
is also a focus on recent advancements towards the development of topoisomerase
chemical inhibitors, underscoring the druggability of unique topoisomerase
subunits that are absent in humans. Plasmodium harbors three
distinct genomes in the nucleus, apicoplast, and mitochondria, respectively, and
undergoes non-canonical cell division during the schizont stage of development.
This review emphasizes the specific developmental stages of
Plasmodium on which future topoisomerase research should
focus.
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4
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Patel PS, Krishnan R, Hakem R. Emerging roles of DNA topoisomerases in the regulation of R-loops. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 876-877:503450. [PMID: 35483781 DOI: 10.1016/j.mrgentox.2022.503450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/24/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
R-loops are comprised of a DNA:RNA hybrid and a displaced single-strand DNA (ssDNA) that reinvades the DNA duplex behind the moving RNA polymerase. Because they have several physiological functions within the cell, including gene expression, chromosomal segregation, and mitochondrial DNA replication, among others, R-loop homeostasis is tightly regulated to ensure normal functioning of cellular processes. Thus, several classes of enzymes including RNases, helicases, topoisomerases, as well as proteins involved in splicing and the biogenesis of messenger ribonucleoproteins, have been implicated in R-loop prevention, suppression, and resolution. There exist six topoisomerase enzymes encoded by the human genome that function to introduce transient DNA breaks to relax supercoiled DNA. In this mini-review, we discuss functions of DNA topoisomerases and their emerging role in transcription, replication, and regulation of R-loops, and we highlight how their role in maintaining genome stability can be exploited for cancer therapy.
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Affiliation(s)
- Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Rehna Krishnan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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5
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Garnier F, Couturier M, Débat H, Nadal M. Archaea: A Gold Mine for Topoisomerase Diversity. Front Microbiol 2021; 12:661411. [PMID: 34113328 PMCID: PMC8185306 DOI: 10.3389/fmicb.2021.661411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
The control of DNA topology is a prerequisite for all the DNA transactions such as DNA replication, repair, recombination, and transcription. This global control is carried out by essential enzymes, named DNA-topoisomerases, that are mandatory for the genome stability. Since many decades, the Archaea provide a significant panel of new types of topoisomerases such as the reverse gyrase, the type IIB or the type IC. These more or less recent discoveries largely contributed to change the understanding of the role of the DNA topoisomerases in all the living world. Despite their very different life styles, Archaea share a quasi-homogeneous set of DNA-topoisomerases, except thermophilic organisms that possess at least one reverse gyrase that is considered a marker of the thermophily. Here, we discuss the effect of the life style of Archaea on DNA structure and topology and then we review the content of these essential enzymes within all the archaeal diversity based on complete sequenced genomes available. Finally, we discuss their roles, in particular in the processes involved in both the archaeal adaptation and the preservation of the genome stability.
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Affiliation(s)
- Florence Garnier
- Département de biologie, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Saclay, UVSQ, Versailles, France
| | - Mohea Couturier
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Hélène Débat
- Département de biologie, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Saclay, UVSQ, Versailles, France
| | - Marc Nadal
- Département de biologie, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université de Paris, Paris, France
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6
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McKie SJ, Neuman KC, Maxwell A. DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis. Bioessays 2021; 43:e2000286. [PMID: 33480441 PMCID: PMC7614492 DOI: 10.1002/bies.202000286] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA-topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single-molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA-associated proteins, supporting the idea that they often function as part of multi-enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini-A. These new findings are advancing our understanding of DNA-related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.
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Affiliation(s)
- Shannon J. McKie
- Department Biological Chemistry, John Innes Centre, Norwich, UK
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Anthony Maxwell
- Department Biological Chemistry, John Innes Centre, Norwich, UK
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7
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Buzun K, Bielawska A, Bielawski K, Gornowicz A. DNA topoisomerases as molecular targets for anticancer drugs. J Enzyme Inhib Med Chem 2020; 35:1781-1799. [PMID: 32975138 PMCID: PMC7534307 DOI: 10.1080/14756366.2020.1821676] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
The significant role of topoisomerases in the control of DNA chain topology has been confirmed in numerous research conducted worldwide. The prevalence of these enzymes, as well as the key importance of topoisomerase in the proper functioning of cells, have made them the target of many scientific studies conducted all over the world. This article is a comprehensive review of knowledge about topoisomerases and their inhibitors collected over the years. Studies on the structure-activity relationship and molecular docking are one of the key elements driving drug development. In addition to information on molecular targets, this article contains details on the structure-activity relationship of described classes of compounds. Moreover, the work also includes details about the structure of the compounds that drive the mode of action of topoisomerase inhibitors. Finally, selected topoisomerases inhibitors at the stage of clinical trials and their potential application in the chemotherapy of various cancers are described.
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Affiliation(s)
- Kamila Buzun
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Bielawska
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Medical University of Bialystok, Bialystok, Poland
| | - Agnieszka Gornowicz
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
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8
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Jaswal S, Nehra B, Kumar S, Monga V. Recent advancements in the medicinal chemistry of bacterial type II topoisomerase inhibitors. Bioorg Chem 2020; 104:104266. [PMID: 33142421 DOI: 10.1016/j.bioorg.2020.104266] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
Replication proteins are sought as a potential targets for antimicrobial agents. Despite their promising target characteristics, only topoisomerase II inhibitors targeting DNA gyrase and/or topoisomerase IV have reached clinical use. Topoisomerases are the enzymes that are essential for cellular functions and various biological activities. A wide range of natural and synthetic compounds have been identified as potential topoisomerase inhibitors but the resistance is most commonly found in these drugs. The emergence of FQ resistance has increased the need for the development of novel topoisomerase inhibitors with efficacy and high potency against FQ-resistant strains. Besides structural modifications of existing FQ scaffolds, novel non-quinolone topoisomerase II inhibitors, known as novel bacterial topoisomerase inhibitors, have been developed which showed remarkable inhibitory activity against DNA gyrase/topoisomerase IV or both with an improved spectrum of antibacterial potency including drug-resistant strains. This review aims to summarize various recent advancements in the medicinal chemistry of topoisomerase inhibitors with the following objectives: (1) To represent inclusive data on types of topoisomerases and various marketed topoisomerase inhibitors as drugs; (2) To discuss the recent advances in the medicinal chemistry of various topoisomerase inhibitors (DNA gyrase and topo IV) belonging to different structural classes as potential antibacterial agents; (3) To summarizes the structure activity relationship (SAR) including in silico and mechanistic studies to afford ideas and to provide focused direction for the development of new chemical entities which are effective against drug-resistant bacterial pathogens and biofilms.
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Affiliation(s)
- Shalini Jaswal
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Bhupender Nehra
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Shubham Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India.
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9
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Abstract
We review the current understanding of the mechanics of DNA and DNA-protein complexes, from scales of base pairs up to whole chromosomes. Mechanics of the double helix as revealed by single-molecule experiments will be described, with an emphasis on the role of polymer statistical mechanics. We will then discuss how topological constraints- entanglement and supercoiling-impact physical and mechanical responses. Models for protein-DNA interactions, including effects on polymer properties of DNA of DNA-bending proteins will be described, relevant to behavior of protein-DNA complexes in vivo. We also discuss control of DNA entanglement topology by DNA-lengthwise-compaction machinery acting in concert with topoisomerases. Finally, the chapter will conclude with a discussion of relevance of several aspects of physical properties of DNA and chromatin to oncology.
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10
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Delgado JL, Lentz SRC, Kulkarni CA, Chheda PR, Held HA, Hiasa H, Kerns RJ. Probing structural requirements for human topoisomerase I inhibition by a novel N1-Biphenyl fluoroquinolone. Eur J Med Chem 2019; 172:109-130. [PMID: 30959322 DOI: 10.1016/j.ejmech.2019.03.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/13/2019] [Accepted: 03/16/2019] [Indexed: 11/28/2022]
Abstract
Fluoroquinolones substituted with N-1 biphenyl and napthyl groups were discovered to act as catalytically inhibitors of human topoisomerases I and II, and to possess anti-proliferative activity in vivo. Structural requirements for these novel quinolones to inhibit catalytic activity of human topoisomerase I have not been explored. In this work novel derivatives of the N-1 biphenyl fluoroquinolone were designed, synthesized and evaluated to understand structural requirements of the C-3 carboxylic acid, C-6 fluorine, C-7 aminomethylpyrrolidine, C-8 methoxy, and the N-1 biphenyl functional groups for hTopoI inhibition. Characterization of each analog for inhibition of hTopoI catalytic inhibition reveals critical insight into structural requirements of these novel quinolones for activity. Additionally, results of DNA binding and modeling studies suggest that N-1 biphenyl fluoroquinolones intercalate between the DNA base pairs with the N-1 biphenyl functional group, rather than the quinolone core, and that this mode of DNA intercalation contributes to inhibition of hTopoI by these novel structures. The results presented here support further development and evaluation of N-1 biphenyl fluoroquinolone analogs as a novel class of anti-cancer agents that act through catalytic inhibition of hTopoI.
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Affiliation(s)
- Justine L Delgado
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA, 52242, USA
| | - Sarah R C Lentz
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Chaitanya A Kulkarni
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA, 52242, USA
| | - Pratik R Chheda
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA, 52242, USA
| | - Hailey A Held
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Robert J Kerns
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA, 52242, USA.
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11
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Chowdhury SR, Majumder HK. DNA Topoisomerases in Unicellular Pathogens: Structure, Function, and Druggability. Trends Biochem Sci 2019; 44:415-432. [PMID: 30609953 DOI: 10.1016/j.tibs.2018.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/20/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Abstract
All organisms, including unicellular pathogens, compulsorily possess DNA topoisomerases for successful nucleic acid metabolism. But particular subtypes of topoisomerases exist, in all prokaryotes and in some unicellular eukaryotes, that are absent in higher eukaryotes. Moreover, topoisomerases from pathogenic members of a niche possess some unique molecular architecture and functionalities completely distinct from their nonpathogenic colleagues. This review will highlight the unique attributes associated with the structures and functions of topoisomerases from the unicellular pathogens, with special reference to bacteria and protozoan parasites. It will also summarise the progress made in the domain pertaining to the druggability of these topoisomerases, upon which a future platform for therapeutic development can be successfully constructed.
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Affiliation(s)
- Somenath Roy Chowdhury
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Hemanta K Majumder
- Laboratory of Molecular Parasitology, Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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12
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Delgado JL, Hsieh CM, Chan NL, Hiasa H. Topoisomerases as anticancer targets. Biochem J 2018; 475:373-398. [PMID: 29363591 PMCID: PMC6110615 DOI: 10.1042/bcj20160583] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/14/2017] [Accepted: 12/21/2017] [Indexed: 12/15/2022]
Abstract
Many cancer type-specific anticancer agents have been developed and significant advances have been made toward precision medicine in cancer treatment. However, traditional or nonspecific anticancer drugs are still important for the treatment of many cancer patients whose cancers either do not respond to or have developed resistance to cancer-specific anticancer agents. DNA topoisomerases, especially type IIA topoisomerases, are proved therapeutic targets of anticancer and antibacterial drugs. Clinically successful topoisomerase-targeting anticancer drugs act through topoisomerase poisoning, which leads to replication fork arrest and double-strand break formation. Unfortunately, this unique mode of action is associated with the development of secondary cancers and cardiotoxicity. Structures of topoisomerase-drug-DNA ternary complexes have revealed the exact binding sites and mechanisms of topoisomerase poisons. Recent advances in the field have suggested a possibility of designing isoform-specific human topoisomerase II poisons, which may be developed as safer anticancer drugs. It may also be possible to design catalytic inhibitors of topoisomerases by targeting certain inactive conformations of these enzymes. Furthermore, identification of various new bacterial topoisomerase inhibitors and regulatory proteins may inspire the discovery of novel human topoisomerase inhibitors. Thus, topoisomerases remain as important therapeutic targets of anticancer agents.
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Affiliation(s)
- Justine L Delgado
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA 52242, U.S.A
| | - Chao-Ming Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, U.S.A.
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13
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Affiliation(s)
- Giovanni Capranico
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Jessica Marinello
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Giovanni Chillemi
- SCAI
SuperComputing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185 Rome, Italy
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14
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Bansal S, Bajaj P, Pandey S, Tandon V. Topoisomerases: Resistance versus Sensitivity, How Far We Can Go? Med Res Rev 2016; 37:404-438. [PMID: 27687257 DOI: 10.1002/med.21417] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/04/2016] [Accepted: 08/29/2016] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases are ubiquitously present remarkable molecular machines that help in altering topology of DNA in living cells. The crucial role played by these nucleases during DNA replication, transcription, and recombination vis-à-vis less sequence similarity among different species makes topoisomerases unique and attractive targets for different anticancer and antibacterial drugs. However, druggability of topoisomerases by the existing class of molecules is increasingly becoming questationable due to resistance development predominated by mutations in the corresponding genes. The current scenario facing a decline in the development of new molecules further comprises an important factor that may challenge topoisomerase-targeting therapy. Thus, it is imperative to wisely use the existing inhibitors lest with this rapid rate of losing grip over the target we may not go too far. Furthermore, it is important not only to design new molecules but also to develop new approaches that may avoid obstacles in therapies due to multiple resistance mechanisms. This review provides a succinct account of different classes of topoisomerase inhibitors, focuses on resistance acquired by mutations in topoisomerases, and discusses the various approaches to increase the efficacy of topoisomerase inhibitors. In a later section, we also suggest the possibility of using bisbenzimidazoles along with efflux pump inhibitors for synergistic bactericidal effects.
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Affiliation(s)
- Sandhya Bansal
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Priyanka Bajaj
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Stuti Pandey
- Department of Chemistry, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Department of Chemistry, University of Delhi, New Delhi, India
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15
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Rajan R, Osterman A, Mondragón A. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site. Nucleic Acids Res 2016; 44:3464-74. [PMID: 26908655 PMCID: PMC4838376 DOI: 10.1093/nar/gkw122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 01/08/2023] Open
Abstract
Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide.
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Affiliation(s)
- Rakhi Rajan
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Amy Osterman
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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16
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Lei L, Egli M. In Situ Proteolysis for Crystallization of Membrane Bound Cytochrome P450 17A1 and 17A2 Proteins from Zebrafish. ACTA ACUST UNITED AC 2016; 84:29.16.1-29.16.19. [PMID: 27038268 DOI: 10.1002/0471140864.ps2916s84] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fish and human cytochrome P450 (P450) 17A1 catalyze both steroid 17α-hydroxylation and 17α,20-lyase reactions. Fish P450 17A2 catalyzes only 17α-hydroxylation. Both enzymes are microsomal-type P450s, integral membrane proteins that bind to the membrane through their N-terminal hydrophobic segment, the signal anchor sequence. The presence of this N-terminal region renders expression of full-length proteins challenging or impossible. For some proteins, variable truncation of the signal anchor sequence precludes expression or results in poor expression levels. To crystallize P450 17A1 and 17A2 in order to gain insight into their different activities, we used an alternative N-terminal sequence to boost expression together with in situ proteolysis. Key features of our approach to identify crystallizable P450 fragments were the use of an N-terminal leader sequence, a screen composed of 12 proteases to establish optimal cleavage, variations of protease concentration in combination with an SDS-PAGE assay, and analysis of the resulting fragments using Edman sequencing. Described in this unit are protocols for vector preparation, expression, purification, and in situ proteolytic crystallization of two membrane-bound P450 proteins.
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Affiliation(s)
- Li Lei
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee
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17
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Abstract
The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed.
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Affiliation(s)
- John F Marko
- Department of Physics & Astronomy and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois USA 60208
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18
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Abstract
DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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19
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Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea. Int J Mol Sci 2014; 15:17162-87. [PMID: 25257534 PMCID: PMC4200833 DOI: 10.3390/ijms150917162] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.
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20
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Rajan R, Osterman AK, Gast AT, Mondragón A. Biochemical characterization of the topoisomerase domain of Methanopyrus kandleri topoisomerase V. J Biol Chem 2014; 289:28898-909. [PMID: 25135643 DOI: 10.1074/jbc.m114.590711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Topoisomerases are ubiquitous enzymes that modify the topological state of DNA inside the cell and are essential for several cellular processes. Topoisomerase V is the sole member of the type IC topoisomerase subtype. The topoisomerase domain has a unique fold among topoisomerases, and the putative active site residues show a distinct arrangement. The present study was aimed at identifying the roles of the putative active site residues in the DNA cleavage/religation process. Residues Arg-131, Arg-144, His-200, Glu-215, Lys-218, and Tyr-226 were mutated individually to a series of conservative and non-conservative amino acids, and the DNA relaxation activity at different pH values, times, and enzyme concentrations was compared with wild-type activity. The results suggest that Arg-144 is essential for protein stability because any substitution at this position was deleterious and that Arg-131 and His-200 are involved in transition state stabilization. Glu-215 reduces the DNA binding ability of topoisomerase V, especially in shorter fragments with fewer helix-hairpin-helix DNA binding motifs. Finally, Lys-218 appears to play a direct role in catalysis but not in charge stabilization of the protein-DNA intermediate complex. The results suggest that although catalytically important residues are oriented in different fashions in the active sites of type IB and type IC topoisomerases, similar amino acids play equivalent roles in both of these subtypes of enzymes, showing convergent evolution of the catalytic mechanism.
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Affiliation(s)
- Rakhi Rajan
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Amy K Osterman
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Alexandra T Gast
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Alfonso Mondragón
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
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21
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Gadelle D, Krupovic M, Raymann K, Mayer C, Forterre P. DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria. Nucleic Acids Res 2014; 42:8578-91. [PMID: 24990376 PMCID: PMC4117785 DOI: 10.1093/nar/gku568] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 11/14/2022] Open
Abstract
Type II DNA topoisomerases are divided into two families, IIA and IIB. Types IIA and IIB enzymes share homologous B subunits encompassing the ATP-binding site, but have non-homologous A subunits catalyzing DNA cleavage. Type IIA topoisomerases are ubiquitous in Bacteria and Eukarya, whereas members of the IIB family are mostly present in Archaea and plants. Here, we report the detection of genes encoding type IIB enzymes in which the A and B subunits are fused into a single polypeptide. These proteins are encoded in several bacterial genomes, two bacterial plasmids and one archaeal plasmid. They form a monophyletic group that is very divergent from archaeal and eukaryotic type IIB enzymes (DNA topoisomerase VI). We propose to classify them into a new subfamily, denoted DNA topoisomerase VIII. Bacterial genes encoding a topoisomerase VIII are present within integrated mobile elements, most likely derived from conjugative plasmids. Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities. In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity. Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.
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Affiliation(s)
- Danièle Gadelle
- Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France
| | - Mart Krupovic
- Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
| | - Kasie Raymann
- Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
| | - Claudine Mayer
- Institut Pasteur, Unité de Microbiologie structurale, Département de Biologie structurale et Chimie, F-75015 Paris, France CNRS, UMR3528, F-75015 Paris, France Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr Roux 75015 Paris, France
| | - Patrick Forterre
- Université Paris-Sud, CNRS UMR8621, Institut de Génétique Microbiologie, 91405 Orsay Cedex, France Institut Pasteur, Unité de Biologie moléculaire du gène chez les extrêmophiles, Département de Microbiologie, F-75015 Paris, France
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22
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PprA contributes to Deinococcus radiodurans resistance to nalidixic acid, genome maintenance after DNA damage and interacts with deinococcal topoisomerases. PLoS One 2014; 9:e85288. [PMID: 24454836 PMCID: PMC3893189 DOI: 10.1371/journal.pone.0085288] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 12/04/2013] [Indexed: 11/19/2022] Open
Abstract
PprA is known to contribute to Deinococcus radiodurans' remarkable capacity to survive a variety of genotoxic assaults. The molecular bases for PprA's role(s) in the maintenance of the damaged D. radiodurans genome are incompletely understood, but PprA is thought to promote D. radiodurans's capacity for DSB repair. PprA is found in a multiprotein DNA processing complex along with an ATP type DNA ligase, and the D. radiodurans toposiomerase IB (DraTopoIB) as well as other proteins. Here, we show that PprA is a key contributor to D. radiodurans resistance to nalidixic acid (Nal), an inhibitor of topoisomerase II. Growth of wild type D. radiodurans and a pprA mutant were similar in the absence of exogenous genotoxic insults; however, the pprA mutant exhibited marked growth delay and a higher frequency of anucleate cells following treatment with DNA-damaging agents. We show that PprA interacts with both DraTopoIB and the Gyrase A subunit (DraGyrA) in vivo and that purified PprA enhances DraTopoIB catalysed relaxation of supercoiled DNA. Thus, besides promoting DNA repair, our findings suggest that PprA also contributes to preserving the integrity of the D. radiodurans genome following DNA damage by interacting with DNA topoisomerases and by facilitating the actions of DraTopoIB.
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23
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Abstract
In situ proteolysis is the method of proactively adding tiny amounts of nonspecific proteases to aid in the crystallization of proteins and protein macromolecular complexes. The simplicity of the procedure and high recovery rate make it a method of first choice for recalcitrant targets. An improved and updated in situ proteolysis protocol used in high-throughput structural biology platforms is described.
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Affiliation(s)
- Yufeng Tong
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Suite 700, Toronto, ON, Canada, M5G 1L7,
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24
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Rajan R, Prasad R, Taneja B, Wilson SH, Mondragón A. Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies. Nucleic Acids Res 2012; 41:657-66. [PMID: 23125368 PMCID: PMC3592480 DOI: 10.1093/nar/gks1017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Topoisomerase V (Topo-V) is the only member of a novel topoisomerase subtype. Topo-V is unique because it is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities within the same protein. Previous studies had shown that the topoisomerase domain spans the N-terminus of the protein and is followed by 12 tandem helix-hairpin-helix [(HhH)(2)] domains. There are at least two DNA repair lyase active sites for apurinic/apyrimidinic (AP) site processing, one within the N-terminal region and the second within the C-terminal domain of Topo-V, but their exact locations and characteristics are unknown. In the present study, the N-terminal 78-kDa fragment of Topo-V (Topo-78), containing the topoisomerase domain and one of the lyase DNA repair domains, was characterized by structural and biochemical studies. The results show that an N-terminal 69-kDa fragment is the minimal fragment with both topoisomerase and AP lyase activities. The lyase active site of Topo-78 is at the junction of the fifth and sixth (HhH)(2) domains. From the biochemical and structural data, it appears that Lys571 is the most probable nucleophile responsible for the lyase activity. Our experiments also suggest that Topo-V most likely acts as a Class I AP endonuclease in vivo.
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Affiliation(s)
- Rakhi Rajan
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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25
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Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end. Proc Natl Acad Sci U S A 2012; 109:16546-51. [PMID: 23011800 DOI: 10.1073/pnas.1203118109] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzyme rates are usually considered to be dependent on local properties of the molecules involved in reactions. However, for large molecules, distant constraints might affect reaction rates by affecting dynamics leading to transition states. In single-molecule experiments we have found that enzymes that relax DNA torsional stress display rates that depend strongly on how the distant ends of the molecule are constrained; experiments with different-sized particles tethered to the end of 10-kb DNAs reveal enzyme rates inversely correlated with particle drag coefficients. This effect can be understood in terms of the coupling between molecule extension and local molecular stresses: The rate of bead thermal motion controls the rate at which transition states are visited in the middle of a long DNA. Importantly, we have also observed this effect for reactions on unsupercoiled DNA; other enzymes show rates unaffected by bead size. Our results reveal a unique mechanism through which enzyme rates can be controlled by constraints on macromolecular or supramolecular substrates.
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26
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Pavlov AR, Pavlova NV, Kozyavkin SA, Slesarev AI. Cooperation between catalytic and DNA binding domains enhances thermostability and supports DNA synthesis at higher temperatures by thermostable DNA polymerases. Biochemistry 2012; 51:2032-43. [PMID: 22320201 DOI: 10.1021/bi2014807] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have previously introduced a general kinetic approach for comparative study of processivity, thermostability, and resistance to inhibitors of DNA polymerases [Pavlov, A. R., et al. (2002) Proc. Natl. Acad. Sci. U.S.A.99, 13510-13515]. The proposed method was successfully applied to characterize hybrid DNA polymerases created by fusing catalytic DNA polymerase domains with various sequence-nonspecific DNA binding domains. Here we use the developed kinetic analysis to assess basic parameters of DNA elongation by DNA polymerases and to further study the interdomain interactions in both previously constructed and new chimeric DNA polymerases. We show that connecting helix-hairpin-helix (HhH) domains to catalytic polymerase domains can increase thermostability, not only of DNA polymerases from extremely thermophilic species but also of the enzyme from a faculatative thermophilic bacterium Bacillus stearothermophilus. We also demonstrate that addition of Topo V HhH domains extends efficient DNA synthesis by chimerical polymerases up to 105 °C by maintaining processivity of DNA synthesis at high temperatures. We found that reversible high-temperature structural transitions in DNA polymerases decrease the rates of binding of these enzymes to the templates. Furthermore, activation energies and pre-exponential factors of the Arrhenius equation suggest that the mechanism of electrostatic enhancement of diffusion-controlled association plays a minor role in binding of templates to DNA polymerases.
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Affiliation(s)
- Andrey R Pavlov
- Fidelity Systems, Inc., Gaithersburg, Maryland 20879, United States.
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27
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Kathiravan MK, Khilare MM, Nikoomanesh K, Chothe AS, Jain KS. Topoisomerase as target for antibacterial and anticancer drug discovery. J Enzyme Inhib Med Chem 2012; 28:419-35. [DOI: 10.3109/14756366.2012.658785] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Muthu K. Kathiravan
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy,
Maharashtra, India
| | - Madhavi M. Khilare
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy,
Maharashtra, India
| | - Kiana Nikoomanesh
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy,
Maharashtra, India
| | - Aparna S. Chothe
- Department of Pharmaceutical Chemistry, AISSMS College of Pharmacy,
Pune, Maharashtra, India
| | - Kishor S. Jain
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy,
Maharashtra, India
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28
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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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29
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Vos SM, Tretter EM, Schmidt BH, Berger JM. All tangled up: how cells direct, manage and exploit topoisomerase function. Nat Rev Mol Cell Biol 2011; 12:827-41. [PMID: 22108601 DOI: 10.1038/nrm3228] [Citation(s) in RCA: 451] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Topoisomerases are complex molecular machines that modulate DNA topology to maintain chromosome superstructure and integrity. Although capable of stand-alone activity in vitro, topoisomerases are frequently linked to larger pathways and systems that resolve specific DNA superstructures and intermediates arising from cellular processes such as DNA repair, transcription, replication and chromosome compaction. Topoisomerase activity is indispensible to cells, but requires the transient breakage of DNA strands. This property has been exploited, often for significant clinical benefit, by various exogenous agents that interfere with cell proliferation. Despite decades of study, surprising findings involving topoisomerases continue to emerge with respect to their cellular function, regulation and utility as therapeutic targets.
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Affiliation(s)
- Seychelle M Vos
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
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30
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Rajan R, Taneja B, Mondragón A. Structures of minimal catalytic fragments of topoisomerase V reveals conformational changes relevant for DNA binding. Structure 2010; 18:829-38. [PMID: 20637419 DOI: 10.1016/j.str.2010.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 03/19/2010] [Accepted: 03/27/2010] [Indexed: 10/19/2022]
Abstract
Topoisomerase V is an archaeal type I topoisomerase that is unique among topoisomerases due to presence of both topoisomerase and DNA repair activities in the same protein. It is organized as an N-terminal topoisomerase domain followed by 24 tandem helix-hairpin-helix (HhH) motifs. Structural studies have shown that the active site is buried by the (HhH) motifs. Here we show that the N-terminal domain can relax DNA in the absence of any HhH motifs and that the HhH motifs are required for stable protein-DNA complex formation. Crystal structures of various topoisomerase V fragments show changes in the relative orientation of the domains mediated by a long bent linker helix, and these movements are essential for the DNA to enter the active site. Phosphate ions bound to the protein near the active site helped model DNA in the topoisomerase domain and show how topoisomerase V may interact with DNA.
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Affiliation(s)
- Rakhi Rajan
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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31
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Abstract
DNA topoisomerases are enzymes that control the topological state of DNA in all cells; they have central roles in DNA replication and transcription. They are classified into two types, I and II, depending on whether they catalyze reactions involving the breakage of one or both strands of DNA. Structural and mechanistic distinctions have led to further classifications: IA, IB, IC, IIA, and IIB. The essence of the topoisomerase reaction is the ability of the enzymes to stabilize transient breaks in DNA, via the formation of tyrosyl-phosphate covalent intermediates. The essential nature of topoisomerases and their ability to stabilize DNA breaks has led to them being key targets for antibacterial and anticancer agents. This chapter reviews the basic features of topoisomerases focussing mainly on the prokaryotic enzymes. We highlight recent structural advances that have given new insight into topoisomerase mechanisms and into the molecular basis of the action of topoisomerase-specific drugs.
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32
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Forterre P, Gadelle D. Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res 2009; 37:679-92. [PMID: 19208647 PMCID: PMC2647321 DOI: 10.1093/nar/gkp032] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Topoisomerases are essential enzymes that solve topological problems arising from the double-helical structure of DNA. As a consequence, one should have naively expected to find homologous topoisomerases in all cellular organisms, dating back to their last common ancestor. However, as observed for other enzymes working with DNA, this is not the case. Phylogenomics analyses indicate that different sets of topoisomerases were present in the most recent common ancestors of each of the three cellular domains of life (some of them being common to two or three domains), whereas other topoisomerases families or subfamilies were acquired in a particular domain, or even a particular lineage, by horizontal gene transfers. Interestingly, two groups of viruses encode topoisomerases that are only distantly related to their cellular counterparts. To explain these observations, we suggest that topoisomerases originated in an ancestral virosphere, and that various subfamilies were later on transferred independently to different ancient cellular lineages. We also proposed that topoisomerases have played a critical role in the origin of modern genomes and in the emergence of the three cellular domains.
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Affiliation(s)
- Patrick Forterre
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, France
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33
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Abstract
Topoisomerases are ubiquitous proteins found in all three domains of life. They change the topology of DNA via transient breaks on either one or two of the DNA strands to allow passage of another single or double DNA strand through the break. Topoisomerases are classified into two types: type I enzymes cleave one DNA strand and pass either one or two DNA strands through the break before resealing it, while type II molecules cleave both DNA strands in concert and pass another double strand through the break followed by religation of the double strand break. Here we review recent work on the structure of type I enzymes. These structural studies are providing atomic details that, together with the existing wealth of biochemical and biophysical data, are bringing our understanding of the mechanism of action of these enzymes to the atomic level.
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Affiliation(s)
- Nicole M Baker
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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34
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Brochier-Armanet C, Gribaldo S, Forterre P. A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya. Biol Direct 2008; 3:54. [PMID: 19105819 PMCID: PMC2621148 DOI: 10.1186/1745-6150-3-54] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 12/23/2008] [Indexed: 01/08/2023] Open
Abstract
DNA topoisomerase IB (TopoIB) was thought for a long time to be a eukaryotic specific enzyme. A shorter version was then found in viruses and later on in several bacteria, but not in archaea. Here, we show that a eukaryotic-like TopoIB is present in the recently sequenced genomes of two archaea of the newly proposed phylum Thaumarchaeota. Phylogenetic analyses suggest that a TopoIB was present in the last common ancestor of Archaea and Eucarya. This finding indicates that the last common ancestor of Archaea and Eucarya may have harboured a DNA genome.
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Affiliation(s)
- Céline Brochier-Armanet
- Laboratoire de Chimie Bactérienne, Université de Provence, Aix-Marseille I, CNRS UPR9043, IFR88, Marseille, France.
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35
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Stuchinskaya T, Mitchenall LA, Schoeffler AJ, Corbett KD, Berger JM, Bates AD, Maxwell A. How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases. J Mol Biol 2008; 385:1397-408. [PMID: 19094994 DOI: 10.1016/j.jmb.2008.11.056] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 11/19/2008] [Accepted: 11/23/2008] [Indexed: 11/16/2022]
Abstract
DNA topoisomerases control the topology of DNA (e.g., the level of supercoiling) in all cells. Type IIA topoisomerases are ATP-dependent enzymes that have been shown to simplify the topology of their DNA substrates to a level beyond that expected at equilibrium (i.e., more relaxed than the product of relaxation by ATP-independent enzymes, such as type I topoisomerases, or a lower-than-equilibrium level of catenation). The mechanism of this effect is currently unknown, although several models have been suggested. We have analyzed the DNA relaxation reactions of type II topoisomerases to further explore this phenomenon. We find that all type IIA topoisomerases tested exhibit the effect to a similar degree and that it is not dependent on the supercoil-sensing C-terminal domains of the enzymes. As recently reported, the type IIB topoisomerase, topoisomerase VI (which is only distantly related to type IIA enzymes), does not exhibit topology simplification. We find that topology simplification is not significantly dependent on circle size in the range approximately 2-9 kbp and is not altered by reducing the free energy available from ATP hydrolysis by varying the ADP:ATP ratio. A direct test of one model (DNA tracking; i.e., sliding of a protein clamp along DNA to trap supercoils) suggests that this is unlikely to be the explanation for the effect. We conclude that geometric selection of DNA segments by the enzymes is likely to be a primary source of the effect, but that it is possible that other kinetic factors contribute. We also speculate whether topology simplification might simply be an evolutionary relic, with no adaptive significance.
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Affiliation(s)
- Tanya Stuchinskaya
- Department of Biological Chemistry, John Innes Centre, Colney, Norwich, UK
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36
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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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Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P, Flodin S, Flores A, Gräslund S, Hammerström M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H. In situ proteolysis for protein crystallization and structure determination. Nat Methods 2007; 4:1019-21. [PMID: 17982461 DOI: 10.1038/nmeth1118] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 10/03/2007] [Indexed: 11/09/2022]
Abstract
We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.
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Affiliation(s)
- Aiping Dong
- Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario M5G 1L5, Canada
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Taneja B, Schnurr B, Slesarev A, Marko JF, Mondragón A. Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism. Proc Natl Acad Sci U S A 2007; 104:14670-5. [PMID: 17804808 PMCID: PMC1976220 DOI: 10.1073/pnas.0701989104] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Topoisomerase V is a type I topoisomerase without structural or sequence similarities to other topoisomerases. Although it belongs to the type I subfamily of topoisomerases, it is unrelated to either type IA or IB enzymes. We used real-time single-molecule micromechanical experiments to show that topoisomerase V relaxes DNA via events that release multiple DNA turns, employing a constrained swiveling mechanism similar to that for type IB enzymes. Relaxation is powered by the torque in the supercoiled DNA and is constrained by friction between the protein and the DNA. Although all type IB enzymes share a common structure and mechanism and type IA and type II enzymes show marked structural and functional similarities, topoisomerase V represents a different type of topoisomerase that relaxes DNA in a similar overall manner as type IB molecules but by using a completely different structural and mechanistic framework.
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Affiliation(s)
- Bhupesh Taneja
- *Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208
| | - Bernhard Schnurr
- Department of Physics, University of Illinois, 845 West Taylor Street, Chicago, IL 60607
- Skirball Institute of Biomolecular Medicine and Department of Pathology, New York University School of Medicine, 540 First Avenue, New York, NY 10016
| | | | - John F. Marko
- *Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208
- Department of Physics, University of Illinois, 845 West Taylor Street, Chicago, IL 60607
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208
| | - Alfonso Mondragón
- *Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208
- **To whom correspondence should be addressed. E-mail:
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Changela A, DiGate RJ, Mondragón A. Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate. J Mol Biol 2007; 368:105-18. [PMID: 17331537 PMCID: PMC1885233 DOI: 10.1016/j.jmb.2007.01.065] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 01/22/2007] [Accepted: 01/26/2007] [Indexed: 11/27/2022]
Abstract
Escherichia coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5' phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an eight-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding.
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Affiliation(s)
- Anita Changela
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208
| | - Russell J. DiGate
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Philadelphia, PA 19104
| | - Alfonso Mondragón
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208
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Bai Y, Auperin TC, Tong L. The use of in situ proteolysis in the crystallization of murine CstF-77. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:135-8. [PMID: 17277459 PMCID: PMC2330134 DOI: 10.1107/s1744309107002904] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 01/18/2007] [Indexed: 02/01/2023]
Abstract
The cleavage-stimulation factor (CstF) is required for the cleavage of the 3'-end of messenger RNA precursors in eukaryotes. During structure determination of the 77 kDa subunit of the murine CstF complex (CstF-77), it was serendipitously discovered that a solution infected by a fungus was crucial for the crystallization of this protein. CstF-77 was partially proteolyzed during crystallization; this was very likely to have been catalyzed by a protease secreted by the fungus. It was found that the fungal protease can be replaced by subtilisin and this in situ proteolysis protocol produced crystals of sufficient size for structural studies. After an extensive search, it was found that 55% glucose can be used as a cryoprotectant while maintaining the diffraction quality of the crystals; most other commonly used cryoprotectants were detrimental to the diffraction quality.
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Affiliation(s)
- Yun Bai
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Thierry C. Auperin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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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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Mandel CR, Gebauer D, Zhang H, Tong L. A serendipitous discovery that in situ proteolysis is essential for the crystallization of yeast CPSF-100 (Ydh1p). Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1041-5. [PMID: 17012808 PMCID: PMC2225192 DOI: 10.1107/s1744309106038152] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 09/18/2006] [Indexed: 11/11/2022]
Abstract
The cleavage and polyadenylation specificity factor (CPSF) complex is required for the cleavage and polyadenylation of the 3'-end of messenger RNA precursors in eukaryotes. During structural studies of the 100 kDa subunit (CPSF-100, Ydh1p) of the yeast CPSF complex, it was serendipitously discovered that a solution that is infected by a fungus (subsequently identified as Penicillium) is crucial for the crystallization of this protein. Further analyses suggest that the protein has undergone partial proteolysis during crystallization, resulting in the deletion of an internal segment of about 200 highly charged and hydrophilic residues, very likely catalyzed by a protease secreted by the fungus. With the removal of this segment, yeast CPSF-100 (Ydh1p) has greatly reduced solubility and can be crystallized in the presence of a minute amount of precipitant.
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Affiliation(s)
- Corey R. Mandel
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Damara Gebauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Hailong Zhang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Correspondence e-mail:
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Forterre P. DNA topoisomerase V: a new fold of mysterious origin. Trends Biotechnol 2006; 24:245-7. [PMID: 16650908 DOI: 10.1016/j.tibtech.2006.04.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Revised: 03/23/2006] [Accepted: 04/13/2006] [Indexed: 10/24/2022]
Abstract
Although all other topoisomerases have a broad phylogenetic distribution, DNA topoisomerase V, the major component of the ThermoFidelase sequencing kit, is presently only known in a single species--the archaeon Methanopyrus kandleri. Resolution of the structure of this enzyme by Taneja and co-workers now reveals that this atypical topoisomerase has no structural similarity with other proteins. So, where did it come from? It is my contention that Topo V, and many other orphan proteins, could have a viral origin.
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Affiliation(s)
- Patrick Forterre
- Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France.
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