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Zhang Z, Zhao W, Cheng Z, Zhang G, Liu H. Olympic gels formed through catenation of dsDNA rings regulated by topoisomerase II: A coarse-grained model. J Chem Phys 2024; 160:054906. [PMID: 38341711 DOI: 10.1063/5.0190580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024] Open
Abstract
Topological regulation of DNA by topoisomerases in cells is very crucial for life. We propose a coarse-grained model to study the catenation process of double-stranded DNA (dsDNA) rings regulated by topoisomerase II (TOP2) and provide a computational method to characterize the topological structures of the Olympic gels obtained. The function of TOP2 in the catenation of dsDNA rings is implicitly fulfilled by operating the length of a stretchable catch bond in the dsDNA ring. After the catenation reaction of initially noncatenated dsDNA rings in the solution, the Olympic gel is obtained and the interlocked topology of the dsDNA rings can be characterized by a computational method derived from the HOMFLY polynomial, based on which the catenation degree and the complexity of catenation are quantified. Detailed dependence of the catenation degree and the complexity of the catenated topology on key parameters, including the size of the transient broken gap and the duration time of the break on the dsDNA ring during operation by TOP2, the initial molar ratio of TOP2 to the dsDNA rings, and the reaction temperature, has been investigated.
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Affiliation(s)
- Zhongyan Zhang
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Wenbo Zhao
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
| | - Zhiyuan Cheng
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
| | - Guojie Zhang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Hong Liu
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
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2
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Characterization of the Emerging Enteropathogen Escherichia Albertii Isolated from Urine Samples of Patients Attending Sapporo Area Hospitals, Japan. Int J Microbiol 2022; 2022:4236054. [PMID: 36160913 PMCID: PMC9507761 DOI: 10.1155/2022/4236054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/06/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Recently, Escherichia albertii has been identified as a causative agent of diarrhea in humans and is often misidentified as diarrheagenic Escherichia coli (DEC), a lactose-nondegrading bacterium. In this study, we performed biochemical characterization, gene possession status, drug susceptibility testing, and sequencing analysis of the strains detected in urine samples. One urea-degrading strain was detected in terms of biochemical characteristics, but was found to be nonurea-degrading by another method, leading to conflicting results. All target strains possessed the E. albertii-specific gene, the DEC common gene eae, and the E. coli 16S rRNA gene. In the drug susceptibility test, all urine-derived strains were sensitive to tetracycline (TC), whereas the JCM 17328 strain was resistant to TC, suggesting that TC is effective against urine-derived E. albertii strains. In 16S rRNA sequencing analysis, the E. albertii strains were ranked at the top of homology, but not in the top one, making it difficult to differentiate them from other strains. In summary, if a suspected lactose-nondegrading E. coli strain was isolated from a urine sample, it could be differentiated from E. albertii by the presence of E. albertii-specific genes.
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Huang SYN, Michaels SA, Mitchell BB, Majdalani N, Vanden Broeck A, Canela A, Tse-Dinh YC, Lamour V, Pommier Y. Exonuclease VII repairs quinolone-induced damage by resolving DNA gyrase cleavage complexes. SCIENCE ADVANCES 2021; 7:7/10/eabe0384. [PMID: 33658195 PMCID: PMC7929499 DOI: 10.1126/sciadv.abe0384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
The widely used quinolone antibiotics act by trapping prokaryotic type IIA topoisomerases, resulting in irreversible topoisomerase cleavage complexes (TOPcc). Whereas the excision repair pathways of TOPcc in eukaryotes have been extensively studied, it is not known whether equivalent repair pathways for prokaryotic TOPcc exist. By combining genetic, biochemical, and molecular biology approaches, we demonstrate that exonuclease VII (ExoVII) excises quinolone-induced trapped DNA gyrase, an essential prokaryotic type IIA topoisomerase. We show that ExoVII repairs trapped type IIA TOPcc and that ExoVII displays tyrosyl nuclease activity for the tyrosyl-DNA linkage on the 5'-DNA overhangs corresponding to trapped type IIA TOPcc. ExoVII-deficient bacteria fail to remove trapped DNA gyrase, consistent with their hypersensitivity to quinolones. We also identify an ExoVII inhibitor that synergizes with the antimicrobial activity of quinolones, including in quinolone-resistant bacterial strains, further demonstrating the functional importance of ExoVII for the repair of type IIA TOPcc.
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Affiliation(s)
- Shar-Yin N Huang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Stephanie A Michaels
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Brianna B Mitchell
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nadim Majdalani
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Arnaud Vanden Broeck
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404, France
| | - Andres Canela
- The Hakubi Center for Advanced Research, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Valerie Lamour
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404, France
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Benyahya F, Nadaud I, Da Ines O, Rimbert H, White C, Sourdille P. SPO11.2 is essential for programmed double-strand break formation during meiosis in bread wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:30-43. [PMID: 32603485 DOI: 10.1111/tpj.14903] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 05/20/2023]
Abstract
Meiotic recombination is initiated by formation of DNA double-strand breaks (DSBs). This involves a protein complex that includes in plants the two similar proteins, SPO11-1 and SPO11-2. We analysed the sequences of SPO11-2 in hexaploid bread wheat (Triticum aestivum), as well as in its diploid and tetraploid progenitors. We investigated its role during meiosis using single, double and triple mutants. The three homoeologous SPO11-2 copies of hexaploid wheat exhibit high nucleotide and amino acid similarities with those of the diploids, tetraploids and Arabidopsis. Interestingly, however, two nucleotides deleted in exon-2 of the A copy lead to a premature stop codon and suggest that it encodes a non-functional protein. Remarkably, the mutation was absent from the diploid A-relative Triticum urartu, but present in the tetraploid Triticum dicoccoides and in different wheat cultivars indicating that the mutation occurred after the first polyploidy event and has since been conserved. We further show that triple mutants with all three copies (A, B, D) inactivated are sterile. Cytological analyses of these mutants show synapsis defects, accompanied by severe reductions in bivalent formation and numbers of DMC1 foci, thus confirming the essential role of TaSPO11-2 in meiotic recombination in wheat. In accordance with its 2-nucleotide deletion in exon-2, double mutants for which only the A copy remained are also sterile. Notwithstanding, some DMC1 foci remain visible in this mutant, suggesting a residual activity of the A copy, albeit not sufficient to restore fertility.
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Affiliation(s)
- Fatiha Benyahya
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Isabelle Nadaud
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Olivier Da Ines
- Génétique, Reproduction et Développement, UMR CNRS 6293 - Université Clermont Auvergne - INSERM U1103, Clermont-Ferrand, 63001, France
| | - Hélène Rimbert
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
| | - Charles White
- Génétique, Reproduction et Développement, UMR CNRS 6293 - Université Clermont Auvergne - INSERM U1103, Clermont-Ferrand, 63001, France
| | - Pierre Sourdille
- Genetics, Diversity & Ecophysiology of Cereals, INRAE, Université Clermont-Auvergne, Clermont-Ferrand, 63000, France
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Andrawus M, Sharvit L, Shekhidem HA, Roichman A, Cohen HY, Atzmon G. The effects of environmental stressors on candidate aging associated genes. Exp Gerontol 2020; 137:110952. [PMID: 32344118 DOI: 10.1016/j.exger.2020.110952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/29/2020] [Accepted: 04/09/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND Aging is defined as a biological and physical complex process that is characterized by the increase in susceptibility to diseases and eventually death. Aging may occur at different rates between and within species, especially or (it varies) among the long-lived ones. Here, we ask whether this diversity (e.g. aging phenotype) stems from genetic or environmental factors or as a combination between the two (epigenetics). Epigenetics play a central role in controlling changes in gene expression during aging. DNA methylation is the most abundant epigenetic modification among vertebrates and is essential to mammalian development. MATERIALS AND METHODS In this study, we utilized the HELPtag assay to identify five candidate genes that were significantly hyper- or hypo-methylated across four different age groups in mice. The candidate genes were annotated using ensemble and their expression was further tested in vitro using the murine RAW 264.7 cell line to examine the effect of three environmental stressors (UV radiation, Hypoxia and fasting) on their expression. RNA was extracted at different time points followed by cDNA synthesis. Changes in gene expression were evaluated using qRT-PCR. RESULTS We show that fasting and UV radiation reduced the viability of RAW264.7 cells. We also found a significant change in three candidate genes' expression levels during fasting (TOP2B, RNF13 and MRPL4). Furthermore, we found a significant change in the four candidate genes' expression levels following UVC treatment (TOP2B, RNF13, PKNOX1 and CREB5) and yet no changes were recorded in hypoxic conditions. CONCLUSION Our results suggest that the model we used was a fitting model for the assessment of environmental stressors on candidate gene expression. In addition, we established a cellular response to the environment via changes in gene expression.
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Affiliation(s)
- Mariana Andrawus
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
| | - Lital Sharvit
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
| | | | - Asael Roichman
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Haim Y Cohen
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Gil Atzmon
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel.
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6
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Weidlich D, Klostermeier D. Functional interactions between gyrase subunits are optimized in a species-specific manner. J Biol Chem 2020; 295:2299-2312. [PMID: 31953321 DOI: 10.1074/jbc.ra119.010245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/03/2020] [Indexed: 11/06/2022] Open
Abstract
DNA gyrase is a bacterial DNA topoisomerase that catalyzes ATP-dependent negative DNA supercoiling and DNA decatenation. The enzyme is a heterotetramer comprising two GyrA and two GyrB subunits. Its overall architecture is conserved, but species-specific elements in the two subunits are thought to optimize subunit interaction and enzyme function. Toward understanding the roles of these different elements, we compared the activities of Bacillus subtilis, Escherichia coli, and Mycobacterium tuberculosis gyrases and of heterologous enzymes reconstituted from subunits of two different species. We show that B. subtilis and E. coli gyrases are proficient DNA-stimulated ATPases and efficiently supercoil and decatenate DNA. In contrast, M. tuberculosis gyrase hydrolyzes ATP only slowly and is a poor supercoiling enzyme and decatenase. The heterologous enzymes are generally less active than their homologous counterparts. The only exception is a gyrase reconstituted from mycobacterial GyrA and B. subtilis GyrB, which exceeds the activity of M. tuberculosis gyrase and reaches the activity of the B. subtilis gyrase, indicating that the activities of enzymes containing mycobacterial GyrB are limited by ATP hydrolysis. The activity pattern of heterologous gyrases is in agreement with structural features present: B. subtilis gyrase is a minimal enzyme, and its subunits can functionally interact with subunits from other bacteria. In contrast, the specific insertions in E. coli and mycobacterial gyrase subunits appear to prevent efficient functional interactions with heterologous subunits. Understanding the molecular details of gyrase adaptations to the specific physiological requirements of the respective organism might aid in the development of species-specific gyrase inhibitors.
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Affiliation(s)
- Daniela Weidlich
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany.
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7
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Stelljes JT, Weidlich D, Gubaev A, Klostermeier D. Gyrase containing a single C-terminal domain catalyzes negative supercoiling of DNA by decreasing the linking number in steps of two. Nucleic Acids Res 2019; 46:6773-6784. [PMID: 29893908 PMCID: PMC6061840 DOI: 10.1093/nar/gky470] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/18/2018] [Indexed: 12/18/2022] Open
Abstract
The topological state of DNA in vivo is regulated by topoisomerases. Gyrase is a bacterial topoisomerase that introduces negative supercoils into DNA at the expense of ATP hydrolysis. According to the strand-passage mechanism, a double-strand of the DNA substrate is cleaved, and a second double-stranded segment is passed through the gap, converting a positive DNA node into a negative node. The correct orientation of these DNA segments for strand passage is achieved by wrapping of the DNA around gyrase, which involves the C-terminal domains (CTDs) of both GyrA subunits in the A2B2 heterotetramer. Gyrase lacking both CTDs cannot introduce negative supercoils into DNA. Here, we analyze the requirements for the two CTDs in individual steps in the supercoiling reaction. Gyrase that contains a single CTD binds, distorts, and cleaves DNA similarly to wildtype gyrase. It also shows wildtype-like DNA-dependent ATPase activity, and undergoes DNA-induced movement of the CTD as well as N-gate narrowing. Most importantly, the enzyme still introduces negative supercoils into DNA in an ATP-dependent reaction, with a velocity similar to wildtype gyrase, and decreases the linking number of the DNA in steps of two. One CTD is thus sufficient to support DNA supercoiling.
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Affiliation(s)
- Jampa Tsedön Stelljes
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Daniela Weidlich
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Airat Gubaev
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, D-48149 Muenster, Germany
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8
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Nitiss KC, Nitiss JL, Hanakahi LA. DNA Damage by an essential enzyme: A delicate balance act on the tightrope. DNA Repair (Amst) 2019; 82:102639. [PMID: 31437813 DOI: 10.1016/j.dnarep.2019.102639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/18/2019] [Accepted: 07/01/2019] [Indexed: 01/07/2023]
Abstract
DNA topoisomerases are essential for DNA metabolic processes such as replication and transcription. Since DNA is double stranded, the unwinding needed for these processes results in DNA supercoiling and catenation of replicated molecules. Changing the topology of DNA molecules to relieve supercoiling or resolve catenanes requires that DNA be transiently cut. While topoisomerases carry out these processes in ways that minimize the likelihood of genome instability, there are several ways that topoisomerases may fail. Topoisomerases can be induced to fail by therapeutic small molecules such as by fluoroquinolones that target bacterial topoisomerases, or a variety of anti-cancer agents that target the eukaryotic enzymes. Increasingly, there have been a large number of agents and processes, including natural products and their metabolites, DNA damage, and the intrinsic properties of the enzymes that can lead to long-lasting DNA breaks that subsequently lead to genome instability, cancer, and other diseases. Understanding the processes that can interfere with topoisomerases and how cells respond when topoisomerases fail will be important in minimizing the consequences when enzymes need to transiently interfere with DNA integrity.
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Affiliation(s)
- Karin C Nitiss
- University of Illinois College of Medicine, Department of Biomedical Sciences, Rockford, IL, 61107, United States; University of Illinois College of Pharmacy, Biopharmaceutical Sciences Department, Rockford IL, 61107, United States
| | - John L Nitiss
- University of Illinois College of Pharmacy, Biopharmaceutical Sciences Department, Rockford IL, 61107, United States.
| | - Leslyn A Hanakahi
- University of Illinois College of Pharmacy, Biopharmaceutical Sciences Department, Rockford IL, 61107, United States.
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9
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Khalil OM, Gedawy EM, El-Malah AA, Adly ME. Novel nalidixic acid derivatives targeting topoisomerase II enzyme; Design, synthesis, anticancer activity and effect on cell cycle profile. Bioorg Chem 2019; 83:262-276. [DOI: 10.1016/j.bioorg.2018.10.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 10/28/2022]
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10
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Deshmukh SU, Kharat KR, Yadav AR, Shisodia SU, Damale MG, Sangshetti JN, Pawar RP. Synthesis of Novel α-Aminophosphonate Derivatives, Biological Evaluation as Potent Antiproliferative Agents and Molecular Docking. ChemistrySelect 2018. [DOI: 10.1002/slct.201800798] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Kiran R. Kharat
- Department of Biotechnology; Deogiri College, Aurangabad; 431005, (MS India
| | - Ashok R. Yadav
- Division of Organic Chemistry; National Chemical Laboratory, (CSIR-NCL); Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Suresh U. Shisodia
- Division of Organic Chemistry; National Chemical Laboratory, (CSIR-NCL); Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Manoj G. Damale
- Shreeyash Institute of Pharmaceutical Education & Research; MS 431001, Aurangabad India
| | | | - Rajendra P. Pawar
- Department of Chemistry; Deogiri College, Aurangabad; 431005, (MS India
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Klostermeier D. Why Two? On the Role of (A-)Symmetry in Negative Supercoiling of DNA by Gyrase. Int J Mol Sci 2018; 19:E1489. [PMID: 29772727 PMCID: PMC5983639 DOI: 10.3390/ijms19051489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/09/2018] [Accepted: 05/12/2018] [Indexed: 11/17/2022] Open
Abstract
Gyrase is a type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme consists of two GyrA and two GyrB subunits. It is believed to introduce negative supercoils into DNA by converting a positive DNA node into a negative node through strand passage: First, it cleaves both DNA strands of a double-stranded DNA, termed the G-segment, and then it passes a second segment of the same DNA molecule, termed the T-segment, through the gap created. As a two-fold symmetric enzyme, gyrase contains two copies of all elements that are key for the supercoiling reaction: The GyrB subunits provide two active sites for ATP binding and hydrolysis. The GyrA subunits contain two C-terminal domains (CTDs) for DNA binding and wrapping to stabilize the positive DNA node, and two catalytic tyrosines for DNA cleavage. While the presence of two catalytic tyrosines has been ascribed to the necessity of cleaving both strands of the G-segment to enable strand passage, the role of the two ATP hydrolysis events and of the two CTDs has been less clear. This review summarizes recent results on the role of these duplicate elements for individual steps of the supercoiling reaction, and discusses the implications for the mechanism of DNA supercoiling.
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Affiliation(s)
- Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany.
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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: 266] [Impact Index Per Article: 44.3] [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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Walker SS, Labroli M, Painter RE, Wiltsie J, Sherborne B, Murgolo N, Sher X, Mann P, Zuck P, Garlisi CG, Su J, Kargman S, Xiao L, Scapin G, Salowe S, Devito K, Sheth P, Buist N, Tan CM, Black TA, Roemer T. Antibacterial small molecules targeting the conserved TOPRIM domain of DNA gyrase. PLoS One 2017; 12:e0180965. [PMID: 28700746 PMCID: PMC5507300 DOI: 10.1371/journal.pone.0180965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/23/2017] [Indexed: 12/21/2022] Open
Abstract
To combat the threat of antibiotic-resistant Gram-negative bacteria, novel agents that circumvent established resistance mechanisms are urgently needed. Our approach was to focus first on identifying bioactive small molecules followed by chemical lead prioritization and target identification. Within this annotated library of bioactives, we identified a small molecule with activity against efflux-deficient Escherichia coli and other sensitized Gram-negatives. Further studies suggested that this compound inhibited DNA replication and selection for resistance identified mutations in a subunit of E. coli DNA gyrase, a type II topoisomerase. Our initial compound demonstrated weak inhibition of DNA gyrase activity while optimized compounds demonstrated significantly improved inhibition of E. coli and Pseudomonas aeruginosa DNA gyrase and caused cleaved complex stabilization, a hallmark of certain bactericidal DNA gyrase inhibitors. Amino acid substitutions conferring resistance to this new class of DNA gyrase inhibitors reside exclusively in the TOPRIM domain of GyrB and are not associated with resistance to the fluoroquinolones, suggesting a novel binding site for a gyrase inhibitor.
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Affiliation(s)
- Scott S. Walker
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
- * E-mail:
| | - Marc Labroli
- Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | | | - Judyann Wiltsie
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Brad Sherborne
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Nicholas Murgolo
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Xinwei Sher
- Merck & Co., Inc., Boston, Massachusetts, United States of America
| | - Paul Mann
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Paul Zuck
- Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | | | - Jing Su
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Stacia Kargman
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Li Xiao
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Giovanna Scapin
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Scott Salowe
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Kristine Devito
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Payal Sheth
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Nichole Buist
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | | | - Todd A. Black
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Terry Roemer
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
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14
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Cuya SM, Bjornsti MA, van Waardenburg RCAM. DNA topoisomerase-targeting chemotherapeutics: what's new? Cancer Chemother Pharmacol 2017; 80:1-14. [PMID: 28528358 DOI: 10.1007/s00280-017-3334-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/03/2017] [Indexed: 02/05/2023]
Abstract
To resolve the topological problems that threaten the function and structural integrity of nuclear and mitochondrial genomes and RNA molecules, human cells encode six different DNA topoisomerases including type IB enzymes (TOP1 and TOP1mt), type IIA enzymes (TOP2α and TOP2β) and type IA enzymes (TOP3α and TOP3β). DNA entanglements and the supercoiling of DNA molecules are regulated by topoisomerases through the introduction of transient enzyme-linked DNA breaks. The covalent topoisomerase-DNA complexes are the cellular targets of a diverse group of cancer chemotherapeutics, which reversibly stabilize these reaction intermediates. Here we review the structure-function and catalytic mechanisms of each family of eukaryotic DNA topoisomerases and the topoisomerase-targeting agents currently approved for patient therapy or in clinical trials, and highlight novel developments and challenges in the clinical development of these agents.
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Affiliation(s)
- Selma M Cuya
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 155 Volker Hall, 1720 2nd Ave. S., Birmingham, AL, 35294-0019, USA
| | - Mary-Ann Bjornsti
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 155 Volker Hall, 1720 2nd Ave. S., Birmingham, AL, 35294-0019, USA
| | - Robert C A M van Waardenburg
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, 155 Volker Hall, 1720 2nd Ave. S., Birmingham, AL, 35294-0019, USA.
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15
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Hou GX, Liu P, Yang J, Wen S. Mining expression and prognosis of topoisomerase isoforms in non-small-cell lung cancer by using Oncomine and Kaplan-Meier plotter. PLoS One 2017; 12:e0174515. [PMID: 28355294 PMCID: PMC5371362 DOI: 10.1371/journal.pone.0174515] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/10/2017] [Indexed: 01/09/2023] Open
Abstract
DNA topoisomerases are essential to modulate DNA topology during various cellular genetic processes. The expression and distinct prognostic value of topoisomerase isoforms in non-small-cell lung cancer (NSCLC) is not well established. In the current study, we have examined the mRNA expression of topoisomerase isoforms by using Oncomine analysis and investigated their prognostic value via the Kaplan–Meier plotter database in NSCLC patients. Our analysis indicated that the expression level of topoisomerases in lung cancer was higher compared with normal tissues. Especially, high expression of two topoisomerase isoforms, TOP2A and TOP3A, was found to be correlated to worse overall survival (OS) in all NSCLC and lung adenocarcinoma (Ade) patients, but not in lung squamous cell carcinoma (SCC) patients. In a contrast, high expression of isoforms TOP1 and TOP2B indicated better OS in all NSCLC and Ade, but not in SCC patients. Meanwhile, high expression of TOP1MT and TOP3B was not correlated with OS in NSCLC patients. Furthermore, we also demonstrated a relationship between topoisomerase isoforms and the clinicopathological features for the NSCLC patients, such as grades, clinical stages, lymph node status, smoking status, gender, chemotherapy and radiotherapy. These results support that TOP2A and TOP3A are associated with worse prognosis in NSCLC patients. In addition, our study also shows that TOP1 and TOP2B contribute to favorable prognosis in NSCLC patients. The exact prognostic significance of TOP1MT and TOP3B need to be further elucidated. Comprehensive evaluation of expression and prognosis of topoisomerase isoforms will be a benefit for the better understanding of heterogeneity and complexity in the molecular biology of NSCLC, paving a way for more accurate prediction of prognosis and discovery of potential drug targets for NSCLC patients.
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Affiliation(s)
- Guo-Xin Hou
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Panpan Liu
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jing Yang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shijun Wen
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail:
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16
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Mogil LS, Becker NA, Maher LJ. Supercoiling Effects on Short-Range DNA Looping in E. coli. PLoS One 2016; 11:e0165306. [PMID: 27783696 PMCID: PMC5081198 DOI: 10.1371/journal.pone.0165306] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 10/10/2016] [Indexed: 11/19/2022] Open
Abstract
DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades. Here we adapt this model to test the hypothesis that negative superhelical strain facilitates the formation of short-range (6-8 DNA turns) repression loops in E. coli. The natural negative superhelicity of E. coli DNA is regulated by the interplay of gyrase and topoisomerase enzymes, adding or removing negative supercoils, respectively. Here, we measured quantitatively DNA looping in three different E. coli strains characterized by different levels of global supercoiling: wild type, gyrase mutant (gyrB226), and topoisomerase mutant (ΔtopA10). DNA looping in each strain was measured by assaying repression of the endogenous lac operon, and repression of ten reporter constructs with DNA loop sizes between 70-85 base pairs. Our data are most simply interpreted as supporting the hypothesis that negative supercoiling facilitates gene repression by small DNA-protein loops in living bacteria.
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MESH Headings
- DNA Gyrase/genetics
- DNA Gyrase/metabolism
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- Electrophoresis, Agar Gel
- Escherichia coli/genetics
- Genes, Reporter
- Lac Operon/genetics
- Mutation
- Nucleic Acid Conformation
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Affiliation(s)
- Lauren S. Mogil
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America
- Biochemistry and Molecular Biology track, Mayo Graduate School, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America
| | - Nicole A. Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America
- * E-mail:
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17
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Chaudhari K, Surana S, Jain P, Patel HM. Mycobacterium Tuberculosis (MTB) GyrB inhibitors: An attractive approach for developing novel drugs against TB. Eur J Med Chem 2016; 124:160-185. [PMID: 27569197 DOI: 10.1016/j.ejmech.2016.08.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/03/2016] [Accepted: 08/17/2016] [Indexed: 01/24/2023]
Abstract
New classes of drugs are needed to treat tuberculosis (TB) in order to combat the emergence of resistance (MDR and XDR) to existing agents and shorten the duration of therapy. Mycobacterial DNA gyrase B subunit has been identified to be one of the potentially under exploited drug targets in the field of antitubercular drug discovery. In the present review, we discussed the synthesis, structural optimization and docking study of effective potent DNA gyrase inhibitor against M. tuberculosis, with improved properties such as enhanced activity against MDR strains, reduced toxicity. Based on this progress, if we can successfully leverage the opportunities in this target, there is hope that we will be able to raise novel gyrase inhibitor in earnest in the long.
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Affiliation(s)
- Kavita Chaudhari
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India
| | - Pritam Jain
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India.
| | - Harun M Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dhule, 425405, Maharashtra, India.
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18
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The Current Case of Quinolones: Synthetic Approaches and Antibacterial Activity. Molecules 2016; 21:268. [PMID: 27043501 PMCID: PMC6274096 DOI: 10.3390/molecules21040268] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/08/2016] [Accepted: 02/15/2016] [Indexed: 11/17/2022] Open
Abstract
Quinolones are broad-spectrum synthetic antibacterial drugs first obtained during the synthesis of chloroquine. Nalidixic acid, the prototype of quinolones, first became available for clinical consumption in 1962 and was used mainly for urinary tract infections caused by Escherichia coli and other pathogenic Gram-negative bacteria. Recently, significant work has been carried out to synthesize novel quinolone analogues with enhanced activity and potential usage for the treatment of different bacterial diseases. These novel analogues are made by substitution at different sites--the variation at the C-6 and C-8 positions gives more effective drugs. Substitution of a fluorine atom at the C-6 position produces fluroquinolones, which account for a large proportion of the quinolones in clinical use. Among others, substitution of piperazine or methylpiperazine, pyrrolidinyl and piperidinyl rings also yields effective analogues. A total of twenty six analogues are reported in this review. The targets of quinolones are two bacterial enzymes of the class II topoisomerase family, namely gyrase and topoisomerase IV. Quinolones increase the concentration of drug-enzyme-DNA cleavage complexes and convert them into cellular toxins; as a result they are bactericidal. High bioavailability, relative low toxicity and favorable pharmacokinetics have resulted in the clinical success of fluoroquinolones and quinolones. Due to these superior properties, quinolones have been extensively utilized and this increased usage has resulted in some quinolone-resistant bacterial strains. Bacteria become resistant to quinolones by three mechanisms: (1) mutation in the target site (gyrase and/or topoisomerase IV) of quinolones; (2) plasmid-mediated resistance; and (3) chromosome-mediated quinolone resistance. In plasmid-mediated resistance, the efflux of quinolones is increased along with a decrease in the interaction of the drug with gyrase (topoisomerase IV). In the case of chromosome-mediated quinolone resistance, there is a decrease in the influx of the drug into the cell.
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19
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Wolański M, Łebkowski T, Kois-Ostrowska A, Zettler J, Apel AK, Jakimowicz D, Zakrzewska-Czerwińska J. Two transcription factors, CabA and CabR, are independently involved in multilevel regulation of the biosynthetic gene cluster encoding the novel aminocoumarin, cacibiocin. Appl Microbiol Biotechnol 2015; 100:3147-64. [PMID: 26637421 DOI: 10.1007/s00253-015-7196-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/19/2015] [Accepted: 11/22/2015] [Indexed: 11/30/2022]
Abstract
Aminocoumarins are potent antibiotics belonging to a relatively small group of secondary metabolites produced by actinomycetes. Genome mining of Catenulispora acidiphila has recently led to the discovery of a gene cluster responsible for biosynthesis of novel aminocoumarins, cacibiocins. However, regulation of the expression of this novel gene cluster has not yet been analyzed. In this study, we identify transcriptional regulators of the cacibiocin gene cluster. Using a heterologous expression system, we show that the CabA and CabR proteins encoded by cabA and cabR genes in the cacibiocin gene cluster control the expression of genes involved in the biosynthesis, modification, regulation, and potentially, efflux/resistance of cacibiocins. CabA positively regulates the expression of cabH (the first gene in the cabHIYJKL operon) and cabhal genes encoding key enzymes responsible for the biosynthesis and halogenation of the aminocoumarin moiety, respectively. We provide evidence that CabA is a direct inducer of cacibiocin production, whereas the second transcriptional factor, CabR, is involved in the negative regulation of its own gene and cabT-the latter of which encodes a putative cacibiocin transporter. We also demonstrate that CabR activity is negatively regulated in vitro by aminocoumarin compounds, suggesting the existence of analogous regulation in vivo. Finally, we propose a model of multilevel regulation of gene transcription in the cacibiocin gene cluster by CabA and CabR.
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Affiliation(s)
- Marcin Wolański
- Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383, Wrocław, Poland.
| | - Tomasz Łebkowski
- Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383, Wrocław, Poland
| | | | - Judith Zettler
- Pharmazeutische Biologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site, Tübingen, Germany
| | - Alexander K Apel
- Pharmazeutische Biologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site, Tübingen, Germany
| | - Dagmara Jakimowicz
- Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383, Wrocław, Poland.,Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Weigla 12, 53-114, Wrocław, Poland
| | - Jolanta Zakrzewska-Czerwińska
- Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, 50-383, Wrocław, Poland.,Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Weigla 12, 53-114, Wrocław, Poland
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20
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Abstract
How eukaryotic genomes are packaged into compact cylindrical chromosomes in preparation for cell divisions has remained one of the major unsolved questions of cell biology. Novel approaches to study the topology of DNA helices inside the nuclei of intact cells, paired with computational modeling and precise biomechanical measurements of isolated chromosomes, have advanced our understanding of mitotic chromosome architecture. In this Review Essay, we discuss - in light of these recent insights - the role of chromatin architecture and the functions and possible mechanisms of SMC protein complexes and other molecular machines in the formation of mitotic chromosomes. Based on the information available, we propose a stepwise model of mitotic chromosome condensation that envisions the sequential generation of intra-chromosomal linkages by condensin complexes in the context of cohesin-mediated inter-chromosomal linkages, assisted by topoisomerase II. The described scenario results in rod-shaped metaphase chromosomes ready for their segregation to the cell poles.
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Affiliation(s)
- Marc Kschonsak
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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21
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Nagano S, Lin TY, Edula JR, Heddle JG. Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum. BMC Bioinformatics 2014; 15:416. [PMID: 25523502 PMCID: PMC4297366 DOI: 10.1186/s12859-014-0416-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/10/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND DNA gyrase, an enzyme once thought to be unique to bacteria, is also found in some eukaryotic plastids including the apicoplast of Apicomplexa such as Plasmodium falciparum and Toxoplasma gondii which are important disease-causing organisms. DNA gyrase is an excellent target for antibacterial drugs, yet such antibacterials seem ineffective against Apicomplexa. Characterisation of the apicoplast gyrases would be a useful step towards understanding why this should be so. While purification of active apicoplast gyrase has proved impossible to date, in silico analyses have allowed us to discover differences in the apicoplast proteins. The resulting predicted structural and functional differences will be a first step towards development of apicoplast-gyrase specific inhibitors. RESULTS We have carried out sequence analysis and structural predictions of the enzymes from the two species and find that P. falciparum gyrase lacks a GyrA box, but T. gondii may retain one. All proteins contained signal/transport peptides for localization to the apicoplast but T. gondii Gyrase B protein lacks the expected hydrophobic region. The most significant difference is in the GyrA C-terminal domain: While the cores of the proteins, including DNA binding and cleavage regions are essentially unchanged, both apicoplast gyrase A proteins have C-terminal domains that are significantly larger than bacterial counterparts and are predicted to have different structures. CONCLUSION The apicoplast gyrases differ significantly from bacterial gyrases while retaining similar core domains. T. gondii Gyrase B may have an unusual or inefficient mechanism of localisation to the apicoplast. P.falciparum gyrase, lacks a GyrA box and is therefore likely to be inefficient in DNA supercoiling. The C-terminal domains of both apicoplast Gyrase A proteins diverge significantly from the bacterial proteins. We predict that an additional structural element is present in the C-terminal domain of both apicoplast Gyrase A proteins, including the possibility of a β-pinwheel with a non-canonical number of blades. These differences undoubtedly will affect the DNA supercoiling mechanism and have perhaps evolved to compensate for the lack of Topoisomerase IV in the apicoplast. These data will be useful first step towards further characterisation and development of inhibitors for apicoplast gyrases.
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Affiliation(s)
- Soshichiro Nagano
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Ting-Yu Lin
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Jyotheeswara Reddy Edula
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Current address: Department of Molecular Protozoology, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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22
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Apostolou P, Toloudi M, Kourtidou E, Mimikakou G, Vlachou I, Chatziioannou M, Kipourou V, Papasotiriou I. Potential role for the Metnase transposase fusion gene in colon cancer through the regulation of key genes. PLoS One 2014; 9:e109741. [PMID: 25333365 PMCID: PMC4198141 DOI: 10.1371/journal.pone.0109741] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/08/2014] [Indexed: 01/06/2023] Open
Abstract
The Metnase fusion gene consists of a SET histone methyltransferase domain and a transposase domain from Mariner transposase. This transposable element is involved in chromosome decatenation, enhances DNA repair, promotes foreign DNA integration, and assists topoisomerase II function. This study investigates the role of Metnase in colon cancer homeostasis and maintenance of the stemness phenotype in colon cancer stem cells (CSCs). Silencing of Metnase was performed in human cancer cell lines before and after treatment with cisplatin, and in colon CSCs. Subsequent changes in the expression of genes involved in repair mechanisms, DNA synthesis, topoisomerase II function, and metastasis as well stemness transcription factors were studied with RT-qPCR experiments. Cellular viability and apoptosis were evaluated by flow cytometry. The results suggest that Metnase influences the expression of many genes involved in the above processes. Furthermore, Metnase levels appear to impact upon expression of NANOG, OCT3/4, and SOX2. Suppression of Metnase also led to an increase in apoptosis. Therefore, Metnase may possess an important role in DNA repair, topoisomerase II function, and the maintenance of stemness during colon cancer development.
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Affiliation(s)
| | - Maria Toloudi
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | - Eleni Kourtidou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | - Georgia Mimikakou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | - Ioanna Vlachou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | | | - Vasiliki Kipourou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
| | - Ioannis Papasotiriou
- Research Genetic Cancer Centre Ltd (R.G.C.C. Ltd), Filotas, Florina, Greece
- * E-mail:
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23
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Gao R, Schellenberg MJ, Huang SYN, Abdelmalak M, Marchand C, Nitiss KC, Nitiss JL, Williams RS, Pommier Y. Proteolytic degradation of topoisomerase II (Top2) enables the processing of Top2·DNA and Top2·RNA covalent complexes by tyrosyl-DNA-phosphodiesterase 2 (TDP2). J Biol Chem 2014; 289:17960-9. [PMID: 24808172 DOI: 10.1074/jbc.m114.565374] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic type II topoisomerases (Top2α and Top2β) are homodimeric enzymes; they are essential for altering DNA topology by the formation of normally transient double strand DNA cleavage. Anticancer drugs (etoposide, doxorubicin, and mitoxantrone) and also Top2 oxidation and DNA helical alterations cause potentially irreversible Top2·DNA cleavage complexes (Top2cc), leading to Top2-linked DNA breaks. Top2cc are the therapeutic mechanism for killing cancer cells. Yet Top2cc can also generate recombination, translocations, and apoptosis in normal cells. The Top2 protein-DNA covalent complexes are excised (in part) by tyrosyl-DNA-phosphodiesterase 2 (TDP2/TTRAP/EAP2/VPg unlinkase). In this study, we show that irreversible Top2cc induced in suicidal substrates are not processed by TDP2 unless they first undergo proteolytic processing or denaturation. We also demonstrate that TDP2 is most efficient when the DNA attached to the tyrosyl is in a single-stranded configuration and that TDP2 can efficiently remove a tyrosine linked to a single misincorporated ribonucleotide or to polyribonucleotides, which expands the TDP2 catalytic profile with RNA substrates. The 1.6-Å resolution crystal structure of TDP2 bound to a substrate bearing a 5'-ribonucleotide defines a mechanism through which RNA can be accommodated in the TDP2 active site, albeit in a strained conformation.
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Affiliation(s)
- Rui Gao
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Matthew J Schellenberg
- the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, and
| | - Shar-Yin N Huang
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Monica Abdelmalak
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Christophe Marchand
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Karin C Nitiss
- the Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, Illinois 61107
| | - John L Nitiss
- the Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, Illinois 61107
| | - R Scott Williams
- the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, and
| | - Yves Pommier
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892,
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24
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Lavery LA, Partridge JR, Ramelot TA, Elnatan D, Kennedy MA, Agard DA. Structural asymmetry in the closed state of mitochondrial Hsp90 (TRAP1) supports a two-step ATP hydrolysis mechanism. Mol Cell 2014; 53:330-43. [PMID: 24462206 PMCID: PMC3947485 DOI: 10.1016/j.molcel.2013.12.023] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 11/04/2013] [Accepted: 12/24/2013] [Indexed: 12/31/2022]
Abstract
While structural symmetry is a prevailing feature of homo-oligomeric proteins, asymmetry provides unique mechanistic opportunities. We present the crystal structure of full-length TRAP1, the mitochondrial Hsp90 molecular chaperone, in a catalytically active closed state. The TRAP1 homodimer adopts a distinct, asymmetric conformation, where one protomer is reconfigured via a helix swap at the middle:C-terminal domain (MD:CTD) interface. This interface plays a critical role in client binding. Solution methods validate the asymmetry and show extension to Hsp90 homologs. Point mutations that disrupt unique contacts at each MD:CTD interface reduce catalytic activity and substrate binding and demonstrate that each protomer needs access to both conformations. Crystallographic data on a dimeric NTD:MD fragment suggests that asymmetry arises from strain induced by simultaneous NTD and CTD dimerization. The observed asymmetry provides the potential for an additional step in the ATPase cycle, allowing sequential ATP hydrolysis steps to drive both client remodeling and client release.
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Affiliation(s)
- Laura A Lavery
- Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James R Partridge
- Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, Miami University Oxford, OH 45056, USA
| | - Daniel Elnatan
- Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University Oxford, OH 45056, USA
| | - David A Agard
- Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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25
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Abstract
In contrast with most bacteria which possess two type II topoisomerases (topoisomerase IV and DNA gyrase), Mycobacterium tuberculosis possesses only one, DNA gyrase, which is functionally a hybrid enzyme. Functional differences between the two type IIA topoisomerases are thought to be specified by a CTD (C-terminal DNA-binding domain), which controls DNA recognition. To explore the molecular mechanism responsible for the hybrid functions of the M. tuberculosis DNA gyrase, we conducted a series of sequence analyses and structural and biochemical experiments with the isolated GyrA CTD and the holoenzyme. Although the CTD displayed a global structure similar to that of bona fide GyrA and ParC paralogues, it harbours a second key motif similar in all respects to that of the conserved GyrA-box sequence motif. Biochemical assays showed that the GyrA-box is responsible for DNA supercoiling, whereas the second GyrA-box-l (GyrA-box-like motif) is responsible for the enhanced decatenation activity, suggesting that the mechanistic originality of M. tuberculosis DNA gyrase depends largely on the particular DNA path around the CTD allowed for by the presence of GyrA-box-l. The results of the present study also provide, through phylogenetic exploration of the entire Corynebacterineae suborder, a new and broader insight into the functional diversity of bacterial type IIA topoisomerases.
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26
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Gyrase subunit B amino acid signatures for the actinobacterial family Streptosporangiaceae. Syst Appl Microbiol 2014; 37:252-60. [PMID: 24423454 DOI: 10.1016/j.syapm.2013.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 12/03/2013] [Accepted: 12/13/2013] [Indexed: 11/24/2022]
Abstract
Higher order taxonomic assignments (family level and above) in the phylum Actinobacteria are currently based only on 16S-rRNA gene sequence analyses. Additional molecular markers need to be identified to increase the number of reference points for defining actinobacterial families and other higher taxa. Furthermore, since most novel actinobacterial taxa are defined at the level of species and genera, it is necessary to define molecular signatures at the genus level to enhance the robustness of genus descriptions. The current use of chemotaxonomic markers to define genera could be improved by the identification of genus-specific molecular signatures. In this study, GyrB amino acid sequences for members of the family Streptosporangiaceae were analysed for molecular signatures. Phylogenetic analyses showed that the gyrB gene tree supported the composition of the currently recognised genera in this family. The catalytically important amino acids were identified in the GyrB sequences, as were the GHKL superfamily motifs. Examination of GyrB protein sequence alignments revealed that there are genus-specific sequences for most of the multi-species genera and genus-defining amino acid insertions for the genera Herbidospora and Microbispora. Furthermore, there are GyrB signature amino acids which distinguish the family Streptosporangiaceae from the family Nocardiopsaceae.
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Mayer C, Janin YL. Non-quinolone inhibitors of bacterial type IIA topoisomerases: a feat of bioisosterism. Chem Rev 2013; 114:2313-42. [PMID: 24313284 DOI: 10.1021/cr4003984] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudine Mayer
- Unité de Microbiologie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur , 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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Abstract
Topoisomerases are ubiquitous enzymes that control DNA supercoiling and entanglements. They are essential during transcription and replication, and topoisomerase inhibitors are among the most effective and most commonly used anticancer and antibacterial drugs. This review consists of two parts. In the first part ("Lessons"), it gives background information on the catalytic mechanisms of the different enzyme families (6 different genes in humans and 4 in most bacteria), describes the "interfacial inhibition" by which topoisomerase-targeted drugs act as topoisomerase poisons, and describes clinically relevant topoisomerase inhibitors. It generalizes the interfacial inhibition principle, which was discovered from the mechanism of action of topoisomerase inhibitors, and discusses how topoisomerase inhibitors kill cells by trapping topoisomerases on DNA rather than by classical enzymatic inhibition. Trapping protein-DNA complexes extends to a novel mechanism of action of PARP inhibitors and could be applied to the targeting of transcription factors. The second part of the review focuses on the challenges for discovery and precise use of topoisomerase inhibitors, including targeting topoisomerase inhibitors using chemical coupling and encapsulation for selective tumor delivery, use of pharmacodynamic biomarkers to follow drug activity, complexity of the response determinants for anticancer activity and patient selection, prospects of rational combinations with DNA repair inhibitors targeting tyrosyl-DNA-phosphodiesterases 1 and 2 (TDP1 and TDP2) and PARP, and the unmet need to develop inhibitors for type IA enzymes.
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Affiliation(s)
- Yves Pommier
- Laboratory of Molecular
Pharmacology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
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ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA. Nat Struct Mol Biol 2012; 19:538-46, S1. [PMID: 22484318 PMCID: PMC5660678 DOI: 10.1038/nsmb.2278] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 03/08/2012] [Indexed: 11/08/2022]
Abstract
DNA gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to introduce negative supercoils into DNA. A critical step in this reaction is the formation of a chiral DNA wrap. Here we observe gyrase structural dynamics using a single-molecule assay in which gyrase drives the processive, stepwise rotation of a nanosphere attached to the side of a stretched DNA molecule. Analysis of rotational pauses and measurements of DNA contraction reveal multiple ATP-modulated structural transitions. DNA wrapping is coordinated with the ATPase cycle and proceeds by way of an unanticipated structural intermediate that dominates the kinetics of supercoiling. Our findings reveal a conformational landscape of loosely coupled transitions funneling the motor toward productive energy transduction, a feature that may be common to the reaction cycles of other DNA and protein remodeling machines.
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DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage. Proc Natl Acad Sci U S A 2011; 108:14085-90. [PMID: 21817063 DOI: 10.1073/pnas.1102100108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
DNA gyrase introduces negative supercoils into DNA in an ATP-dependent reaction. DNA supercoiling is catalyzed by a strand-passage mechanism, in which a T-segment of DNA is passed through the gap in a transiently cleaved G-segment. Strand passage requires the coordinated closing and opening of three protein interfaces in gyrase, the N-gate, DNA-gate, and C-gate. We show here that DNA binding to the DNA-gate of gyrase and wrapping of DNA around the C-terminal domains of GyrA induces a narrowing of the N-gate. This half-closed state prepares capture of a T-segment in the upper cavity of gyrase. Subsequent N-gate closure upon binding of ATP then poises the reaction toward strand passage. The N-gate reopens after ATP hydrolysis, allowing for further catalytic cycles. DNA binding, cleavage, and wrapping and N-gate narrowing are intimately linked events that coordinate conformational changes at the DNA and the N-gate.
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31
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Wong A, Kassen R. Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2011; 157:937-944. [PMID: 21292748 DOI: 10.1099/mic.0.046870-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The emergence and spread of antibiotic resistance in pathogens is a major impediment to the control of microbial disease. Here, we review mechanisms of quinolone resistance in Pseudomonas aeruginosa, an important nosocomial pathogen and a major cause of morbidity in cystic fibrosis (CF) patients. In this quantitative literature review, we find that mutations in DNA gyrase A, the primary target of quinolones in Gram-negative bacteria, are the most common resistance mutations identified in clinical samples of all origins, in keeping with previous observations. However, the identities of non-gyrase resistance mutations vary systematically between samples isolated from CF patients and those isolated from acute infections. CF-derived strains tend to harbour mutations in the efflux pump regulator nfxB, while non-CF strains tend to bear mutations in the efflux regulator mexR or in parC, which encodes one of two subunits of DNA topoisomerase IV. We suggest that differences in resistance mechanisms between CF and non-CF strains result either from local adaptation to different sites of infection or from differences in mutational processes between different environments. We further discuss the therapeutic implications of local differentiation in resistance mechanisms to a common antibiotic.
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Affiliation(s)
- Alex Wong
- Center for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Rees Kassen
- Center for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada
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Glaser BT, Malerich JP, Duellman SJ, Fong J, Hutson C, Fine RM, Keblansky B, Tang MJ, Madrid PB. A high-throughput fluorescence polarization assay for inhibitors of gyrase B. ACTA ACUST UNITED AC 2011; 16:230-8. [PMID: 21245469 DOI: 10.1177/1087057110392038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
DNA gyrase, a type II topoisomerase that introduces negative supercoils into DNA, is a validated antibacterial drug target. The holoenzyme is composed of 2 subunits, gyrase A (GyrA) and gyrase B (GyrB), which form a functional A(2)B(2) heterotetramer required for bacterial viability. A novel fluorescence polarization (FP) assay has been developed and optimized to detect inhibitors that bind to the adenosine triphosphate (ATP) binding domain of GyrB. Guided by the crystal structure of the natural product novobiocin bound to GyrB, a novel novobiocin-Texas Red probe (Novo-TRX) was designed and synthesized for use in a high-throughput FP assay. The binding kinetics of the interaction of Novo-TRX with GyrB from Francisella tularensis has been characterized, as well as the effect of common buffer additives on the interaction. The assay was developed into a 21-µL, 384-well assay format and has been validated for use in high-throughput screening against a collection of Food and Drug Administration-approved compounds. The assay performed with an average Z' factor of 0.80 and was able to identify GyrB inhibitors from a screening library.
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A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs. Proc Natl Acad Sci U S A 2010; 107:22055-9. [PMID: 21076033 DOI: 10.1073/pnas.1012938107] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria frequently possess two type IIA DNA topoisomerases, gyrase and topo IV, which maintain chromosome topology by variously supercoiling, relaxing, and disentangling DNA. DNA recognition and functional output is thought to be controlled by the C-terminal domain (CTD) of the topoisomerase DNA binding subunit (GyrA/ParC). The deeply rooted organism Aquifex aeolicus encodes one type IIA topoisomerase conflictingly categorized as either DNA gyrase or topo IV. To resolve this enzyme's catalytic properties and heritage, we conducted a series of structural and biochemical studies on the isolated GyrA/ParC CTD and the holoenzyme. Whereas the CTD displays a global structure similar to that seen in bone fide GyrA and ParC paralogs, it lacks a key functional motif (the "GyrA-box") and fails to wrap DNA. Biochemical assays show that the A. aeolicus topoisomerase cannot supercoil DNA, but robustly removes supercoils and decatenates DNA, two hallmark activities of topo IV. Despite these properties, phylogenetic analyses place all functional domains except the CTD squarely within a gyrase lineage, and the A. aeolicus GyrB subunit is capable of supporting supercoiling with Escherichia coli GyrA, but not DNA relaxation with E. coli ParC. Moreover, swapping the A. aeolicus GyrA/ParC CTD with the GyrA CTD from Thermotoga maritima creates an enzyme that negatively supercoils DNA. These findings identify A. aeolicus as the first bacterial species yet found to exist without a functional gyrase, and suggest an evolutionary path for generation of bacterial type IIA paralogs.
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Piton J, Petrella S, Delarue M, André-Leroux G, Jarlier V, Aubry A, Mayer C. Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase. PLoS One 2010; 5:e12245. [PMID: 20805881 PMCID: PMC2923608 DOI: 10.1371/journal.pone.0012245] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 07/21/2010] [Indexed: 12/04/2022] Open
Abstract
Mycobacterium tuberculosis DNA gyrase, an indispensable nanomachine involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and is hence the sole target for quinolone action, a crucial drug active against multidrug-resistant tuberculosis. To understand at an atomic level the quinolone resistance mechanism, which emerges in extensively drug resistant tuberculosis, we performed combined functional, biophysical and structural studies of the two individual domains constituting the catalytic DNA gyrase reaction core, namely the Toprim and the breakage-reunion domains. This allowed us to produce a model of the catalytic reaction core in complex with DNA and a quinolone molecule, identifying original mechanistic properties of quinolone binding and clarifying the relationships between amino acid mutations and resistance phenotype of M. tuberculosis DNA gyrase. These results are compatible with our previous studies on quinolone resistance. Interestingly, the structure of the entire breakage-reunion domain revealed a new interaction, in which the Quinolone-Binding Pocket (QBP) is blocked by the N-terminal helix of a symmetry-related molecule. This interaction provides useful starting points for designing peptide based inhibitors that target DNA gyrase to prevent its binding to DNA.
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Affiliation(s)
- Jérémie Piton
- Unité de Dynamique Structurale des Macromolécules, Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
- URA 2185, CNRS, Paris, France
- UPMC Univ Paris 06, Paris, France
| | | | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
- URA 2185, CNRS, Paris, France
| | - Gwénaëlle André-Leroux
- URA 2185, CNRS, Paris, France
- Unité de Biochimie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
| | - Vincent Jarlier
- UPMC Univ Paris 06, EA1541, Bactériologie-Hygiène, Paris, France
| | - Alexandra Aubry
- UPMC Univ Paris 06, EA1541, Bactériologie-Hygiène, Paris, France
| | - Claudine Mayer
- Unité de Dynamique Structurale des Macromolécules, Département de Biologie Structurale et Chimie, Institut Pasteur, Paris, France
- URA 2185, CNRS, Paris, France
- Université Paris Diderot Paris 7, Paris, France
- * E-mail:
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35
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Sissi C, Palumbo M. In front of and behind the replication fork: bacterial type IIA topoisomerases. Cell Mol Life Sci 2010; 67:2001-24. [PMID: 20165898 PMCID: PMC11115839 DOI: 10.1007/s00018-010-0299-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 01/26/2010] [Accepted: 02/01/2010] [Indexed: 01/03/2023]
Abstract
Topoisomerases are vital enzymes specialized in controlling DNA topology, in particular supercoiling and decatenation, to properly handle nucleic acid packing and cell dynamics. The type IIA enzymes act by cleaving both strands of a double helix and having another strand from the same or another molecule cross the DNA gate before a re-sealing event completes the catalytic cycle. Here, we will consider the two types of IIA prokaryotic topoisomerases, DNA Gyrase and Topoisomerase IV, as crucial regulators of bacterial cell cycle progression. Their synergistic action allows control of chromosome packing and grants occurrence of functional transcription and replication processes. In addition to displaying a fascinating molecular mechanism of action, which transduces chemical energy into mechanical energy by means of large conformational changes, these enzymes represent attractive pharmacological targets for antibacterial chemotherapy.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131, Padua, Italy.
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36
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Abstract
Type II topoisomerases are essential enzymes that regulate DNA under- and overwinding and remove knots and tangles from the genetic material. In order to carry out their critical physiological functions, these enzymes utilize a double-stranded DNA passage mechanism that requires them to generate a transient double-stranded break. Consequently, while necessary for cell survival, type II topoisomerases also have the capacity to fragment the genome. This feature of the prokaryotic and eukaryotic enzymes, respectively, is exploited to treat a variety of bacterial infections and cancers in humans. All type II topoisomerases require divalent metal ions for catalytic function. These metal ions function in two separate active sites and are necessary for the ATPase and DNA cleavage/ligation activities of the enzymes. ATPase activity is required for the strand passage process and utilizes the metal-dependent binding and hydrolysis of ATP to drive structural rearrangements in the protein. Both the DNA cleavage and ligation activities of type II topoisomerases require divalent metal ions and appear to utilize a novel variant of the canonical two-metal-ion phosphotransferase/hydrolase mechanism to facilitate these reactions. This article will focus primarily on eukaryotic type II topoisomerases and the roles of metal ions in the catalytic functions of these enzymes.
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Affiliation(s)
- Joseph E Deweese
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy, Nashville, TN 37204-3951, USA
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37
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Park JS, Kim HS, Park MY, Kim CH, Chung YJ, Hong YK, Kim TG. Topoisomerase II alpha as a universal tumor antigen: antitumor immunity in murine tumor models and H-2K(b)-restricted T cell epitope. Cancer Immunol Immunother 2010; 59:747-57. [PMID: 19936747 PMCID: PMC11030946 DOI: 10.1007/s00262-009-0795-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 10/31/2009] [Indexed: 10/20/2022]
Abstract
Topoisomerase II alpha (Top2alpha) is an attractive candidate to be used as a tumor antigen for cancer immunotherapy, because it is abundantly expressed in various tumors and serves as a target for a number of chemotherapeutic agents. In this study, we demonstrated the immunogenicity of Top2alpha, using dendritic cells (DC) electroporated with RNA encoding the Top2alpha C-terminus (Top2alphaCRNA/DC). Top2alphaCRNA/DC were able to demonstrate in vitro stimulation of T cells from mice that were previously vaccinated with Top2alpha-expressing tumor lysate-pulsed DC. Vaccination with Top2alphaCRNA/DC induced Top2alpha-specific T cell responses in vivo as well as antitumor effects in various murine tumor models including MC-38, B16F10, and GL26. DC pulsed with p1327 (DSDEDFSGL), defined as an epitope presented by H-2K(b), also induced Top2alpha-specific immune responses and antitumor effects. Based on these data, Top2alpha is suggested to be a universal target for cancer immunotherapy.
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Affiliation(s)
- Jung-Sun Park
- Department of Microbiology and Immunology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul, 137-701 Korea
| | - Hye-Sung Kim
- Department of Microbiology and Immunology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul, 137-701 Korea
| | - Mi-Young Park
- Department of Microbiology and Immunology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul, 137-701 Korea
| | - Chang-Hyun Kim
- Department of Microbiology and Immunology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul, 137-701 Korea
| | - Yeun-Jun Chung
- Department of Microbiology and Immunology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul, 137-701 Korea
| | - Yong-Kil Hong
- Department of Neurosurgery, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul, 137-701 Korea
| | - Tai-Gyu Kim
- Department of Microbiology and Immunology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul, 137-701 Korea
- Catholic Hematopoietic Stem Cell Bank, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul, 137-701 Korea
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38
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Xie P. Dynamics of strand passage catalyzed by topoisomerase II. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1251-9. [PMID: 20127325 DOI: 10.1007/s00249-010-0578-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 12/17/2009] [Accepted: 01/13/2010] [Indexed: 11/25/2022]
Abstract
DNA topoisomerase II is a homodimeric molecular machine that uses ATP hydrolysis to untangle DNA by passing one double-stranded DNA duplex (T-segment) through another double-stranded duplex (G-segment). However, despite extensive studies, the dynamics of ATP-dependent T-transport is still not very clear. Here, based on the proposal that transport of the T-segment through the transiently cleaved G-segment and the opened C-gate of the enzyme is via a free diffusion mechanism, the dynamics of T-transport are studied theoretically. Our results show that, to complete passage of the strand with nearly 100% efficiency, the C-gate is required to open by a width that is only slightly larger than the width of DNA duplex and for a time shorter than 100 micros in the presence of several k (B) T binding affinities of the T-segment for the B' domains. The results are implied by our understanding of the opening and closing dynamics of the C-gate. Moreover, the dependence of chemomechanical coupling efficiency on degrees of DNA supercoiling by gyrases can also be explained by using our results. On the basis of these theoretical results and previous experimental data, a modified two-gate model for chemomechanical coupling of the topoisomerase II enzyme is proposed.
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Affiliation(s)
- Ping Xie
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190, Beijing, China.
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Bigot S, Marians KJ. DNA chirality-dependent stimulation of topoisomerase IV activity by the C-terminal AAA+ domain of FtsK. Nucleic Acids Res 2010; 38:3031-40. [PMID: 20081205 PMCID: PMC2875013 DOI: 10.1093/nar/gkp1243] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We have studied the stimulation of topoisomerase IV (Topo IV) by the C-terminal AAA+ domain of FtsK. These two proteins combine to assure proper chromosome segregation in the cell. Stimulation of Topo IV activity was dependent on the chirality of the DNA substrate: FtsK stimulated decatenation of catenated DNA and relaxation of positively supercoiled [(+)ve sc] DNA, but inhibited relaxation of negatively supercoiled [(−)ve sc] DNA. The DNA translocation activity of FtsK was not required for stimulation, but was required for inhibition. DNA chirality did not affect any of the activities of FtsK, suggesting that FtsK possesses an inherent Topo IV stimulatory activity that is presumably mediated by protein–protein interactions, the stability of Topo IV on the DNA substrate dictated the effect observed. Inhibition occurs because FtsK can strip distributively acting topoisomerase off (−)ve scDNA, but not from either (+)ve scDNA or catenated DNA where the enzyme acts processively. Our analyses suggest that FtsK increases the efficiency of trapping of the transfer segment of DNA during the catalytic cycle of the topoisomerase.
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Affiliation(s)
- Sarah Bigot
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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40
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Lanoue L, Green KK, Kwik-Uribe C, Keen CL. Dietary factors and the risk for acute infant leukemia: evaluating the effects of cocoa-derived flavanols on DNA topoisomerase activity. Exp Biol Med (Maywood) 2010; 235:77-89. [DOI: 10.1258/ebm.2009.009184] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
There is cumulative strong evidence that diets rich in flavanols can provide certain positive health benefits, particularly with respect to the cardiovascular system. Consequently, it has been suggested that increasing one's dietary intake of flavanols may be of benefit. Complicating this idea, there are reports that high intakes of certain flavonoids during pregnancy are associated with an increased risk for acute infant leukemia due to a poison effect of select polyphenolic compounds on DNA topoisomerase (topo) II activity that promotes aberrant chromosomal translocations. In the current study, we characterized the effects of select flavanols (epicatechin and catechin monomers), and select flavanol dimers and longer oligomers, on topo II activity, and on cellular toxicity in vitro. In contrast to the chemotherapeutic drug etoposide (VP16) and the flavonol quercetin, which strongly inhibited topo II activity and increased the formation of cleavage complexes demonstrating a poison effect, the flavanols epicatechin and catechin had little effect on topo II enzyme activity. Accordingly, several fold greater concentrations of the flavanols were required to achieve cellular toxicity similar to that of quercetin and VP16 in cultures of myeloid and lymphoid cells. Low cellular toxicity and limited topo II inhibition were also observed with a procyanidin-rich cocoa extract. Of all the flavanols tested, the dimers (B2, B5 and a mix of both) exerted the greatest inhibition of topo II and inhibited cellular proliferation rates at concentrations similar to quercetin. However, in contrast to quercetin, the dimers did not function as topo II poisons. Collectively, our in vitro data show that cocoa-derived flavanols have limited effects on topo II activity and cellular proliferation in cancer cell lines. We predict that these compounds are likely to have limited leukemogenic potential at physiological concentrations.
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Affiliation(s)
- Louise Lanoue
- Department of Nutrition, University of California, Davis, One Shields Ave Davis, CA 95616
| | - Kerri K Green
- Department of Nutrition, University of California, Davis, One Shields Ave Davis, CA 95616
| | | | - Carl L Keen
- Department of Nutrition, University of California, Davis, One Shields Ave Davis, CA 95616
- Department of Internal Medicine, University of California, Davis, One Shields Ave Davis, CA 95616, USA
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41
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Dalla Via L, Magno SM, Gia O, Marini AM, Da Settimo F, Salerno S, La Motta C, Simorini F, Taliani S, Lavecchia A, Di Giovanni C, Brancato G, Barone V, Novellino E. Benzothiopyranoindole-based antiproliferative agents: synthesis, cytotoxicity, nucleic acids interaction, and topoisomerases inhibition properties. J Med Chem 2009; 52:5429-41. [PMID: 19725581 DOI: 10.1021/jm900627v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Novel benzo[3',2':5,6]thiopyrano[3,2-b]indol-10(11H)-ones 1a-v were synthesized and evaluated for their antiproliferative activity in an in vitro assay of human tumor cell lines (HL-60 and HeLa). Compounds 1e-v, substituted at the 11-position with a basic side chain, showed a significant ability to inhibit cell growth with IC(50) values in the low micromolar range. Linear dichroism measurements showed that all 11-dialkylaminoalkyl substituted derivatives 1e-v behave as DNA-intercalating agents. Fluorimetric titrations demonstrated their specificity in binding to A-T rich regions, and molecular modeling studies were performed on the most active derivatives (1e, 1i, 1p) to characterize in detail the complexation mechanism of these benzothiopyranoindoles to DNA. A relaxation assay evidenced a dose-dependent inhibition of topoisomerase II activity that appeared in accordance with the antiproliferative capacity. Finally, for the most cytotoxic derivative, 1e, a topoisomerase II poisoning effect was also demonstrated, along with a weak inhibition of topoisomerase I-mediated relaxation.
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Affiliation(s)
- Lisa Dalla Via
- Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy.
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The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction. Proc Natl Acad Sci U S A 2009; 106:13278-83. [PMID: 19666507 DOI: 10.1073/pnas.0902493106] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gyrase is the only type II topoisomerase that introduces negative supercoils into DNA. Supercoiling is catalyzed via a strand-passage mechanism, in which the gate DNA (gDNA) is transiently cleaved, and a second DNA segment, the transfer DNA (tDNA), is passed through the gap before the gDNA is religated. Strand passage requires an opening of the so-called DNA-gate by approximately 2 nm. A single-molecule FRET study reported equal populations of open and closed DNA-gate in topoisomerase II. We present here single-molecule FRET experiments that monitor the conformation of DNA bound to the DNA-gate of Bacillus subtilis gyrase and the conformation of the DNA-gate itself. DNA bound to gyrase adopts two different conformations, one slightly, one severely distorted. DNA distortion requires cleavage, but neither ATP nor the presence of a tDNA. At the same time, the DNA-gate of gyrase is predominantly in the closed conformation. In agreement with the single molecule data and with the danger of dsDNA breaks for genome integrity, <5% of cleavage complexes are detected in equilibrium. Quinolone inhibitors favor DNA cleavage by B. subtilis gyrase, but disfavor DNA distortion, and the DNA-gate remains in the closed conformation. Our results demonstrate that DNA binding, distortion and cleavage, and gate-opening are mechanistically distinct events. During the relaxation and supercoiling reactions, gyrase with an open DNA-gate is not significantly populated, consistent with gate-opening as a very rare event that only occurs briefly to allow for strand passage.
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43
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Affiliation(s)
- Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.
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Simic M, De Jonge N, Loris R, Vesnaver G, Lah J. Driving forces of gyrase recognition by the addiction toxin CcdB. J Biol Chem 2009; 284:20002-10. [PMID: 19465484 DOI: 10.1074/jbc.m109.014035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gyrase, an essential bacterial topoisomerase, is the target of several antibiotics (e.g. quinolones) as well as of bacterial toxin CcdB. This toxin, encoded by Escherichia coli toxin-antitoxin module ccd, poisons gyrase by causing inhibition of both transcription and replication. Because the molecular driving forces of gyrase unfolding and CcdB-gyrase binding were unknown, the nature of the CcdB-gyrase recognition remained elusive. Therefore, we performed a detailed thermodynamic analysis of CcdB binding to several fragments of gyrase A subunit (GyrA) that contain the CcdB-binding site. Binding of CcdB to the shorter fragments was studied directly by isothermal titration calorimetry. Its binding to the longer GyrA59 fragment in solution is kinetically limited and was therefore investigated via urea induced unfolding of the GyrA59-CcdB complex and unbound GyrA59 and CcdB, monitored by circular dichroism spectroscopy. Model analysis of experimental data, in combination with the relevant structural information, indicates that CcdB binding to gyrase is an enthalpic process driven mainly by specific interactions between CcdB and the highly stable dimerization domain of the GyrA. The dissection of binding energetics indicates that CcdB-gyrase recognition is accompanied by opening of the tower and catalytic domain of GyrA. Such extensive structural rearrangements appear to be crucial driving forces for the functioning of the ccd toxin-antitoxin module.
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Affiliation(s)
- Mario Simic
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, 1000 Ljubljana, Slovenia
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Vologodskii A. Theoretical models of DNA topology simplification by type IIA DNA topoisomerases. Nucleic Acids Res 2009; 37:3125-33. [PMID: 19383879 PMCID: PMC2691845 DOI: 10.1093/nar/gkp250] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It was discovered 12 years ago that type IIA topoisomerases can simplify DNA topology--the steady-state fractions of knots and links created by the enzymes are many times lower than the corresponding equilibrium fractions. Though this property of the enzymes made clear biological sense, it was not clear how small enzymes could selectively change the topology of very large DNA molecules, since topology is a global property and cannot be determined by a local DNA-protein interaction. A few models, suggested to explain the phenomenon, are analyzed in this review. We also consider experimental data that both support and contravene these models.
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Deweese JE, Osheroff N. Coordinating the two protomer active sites of human topoisomerase IIalpha: nicks as topoisomerase II poisons. Biochemistry 2009; 48:1439-41. [PMID: 19166355 DOI: 10.1021/bi8021679] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Topoisomerase II modulates DNA topology by generating double-stranded breaks in DNA. Results of the current study indicate that the presence of a nick at one scissile bond dramatically increases the rate of cleavage by human topoisomerase IIalpha at the scissile bond on the opposite strand. We propose that this enhanced activity at the second strand coordinates the two protomer subunits of topoisomerase II and allows the enzyme to create double-stranded breaks. Finally, the presence of a nick on one strand induces cleavage on the opposite strand. Thus, nicks are topoisomerase II poisons that generate novel sites of DNA cleavage.
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Affiliation(s)
- Joseph E Deweese
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Chène P, Rudloff J, Schoepfer J, Furet P, Meier P, Qian Z, Schlaeppi JM, Schmitz R, Radimerski T. Catalytic inhibition of topoisomerase II by a novel rationally designed ATP-competitive purine analogue. BMC CHEMICAL BIOLOGY 2009; 9:1. [PMID: 19128485 PMCID: PMC2628638 DOI: 10.1186/1472-6769-9-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2008] [Accepted: 01/07/2009] [Indexed: 01/10/2023]
Abstract
Background Topoisomerase II poisons are in clinical use as anti-cancer therapy for decades and work by stabilizing the enzyme-induced DNA breaks. In contrast, catalytic inhibitors block the enzyme before DNA scission. Although several catalytic inhibitors of topoisomerase II have been described, preclinical concepts for exploiting their anti-proliferative activity based on molecular characteristics of the tumor cell have only recently started to emerge. Topoisomerase II is an ATPase and uses the energy derived from ATP hydrolysis to orchestrate the movement of the DNA double strands along the enzyme. Thus, interfering with ATPase function with low molecular weight inhibitors that target the nucleotide binding pocket should profoundly affect cells that are committed to undergo mitosis. Results Here we describe the discovery and characterization of a novel purine diamine analogue as a potent ATP-competitive catalytic inhibitor of topoisomerase II. Quinoline aminopurine compound 1 (QAP 1) inhibited topoisomerase II ATPase activity and decatenation reaction at sub-micromolar concentrations, targeted both topoisomerase II alpha and beta in cell free assays and, using a quantitative cell-based assay and a chromosome segregation assay, displayed catalytic enzyme inhibition in cells. In agreement with recent hypothesis, we show that BRCA1 mutant breast cancer cells have increased sensitivity to QAP 1. Conclusion The results obtained with QAP 1 demonstrate that potent and selective catalytic inhibition of human topoisomerase II function with an ATP-competitive inhibitor is feasible. Our data suggest that further drug discovery efforts on ATP-competitive catalytic inhibitors are warranted and that such drugs could potentially be developed as anti-cancer therapy for tumors that bear the appropriate combination of molecular alterations.
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Affiliation(s)
- Patrick Chène
- Department of Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Joëlle Rudloff
- Department of Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Joseph Schoepfer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Pascal Furet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Peter Meier
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Zhiyan Qian
- Department of Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jean-Marc Schlaeppi
- Biologics Center, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Rita Schmitz
- Biologics Center, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thomas Radimerski
- Department of Oncology, Novartis Institutes for BioMedical Research, Basel, Switzerland
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Trovatti E, Cotrim CA, Garrido SS, Barros RS, Marchetto R. Peptides based on CcdB protein as novel inhibitors of bacterial topoisomerases. Bioorg Med Chem Lett 2008; 18:6161-4. [PMID: 18938079 DOI: 10.1016/j.bmcl.2008.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 10/02/2008] [Indexed: 10/21/2022]
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Sohi MK, Veselkov DA, Laponogov I, Pan XS, Fisher LM, Sanderson MR. The difficult case of crystallization and structure solution for the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae. PLoS One 2008; 3:e3201. [PMID: 18787651 PMCID: PMC2527675 DOI: 10.1371/journal.pone.0003201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 07/08/2008] [Indexed: 11/19/2022] Open
Abstract
Background Streptococcus pneumoniae is the major cause of community-acquired pneumonia and is also associated with bronchitis, meningitis, otitis and sinusitis. The emergence and increasing prevalence of resistance to penicillin and other antibiotics has led to interest in other anti-pneumonococcal drugs such as quinolones that target the enzymes DNA gyrase and topoisomerase IV. During crystallization and in the avenues to finding a method to determine phases for the structure of the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae, obstacles were faced at each stage of the process. These problems included: majority of the crystals being twinned, either non-diffracting or exhibiting a high mosaic spread. The crystals, which were grown under conditions that favoured diffraction, were difficult to flash-freeze without loosing diffraction. The initial structure solution by molecular replacement failed and the approach proved to be unviable due to the complexity of the problem. In the end the successful structure solution required an in-depth data analysis and a very detailed molecular replacement search. Methodology/Principal Findings Crystal anti-twinning agents have been tested and two different methods of flash freezing have been compared. The fragility of the crystals did not allow the usual method of transferring the crystals into the heavy atom solution. Consequently, it was necessary to co-crystallize in the presence of the heavy atom compound. The multiple isomorphous replacement approach was unsuccessful because the 7 cysteine mutants which were engineered could not be successfully derivatized. Ultimately, molecular replacement was used to solve the structure by sorting through a large number of solutions in space group P1 using CNS. Conclusions/Significance The main objective of this paper is to describe the obstacles which were faced and overcome in order to acquire data sets on such difficult crystals and determine phases for successful structure solution.
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Affiliation(s)
- Maninder K. Sohi
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Dennis A. Veselkov
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Xiao-Su Pan
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London, United Kingdom
| | - L. Mark Fisher
- Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London, United Kingdom
- * E-mail: (LMF); (MRS)
| | - Mark R. Sanderson
- Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
- * E-mail: (LMF); (MRS)
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50
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Wang W, Rupasinghe SG, Schuler MA, Gonzalez de Mejia E. Identification and characterization of topoisomerase II inhibitory peptides from soy protein hydrolysates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:6267-6277. [PMID: 18593177 DOI: 10.1021/jf8005195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Topoisomerases are targets of several anticancer agents because their inhibition impedes the processes of cell proliferation and differentiation in carcinogenesis. With very limited information available on the inhibitory activities of peptides derived from dietary proteins, the objectives of this study were to employ co-immunoprecipitation to identify inhibitory peptides in soy protein hydrolysates in a single step and to investigate their molecular interactions with topoisomerase II. For this, soy protein isolates were subjected to simulated gastrointestinal digestion with pepsin and pancreatin, and the human topoisomerase II inhibitory peptides were co-immunoprecipitated and identified on a CapLC- Micromass Q-TOF Ultima API system. The inhibitory activity of these peptides from soy isolates toward topoisomerase II was confirmed using three synthetic peptides, FEITPEKNPQ, IETWNPNNKP,and VFDGEL, which have IC 50 values of 2.4, 4.0, and 7.9 mM, respectively. The molecular interactions of these peptides evaluated by molecular docking revealed interaction energies with the topoisomerase II C-terminal domain (CTD) (-186 to -398 kcal/mol) that were smaller than for the ATPase domain (-169 to -357 kcal/mol) and that correlated well with our experimental IC 50 values ( R (2) = 0.99). In conclusion, three peptides released from in vitro gastrointestinal enzyme digestion of soy proteins inhibited human topoisomerase II activity through binding to the active site of the CTD domain.
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Affiliation(s)
- Wenyi Wang
- Department of Food Science and Human Nutrition and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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