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Unraveling topoisomerase IA gate dynamics in presence of PPEF and its preclinical evaluation against multidrug-resistant pathogens. Commun Biol 2023; 6:195. [PMID: 36807602 PMCID: PMC9938908 DOI: 10.1038/s42003-023-04412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 01/03/2023] [Indexed: 02/20/2023] Open
Abstract
Type IA topoisomerases maintain DNA topology by cleaving ssDNA and relaxing negative supercoils. The inhibition of its activity in bacteria prevents the relaxation of negative supercoils, which in turn impedes DNA metabolic processes leading to cell death. Using this hypothesis, two bisbenzimidazoles, PPEF and BPVF are synthesized, selectively inhibiting bacterial TopoIA and TopoIII. PPEF stabilizes the topoisomerase and topoisomerase-ssDNA complex, acts as an interfacial inhibitor. PPEF display high efficacy against ~455 multi-drug resistant gram positive and negative bacteria. To understand molecular mechanism of inhibition of TopoIA and PPEF, accelerated MD simulation is carried out, and results suggested that PPEF binds, stabilizes the closed conformation of TopoIA with -6Kcal/mol binding energy and destabilizes the binding of ssDNA. The TopoIA gate dynamics model can be used as a tool to screen TopoIA inhibitors as therapeutic candidates. PPEF and BPVF cause cellular filamentation and DNA fragmentation leading to bacterial cell death. PPEF and BPVF show potent efficacy against systemic and neutropenic mouse models harboring E. coli, VRSA, and MRSA infection without cellular toxicity.
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2
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Li Y, Rong Z, Li Z, Cui H, Li J, Xu XW. Structural insights into catalytical capability for CPT11 hydrolysis and substrate specificity of a novel marine microbial carboxylesterase, E93. Front Microbiol 2023; 13:1081094. [PMID: 36756200 PMCID: PMC9901791 DOI: 10.3389/fmicb.2022.1081094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction CPT11 (Irinotecan; 7-ethyl-10-[4-(1-piperidino)-1-piperidino] carbonyloxycamptothecin) is an important camptothecin-based broad-spectrum anticancer prodrug. The activation of its warhead, SN38 (7-ethyl-10-hydroxycamptothecin), requires hydrolysis by carboxylesterases. NPC (7-ethyl-10-[4-(1-piperidino)-1-amino] carbonyloxycamptothecin) is a metabolic derivative of CPT11 and is difficult to be hydrolyzed by human carboxylesterase. Microbial carboxylesterase with capability on both CPT11 and NPC hydrolysis is rarely reported. A marine microbial carboxylesterase, E93, was identified to hydrolyze both substrates in this study. This enzyme was an appropriate subject for uncovering the catalytic mechanism of carboxylesterases to CPT11 and NPC hydrolysis. Methods X-ray diffraction method was applied to obtain high-resolution structure of E93. Molecular docking was adopted to analyze the interaction of E93 with p-NP (p-nitrophenyl), CPT11, and NPC substrates. Mutagenesis and enzymatic assay were adopted to verify the binding pattern of substrates. Results Three core regions (Region A, B, and C) of the catalytic pocket were identified and their functions on substrates specificity were validated via mutagenesis assays. The Region A was involved in the binding with the alcohol group of all tested substrates. The size and hydrophobicity of the region determined the binding affinity. The Region B accommodated the acyl group of p-NP and CPT11 substrates. The polarity of this region determined the catalytic preference to both substrates. The Region C specifically accommodated the acyl group of NPC. The interaction from the acidic residue, E428, contributed to the binding of E93 with NPC. Discussion The study analyzed both unique and conserved structures of the pocket in E93, for the first time demonstrating the discrepancy of substrate-enzyme interaction between CPT11 and NPC. It also expanded the knowledge about the substrate specificity and potential application of microbial Family VII carboxylesterases.
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Affiliation(s)
- Yang Li
- School of Oceanography, Zhejiang University, Zhoushan, China,Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zhen Rong
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Henglin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China,*Correspondence: Jixi Li,
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China,Xue-Wei Xu,
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3
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Yue B, Gao R, Wang Z, Dou W. Microbiota-Host-Irinotecan Axis: A New Insight Toward Irinotecan Chemotherapy. Front Cell Infect Microbiol 2021; 11:710945. [PMID: 34722328 PMCID: PMC8553258 DOI: 10.3389/fcimb.2021.710945] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/23/2021] [Indexed: 12/19/2022] Open
Abstract
Irinotecan (CPT11) and its active metabolite ethyl-10-hydroxy-camptothecin (SN38) are broad-spectrum cytotoxic anticancer agents. Both cause cell death in rapidly dividing cells (e.g., cancer cells, epithelial cells, hematopoietic cells) and commensal bacteria. Therefore, CPT11 can induce a series of toxic side-effects, of which the most conspicuous is gastrointestinal toxicity (nausea, vomiting, diarrhea). Studies have shown that the gut microbiota modulates the host response to chemotherapeutic drugs. Targeting the gut microbiota influences the efficacy and toxicity of CPT11 chemotherapy through three key mechanisms: microbial ecocline, catalysis of microbial enzymes, and immunoregulation. This review summarizes and explores how the gut microbiota participates in CPT11 metabolism and mediates host immune dynamics to affect the toxicity and efficacy of CPT11 chemotherapy, thus introducing a new concept that is called "microbiota-host-irinotecan axis". Also, we emphasize the utilization of bacterial β-glucuronidase-specific inhibitor, dietary interventions, probiotics and strain-engineered interventions as emergent microbiota-targeting strategies for the purpose of improving CPT11 chemotherapy efficiency and alleviating toxicity.
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Affiliation(s)
- Bei Yue
- The MOE Key Laboratory of Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines, and the SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China
| | - Ruiyang Gao
- The MOE Key Laboratory of Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines, and the SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China
| | - Zhengtao Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines, and the SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China
| | - Wei Dou
- The MOE Key Laboratory of Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines, and the SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China
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4
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Flor A, Wolfgeher D, Li J, Hanakahi LA, Kron SJ. Lipid-derived electrophiles mediate the effects of chemotherapeutic topoisomerase I poisons. Cell Chem Biol 2021; 28:776-787.e8. [PMID: 33352117 PMCID: PMC8206239 DOI: 10.1016/j.chembiol.2020.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/13/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022]
Abstract
Topoisomerase 1 (Top1) reversibly nicks chromosomal DNA to relax strain accumulated during transcription, replication, chromatin assembly, and chromosome condensation. The Top1 poison camptothecin targets cancer cells by trapping the enzyme in the covalent complex Top1cc, tethered to cleaved DNA by a tyrosine-3'-phosphate bond. In vitro mechanistic studies point to interfacial inhibition, where camptothecin binding to the Top1-DNA interface stabilizes Top1cc. Here we present a complementary covalent mechanism that is critical in vivo. We observed that camptothecins induce oxidative stress, leading to lipid peroxidation, lipid-derived electrophile accumulation, and Top1 poisoning via covalent modification. The electrophile 4-hydroxy-2-nonenal can induce Top1cc on its own and forms a Michael adduct to a cysteine thiol in the Top1 active site, potentially blocking tyrosine dephosphorylation and 3' DNA phosphate release. Thereby, camptothecins may leverage a physiological cysteine-based redox switch in Top1 to mediate their selective toxicity to rapidly proliferating cancer cells.
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Affiliation(s)
- Amy Flor
- University of Chicago, Department of Molecular Genetics and Cell Biology, Chicago IL 60637, USA,Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Amy Flor ()
| | - Donald Wolfgeher
- University of Chicago, Department of Molecular Genetics and Cell Biology, Chicago IL 60637, USA
| | - Jing Li
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences, Rockford IL 61107, USA
| | - Leslyn A. Hanakahi
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences, Rockford IL 61107, USA
| | - Stephen J. Kron
- University of Chicago, Department of Molecular Genetics and Cell Biology, Chicago IL 60637, USA,Corresponding author: 929 E. 57th St. W522A, Chicago IL 60637, USA;
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5
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Gao HY, Wang W, Luo XG, Jiang YF, He X, Xu P, Chen X, Li XY. Screening of prognostic risk microRNAs for acute myeloid leukemia. ACTA ACUST UNITED AC 2018; 23:747-755. [PMID: 29781401 DOI: 10.1080/10245332.2018.1475860] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Objectives This study aimed to investigate the risk miRNAs (microRNAs) for AML (acute myeloid leukemia) prognosis and related regulatory mechanisms. Methods MiRNA and gene expression data, as well as clinical data of 176 patients were first downloaded from TCGA. Then miRNAs and genes significantly affecting the survival time based on KM survival curve were identified using Log Rank test. Next, COX proportional-hazard regression analysis was performed to screen the risk miRNAs (P-value < 0.05). Common genes from survival analysis and predicted by miRWalk were used to construct the miRNA regulatory network with the risk miRNAs. Finally, a protein-protein interaction (PPI) network was constructed, as well as functional annotation and pathway enrichment analysis. Results The survival analysis revealed 33 miRNAs and 1,377 genes significantly affecting the survival time. HR values of nine miRNAs (up-regulated hsa-mir-606, 520a, 137, 362, 599, 600, 202, 639and down-regulated 502) were either >1 or <1. The miRNA regulatory network contained 477 nodes and 944 edges. The top ten genes of the constructed PPI network were EGFR, EIF4G1, REL, TOP1, COL14A1, HDAC3, MRPL49, PSMA2, TOP2A and VCAM1 successively. According to pathway enrichment analysis, 6 KEGG pathways and 6 REACTOME pathways were obtained respectively. Conclusion Up-regulated hsa-mir-520a, 599, 606, 137 and 362 may increase the prognostic risk for AML patients via regulating the expression of corresponding target genes, especially COL14A1, HDAC3, REL, EGFR, PSMA2, EIF4G1, MRPL49 and TOP1.
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Affiliation(s)
- Hai-Yan Gao
- a Department of Hematology , The Second Affiliated Hospital of Harbin Medical University , Harbin , People's Republic of China
| | - Wei Wang
- a Department of Hematology , The Second Affiliated Hospital of Harbin Medical University , Harbin , People's Republic of China
| | - Xin-Guo Luo
- b Department of Hematology , Jinhua People's Hospital , Jinhua , People's Republic of China
| | - Yong-Fang Jiang
- a Department of Hematology , The Second Affiliated Hospital of Harbin Medical University , Harbin , People's Republic of China
| | - Xin He
- a Department of Hematology , The Second Affiliated Hospital of Harbin Medical University , Harbin , People's Republic of China
| | - Ping Xu
- a Department of Hematology , The Second Affiliated Hospital of Harbin Medical University , Harbin , People's Republic of China
| | - Xi Chen
- a Department of Hematology , The Second Affiliated Hospital of Harbin Medical University , Harbin , People's Republic of China
| | - Xiao-Yun Li
- a Department of Hematology , The Second Affiliated Hospital of Harbin Medical University , Harbin , People's Republic of China
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Das SK, Ghosh A, Paul Chowdhuri S, Halder N, Rehman I, Sengupta S, Sahoo KC, Rath H, Das BB. Neutral Porphyrin Derivative Exerts Anticancer Activity by Targeting Cellular Topoisomerase I (Top1) and Promotes Apoptotic Cell Death without Stabilizing Top1-DNA Cleavage Complexes. J Med Chem 2018; 61:804-817. [PMID: 29290109 PMCID: PMC5808360 DOI: 10.1021/acs.jmedchem.7b01297] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Camptothecin (CPT) selectively traps
topoisomerase 1-DNA cleavable
complexes (Top1cc) to promote anticancer activity. Here, we report
the design and synthesis of a new class of neutral porphyrin derivative
5,10-bis(4-carboxyphenyl)-15, 20-bis(4-dimethylaminophenyl)porphyrin
(compound 8) as a potent catalytic inhibitor of human
Top1. In contrast to CPT, compound 8 reversibly binds
with the free enzyme and inhibits the formation of Top1cc and promotes
reversal of the preformed Top1cc with CPT. Compound 8 induced inhibition of Top1cc formation in live cells was substantiated
by fluorescence recovery after photobleaching (FRAP) assays. We established
that MCF7 cells treated with compound 8 trigger proteasome-mediated
Top1 degradation, accumulate higher levels of reactive oxygen species
(ROS), PARP1 cleavage, oxidative DNA fragmentation, and stimulate
apoptotic cell death without stabilizing apoptotic Top1-DNA cleavage
complexes. Finally, compound 8 shows anticancer activity
by targeting cellular Top1 and preventing the enzyme from directly
participating in the apoptotic process.
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Affiliation(s)
| | | | | | | | | | - Souvik Sengupta
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University , Central Campus, Navrangpura, Ahmedabad, Gujarat 380009, India
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7
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Young MJ. Off-Target Effects of Drugs that Disrupt Human Mitochondrial DNA Maintenance. Front Mol Biosci 2017; 4:74. [PMID: 29214156 PMCID: PMC5702650 DOI: 10.3389/fmolb.2017.00074] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) were the first drugs used to treat human immunodeficiency virus (HIV) the cause of acquired immunodeficiency syndrome. Development of severe mitochondrial toxicity has been well documented in patients infected with HIV and administered NRTIs. In vitro biochemical experiments have demonstrated that the replicative mitochondrial DNA (mtDNA) polymerase gamma, Polg, is a sensitive target for inhibition by metabolically active forms of NRTIs, nucleotide reverse transcriptase inhibitors (NtRTIs). Once incorporated into newly synthesized daughter strands NtRTIs block further DNA polymerization reactions. Human cell culture and animal studies have demonstrated that cell lines and mice exposed to NRTIs display mtDNA depletion. Further complicating NRTI off-target effects on mtDNA maintenance, two additional DNA polymerases, Pol beta and PrimPol, were recently reported to localize to mitochondria as well as the nucleus. Similar to Polg, in vitro work has demonstrated both Pol beta and PrimPol incorporate NtRTIs into nascent DNA. Cell culture and biochemical experiments have also demonstrated that antiviral ribonucleoside drugs developed to treat hepatitis C infection act as off-target substrates for POLRMT, the mitochondrial RNA polymerase and primase. Accompanying the above-mentioned topics, this review examines: (1) mtDNA maintenance in human health and disease, (2) reports of DNA polymerases theta and zeta (Rev3) localizing to mitochondria, and (3) additional drugs with off-target effects on mitochondrial function. Lastly, mtDNA damage may induce cell death; therefore, the possibility of utilizing compounds that disrupt mtDNA maintenance to kill cancer cells is discussed.
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Affiliation(s)
- Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States
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8
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El-Sayed A, Awad W, Abdou NE, Castañeda Vázquez H. Molecular biological tools applied for identification of mastitis causing pathogens. Int J Vet Sci Med 2017; 5:89-97. [PMID: 30255056 PMCID: PMC6137832 DOI: 10.1016/j.ijvsm.2017.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/13/2017] [Accepted: 08/13/2017] [Indexed: 12/19/2022] Open
Abstract
The molecular diagnostic tools became the gold standard of mastitis diagnosis in the last few years. They enable rapid, qualitative, quantitative and large scale diagnosis. In addition to their role in diagnosis, they can identify pathogens at the subspecies level which is necessary for the epidemiological studies. They are increasingly used in mastitis control programs through identification of suitable candidates for vaccine production and through the selection of mastitis resistant cattle breeds. The present molecular techniques are continuously improved and new techniques are developed in order to provide higher sensitivity and specificity and to minimize the costs. The present work aims to provide an overview of the modern molecular tools, discuss why they replaced the traditional tools and became the new gold standard in mastitis diagnosis through comparing both traditional and molecular tools, explore the prospective of the molecular diagnostic techniques in mastitis diagnosis and control and to explore new horizons of using molecular assays in near future.
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Affiliation(s)
- Amr El-Sayed
- Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Egypt.,Hessian State Laboratory (LHL), Giessen, Germany
| | - Walid Awad
- Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Egypt
| | - Nadra-Elwgoud Abdou
- Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Egypt.,Veterinary Laboratories, Public Authority of Agriculture Affairs and Fish Resources, Kuwait
| | - Hugo Castañeda Vázquez
- Universitario de Ciencias Biológicas y Agropecuarias de la Universidad de Guadalajara, Mexico
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9
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Synthesis of novel indole derivatives as promising DNA-binding agents and evaluation of antitumor and antitopoisomerase I activities. Eur J Med Chem 2017; 136:511-522. [DOI: 10.1016/j.ejmech.2017.05.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/03/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022]
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10
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Seol Y, Neuman KC. The dynamic interplay between DNA topoisomerases and DNA topology. Biophys Rev 2016; 8:101-111. [PMID: 28510219 DOI: 10.1007/s12551-016-0240-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/07/2016] [Indexed: 01/03/2023] Open
Abstract
Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 50 South Dr., Room 3517, Bethesda, MD, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 50 South Dr., Room 3517, Bethesda, MD, 20892, USA.
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11
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Szumilak M, Merecz A, Strek M, Stanczak A, Inglot TW, Karwowski BT. DNA Interaction Studies of Selected Polyamine Conjugates. Int J Mol Sci 2016; 17:E1560. [PMID: 27657041 PMCID: PMC5037830 DOI: 10.3390/ijms17091560] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/09/2016] [Accepted: 09/09/2016] [Indexed: 01/26/2023] Open
Abstract
The interaction of polyamine conjugates with DNA double helix has been studied. Binding properties were examined by ethidium bromide (EtBr) displacement and DNA unwinding/topoisomerase I/II (Topo I/II) activity assays, as well as dsDNA thermal stability studies and circular dichroism spectroscopy. Genotoxicity of the compounds was estimated by a comet assay. It has been shown that only compound 2a can interact with dsDNA via an intercalative binding mode as it displaced EtBr from the dsDNA-dye complex, with Kapp = 4.26 × 10⁶ M-1; caused an increase in melting temperature; changed the circular dichroism spectrum of dsDNA; converted relaxed plasmid DNA into a supercoiled molecule in the presence of Topo I and reduced the amount of short oligonucleotide fragments in the comet tail. Furthermore, preliminary theoretical study has shown that interaction of the discussed compounds with dsDNA depends on molecule linker length and charge distribution over terminal aromatic chromophores.
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Affiliation(s)
- Marta Szumilak
- Department of Hospital Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
| | - Anna Merecz
- Food Science Department, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
| | - Malgorzata Strek
- Department of Nucleic Acids Biochemistry, Medical University of Lodz, 251 Pomorska Street, 92-213 Lodz, Poland.
| | - Andrzej Stanczak
- Department of Hospital Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
| | - Tadeusz W Inglot
- Department of Medicinal Chemistry, Medical University of Lublin, 4 Jaczewskiego Street, 20-090 Lublin, Poland.
| | - Boleslaw T Karwowski
- Food Science Department, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
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12
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Abstract
Topological properties of DNA influence its structure and biochemical interactions. Within the cell DNA topology is constantly in flux. Transcription and other essential processes including DNA replication and repair, alter the topology of the genome, while introducing additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases, is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that established the fundamental mechanistic basis of topoisomerase activity, the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases have begun to be explored. In this review we survey established and emerging DNA topology dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, U.S.A
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, U.S.A
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13
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Khiati S, Seol Y, Agama K, Dalla Rosa I, Agrawal S, Fesen K, Zhang H, Neuman KC, Pommier Y. Poisoning of mitochondrial topoisomerase I by lamellarin D. Mol Pharmacol 2014; 86:193-9. [PMID: 24890608 DOI: 10.1124/mol.114.092833] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Lamellarin D (Lam-D) is a hexacyclic pyrole alkaloid isolated from marine invertebrates, whose biologic properties have been attributed to mitochondrial targeting. Mitochondria contain their own DNA (mtDNA), and the only specific mitochondrial topoisomerase in vertebrates is mitochondrial topoisomerase I (Top1mt). Here, we show that Top1mt is a direct mitochondrial target of Lam-D. In vitro Lam-D traps Top1mt and induces Top1mt cleavage complexes (Top1mtcc). Using single-molecule analyses, we also show that Lam-D slows down supercoil relaxation of Top1mt and strongly inhibits Top1mt religation in contrast to the inefficacy of camptothecin on Top1mt. In living cells, we show that Lam-D accumulates rapidly inside mitochondria, induces cellular Top1mtcc, and leads to mtDNA damage. This study provides evidence that Top1mt is a direct mitochondrial target of Lam-D and suggests that developing Top1mt inhibitors represents a novel strategy for targeting mitochondrial DNA.
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Affiliation(s)
- Salim Khiati
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Yeonee Seol
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Ilaria Dalla Rosa
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Surbhi Agrawal
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Katherine Fesen
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Keir C Neuman
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
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14
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Das S, Parveen S, Pradhan AB. An insight into the interaction of phenanthridine dyes with polyriboadenylic acid: spectroscopic and thermodynamic approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:356-366. [PMID: 24060481 DOI: 10.1016/j.saa.2013.08.106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/17/2013] [Accepted: 08/23/2013] [Indexed: 06/02/2023]
Abstract
Interaction of two phenanthridine dyes, namely ethidium bromide (EB) and propidium iodide (PI) with polyriboadenylic acid was investigated using various spectroscopic techniques. They were found to bind only with the single stranded form of the polymer, while no affinity was observed for the double stranded form. Enhanced binding observed for PI compared to EB may be attributed to the presence of external alkyl chain in PI. Thermodynamic studies showed negative enthalpy and negative entropy changes for the binding of both the dyes. Salt dependent studies revealed a lesser electrolytic contribution compared to the nonelectrolytic contribution to the total Gibbs free energy change in each case. This indicated importance of hydrophobic and van der Waal's interaction for the binding process. Overall, the binding data and detail energetics of interaction presented here would be helpful in the design of phenanthridine based molecules that interact with specific RNA structure.
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Affiliation(s)
- Suman Das
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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15
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Rescifina A, Zagni C, Varrica MG, Pistarà V, Corsaro A. Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling. Eur J Med Chem 2014; 74:95-115. [PMID: 24448420 DOI: 10.1016/j.ejmech.2013.11.029] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
The interaction of small molecules with DNA plays an essential role in many biological processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study about the interaction of drug and DNA has a key role in pharmacology. Moreover, understanding the interactions of small molecules with DNA is of prime significance in the rational design of more powerful and selective anticancer agents. Two of the most important and promising targets in cancer chemotherapy include DNA alkylating agents and DNA intercalators. For these last the DNA recognition is a critical step in their anti-tumor action and the intercalation is not only one kind of the interactions in DNA recognition but also a pivotal step of several clinically used anti-tumor drugs such as anthracyclines, acridines and anthraquinones. To push clinical cancer therapy, the discovery of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. The intercalative binding properties of such molecules can also be harnessed as diagnostic probes for DNA structure in addition to DNA-directed therapeutics. Moreover, the problem of intercalation site formation in the undistorted B-DNA of different length and sequence is matter of tremendous importance in molecular modeling studies and, nowadays, three models of DNA intercalation targets have been proposed that account for the binding features of intercalators. Finally, despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. Therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.
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Affiliation(s)
- Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
| | - Chiara Zagni
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Maria Giulia Varrica
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Venerando Pistarà
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Antonino Corsaro
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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16
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Saeidnia S, Abdollahi M. Are other fluorescent tags used instead of ethidium bromide safer? ACTA ACUST UNITED AC 2013; 21:71. [PMID: 24355254 PMCID: PMC4028844 DOI: 10.1186/2008-2231-21-71] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 09/02/2013] [Indexed: 11/10/2022]
Abstract
Ethidium bromide (EtBr) is a well-known fluorescent tag usually applied in molecular biological techniques like agarose gel electrophoresis. The mechanism of action for such compounds is known, in which these compounds are able to bind to the kinetoplastid DNA and to alter their conformation to Z-DNA molecules that stop replication of kinetoplastid DNA leading to Trypanosoma death. Although the usual amounts used in laboratories are considered as below the level required to cause toxicity (LD50 in oral administration in rat is 1.5 g/Kg), the mentioned concentrations are high enough to involve in replication of mitochondrial DNA in some human cell lines. Regarding the points that EtBr is very stable in the environment and if degraded especially by use of bleaches that result in formation of mutagenic compounds, there is a big concern about its use. Although application of EtBr is going to be restricted and replaced with other tags such as SYBR® products, the safety of the new substituted compounds are still in doubt and except a few data, there is no essential evidence available to confirm that they are safer than EtBr. Further investigations are recommended to compare their relative biosafety hazards.
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Affiliation(s)
| | - Mohammad Abdollahi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran 1417614411, Iran.
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17
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Patel D, Rahman S, Savva M. Kinetic and thermodynamic studies of 9-aminocamptothecin hydrolysis at physiological pH in the presence of human serum albumin. Eur J Pharm Sci 2013; 49:858-63. [DOI: 10.1016/j.ejps.2013.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 05/09/2013] [Accepted: 06/07/2013] [Indexed: 01/07/2023]
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18
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Juul S, Nielsen CJF, Labouriau R, Roy A, Tesauro C, Jensen PW, Harmsen C, Kristoffersen EL, Chiu YL, Frøhlich R, Fiorani P, Cox-Singh J, Tordrup D, Koch J, Bienvenu AL, Desideri A, Picot S, Petersen E, Leong KW, Ho YP, Stougaard M, Knudsen BR. Droplet microfluidics platform for highly sensitive and quantitative detection of malaria-causing Plasmodium parasites based on enzyme activity measurement. ACS NANO 2012; 6:10676-83. [PMID: 23121492 PMCID: PMC3528816 DOI: 10.1021/nn3038594] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present an attractive new system for the specific and sensitive detection of the malaria-causing Plasmodium parasites. The system relies on isothermal conversion of single DNA cleavage-ligation events catalyzed specifically by the Plasmodium enzyme topoisomerase I to micrometer-sized products detectable at the single-molecule level. Combined with a droplet microfluidics lab-on-a-chip platform, this design allowed for sensitive, specific, and quantitative detection of all human-malaria-causing Plasmodium species in single drops of unprocessed blood with a detection limit of less than one parasite/μL. Moreover, the setup allowed for detection of Plasmodium parasites in noninvasive saliva samples from infected patients. During recent years malaria transmission has declined worldwide, and with this the number of patients with low-parasite density has increased. Consequently, the need for accurate detection of even a few parasites is becoming increasingly important for the continued combat against the disease. We believe that the presented droplet microfluidics platform, which has a high potential for adaptation to point-of-care setups suitable for low-resource settings, may contribute significantly to meet this demand. Moreover, potential future adaptation of the presented setup for the detection of other microorganisms may form the basis for the development of a more generic platform for diagnosis, fresh water or food quality control, or other purposes within applied or basic science.
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Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | | | - Rodrigo Labouriau
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Amit Roy
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Cinzia Tesauro
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Pia W. Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Charlotte Harmsen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | | | - Ya-Ling Chiu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Rome, Italy
| | - Janet Cox-Singh
- School of Medicine, University of St Andrews, Fife KY16 9TF, Scotland and The Malaria Research Centre, University Malaysia Sarawak, Kuching, Sarawak, Malaysia
| | - David Tordrup
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jørn Koch
- Department of Pathology, Aarhus University Hospital, Denmark
| | - Anne-Lise Bienvenu
- Malaria Research Unit, SMITH, ICBMS, UMR CNRS 5246, University Lyon1, and Hospices civils de Lyon, Lyon, France
| | - Alessandro Desideri
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Stephane Picot
- Malaria Research Unit, SMITH, ICBMS, UMR CNRS 5246, University Lyon1, and Hospices civils de Lyon, Lyon, France
| | - Eskild Petersen
- Department of Infectious Diseases, Institute of Clinical Medicine, Aarhus University Hospital-Skejby, Denmark
| | - Kam W. Leong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark
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Grierson PM, Acharya S, Groden J. Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription. Mutat Res 2012; 743-744:89-96. [PMID: 23261817 DOI: 10.1016/j.mrfmmm.2012.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 12/07/2012] [Accepted: 12/08/2012] [Indexed: 02/03/2023]
Abstract
Bloom's syndrome (BS) is an inherited disorder caused by loss of function of the recQ-like BLM helicase. It is characterized clinically by severe growth retardation and cancer predisposition. BLM localizes to PML nuclear bodies and to the nucleolus; its deficiency results in increased intra- and inter-chromosomal recombination, including hyper-recombination of rDNA repeats. Our previous work has shown that BLM facilitates RNA polymerase I-mediated rRNA transcription in the nucleolus (Grierson et al., 2012 [18]). This study uses protein co-immunoprecipitation and in vitro transcription/translation (IVTT) to identify a direct interaction of DNA topoisomerase I with the C-terminus of BLM in the nucleolus. In vitro helicase assays demonstrate that DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid, but has an insignificant effect on BLM helicase activity on a control DNA:DNA duplex substrate. Reciprocally, BLM enhances the DNA relaxation activity of DNA topoisomerase I on supercoiled DNA substrates. Our study suggests that BLM and DNA topoisomerase I function coordinately to modulate RNA:DNA hybrid formation as well as relaxation of DNA supercoils in the context of nucleolar transcription.
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Affiliation(s)
- Patrick M Grierson
- Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Samir Acharya
- Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
| | - Joanna Groden
- Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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20
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A kinetic clutch governs religation by type IB topoisomerases and determines camptothecin sensitivity. Proc Natl Acad Sci U S A 2012; 109:16125-30. [PMID: 22991469 DOI: 10.1073/pnas.1206480109] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Type IB topoisomerases (Top1Bs) relax excessive DNA supercoiling associated with replication and transcription by catalyzing a transient nick in one strand to permit controlled rotation of the DNA about the intact strand. The natural compound camptothecin (CPT) and the cancer chemotherapeutics derived from it, irinotecan and topotecan, are highly specific inhibitors of human nuclear Top1B (nTop1). Previous work on vaccinia Top1B led to an elegant model that describes a straightforward dependence of rotation and religation on the torque caused by supercoiling. Here, we used a single-molecule DNA supercoil relaxation assay to measure the torque dependence of nTop1 and its inhibition by CPT. For comparison, we also examined mitochondrial Top1B and an N-terminal deletion mutant of nTop1. Despite substantial sequence homology in their core domains, nTop1 and mitochondrial Top1B exhibit dramatic differences in sensitivity to torque and CPT, with the N-terminal deletion mutant of nTop1 showing intermediate characteristics. In particular, nTop1 displays nearly torque-independent religation probability, distinguishing it from other Top1B enzymes studied to date. Kinetic modeling reveals a hitherto unobserved torque-independent transition linking the DNA rotation and religation phases of the enzymatic cycle. The parameters of this transition determine the torque sensitivity of religation and the efficiency of CPT binding. This "kinetic clutch" mechanism explains the molecular basis of CPT sensitivity and more generally provides a framework with which to interpret Top1B activity and inhibition.
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21
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Marchand C, Pommier Y. Topoisomerases Inhibitors: A Paradigm for Interfacial Inhibition. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-1-4614-0323-4_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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