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Shao Z, Su S, Yang J, Zhang W, Gao Y, Zhao X, Zhang Y, Shao Q, Cao C, Li H, Liu H, Zhang J, Lin J, Ma J, Gan J. Structures and implications of the C962R protein of African swine fever virus. Nucleic Acids Res 2023; 51:9475-9490. [PMID: 37587714 PMCID: PMC10516667 DOI: 10.1093/nar/gkad677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/01/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023] Open
Abstract
African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. Although it has been extensively studied in the past, no vaccine or other useful treatment against ASFV is available. The genome of ASFV encodes more than 170 proteins, but the structures and functions for the majority of the proteins remain elusive, which hindered our understanding on the life cycle of ASFV and the development of ASFV-specific inhibitors. Here, we report the structural and biochemical studies of the highly conserved C962R protein of ASFV, showing that C962R is a multidomain protein. The N-terminal AEP domain is responsible for the DNA polymerization activity, whereas the DNA unwinding activity is catalyzed by the central SF3 helicase domain. The middle PriCT2 and D5_N domains and the C-terminal Tail domain all contribute to the DNA unwinding activity of C962R. C962R preferentially works on forked DNA, and likely functions in Base-excision repair (BER) or other repair pathway in ASFV. Although it is not essential for the replication of ASFV, C962R can serve as a model and provide mechanistic insight into the replicative primase proteins from many other species, such as nitratiruptor phage NrS-1, vaccinia virus (VACV) and other viruses.
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Affiliation(s)
- Zhiwei Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Weizhen Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin Zhao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yixi Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiyuan Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chulei Cao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huili Li
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinru Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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Moreira F, Arenas M, Videira A, Pereira F. Evolution of TOP1 and TOP1MT Topoisomerases in Chordata. J Mol Evol 2023; 91:192-203. [PMID: 36651963 PMCID: PMC10081982 DOI: 10.1007/s00239-022-10091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023]
Abstract
Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos S/N 4450-208, Matosinhos, Portugal
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal.
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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3
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Seddek A, Madeira C, Annamalai T, Mederos C, Tiwari PB, Welch AZ, Tse-Dinh YC. A Yeast-Based Screening System for Differential Identification of Poisons and Suppressors of Human Topoisomerase I. FRONT BIOSCI-LANDMRK 2022; 27:93. [PMID: 35345325 DOI: 10.31083/j.fbl2703093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Inhibition of human topoisomerase I (TOP1) by camptothecin and topotecan has been shown to reduce excessive transcription of PAMP (Pathogen-Associated Molecular Pattern)-induced genes in prior studies, preventing death from sepsis in animal models of bacterial and SARS-CoV-2 infections. The TOP1 catalytic activity likely resolves the topological constraints on DNA that encodes these genes to facilitate the transcription induction that leads to excess inflammation. The increased accumulation of TOP1-DNA covalent complex (TOP1cc) following DNA cleavage is the basis for the anticancer efficacy of the TOP1 poisons developed for anticancer treatment. The potential cytotoxicity and mutagenicity of TOP1 targeting cancer drugs pose serious concerns for employing them as therapies in sepsis prevention. METHODS In this study we set up a novel yeast-based screening system that employs yeast strains expressing wild-type or a dominant lethal mutant recombinant human TOP1. The effect of test compounds on growth is monitored with and without overexpression of the recombinant human TOP1. RESULTS This yeast-based screening system can identify human TOP1 poisons for anticancer efficacy as well as TOP1 suppressors that can inhibit TOP1 DNA binding or cleavage activity in steps prior to the formation of the TOP1cc. CONCLUSIONS This yeast-based screening system can distinguish between TOP1 suppressors and TOP1 poisons. The assay can also identify compounds that are likely to be cytotoxic based on their effect on yeast cell growth that is independent of recombinant human TOP1 overexpression.
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Affiliation(s)
- Ahmed Seddek
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Christian Madeira
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Christopher Mederos
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Aaron Z Welch
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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Soren BC, Babu Dasari J, Ottaviani A, Messina B, Andreotti G, Romeo A, Iacovelli F, Falconi M, Desideri A, Fiorani P. In Vitro and In Silico Characterization of an Antimalarial Compound with Antitumor Activity Targeting Human DNA Topoisomerase IB. Int J Mol Sci 2021; 22:7455. [PMID: 34299074 PMCID: PMC8306514 DOI: 10.3390/ijms22147455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/18/2022] Open
Abstract
Human DNA topoisomerase IB controls the topological state of supercoiled DNA through a complex catalytic cycle that consists of cleavage and religation reactions, allowing the progression of fundamental DNA metabolism. The catalytic steps of human DNA topoisomerase IB were analyzed in the presence of a drug, obtained by the open-access drug bank Medicines for Malaria Venture. The experiments indicate that the compound strongly and irreversibly inhibits the cleavage step of the enzyme reaction and reduces the cell viability of three different cancer cell lines. Molecular docking and molecular dynamics simulations suggest that the drug binds to the human DNA topoisomerase IB-DNA complex sitting inside the catalytic site of the enzyme, providing a molecular explanation for the cleavage-inhibition effect. For all these reasons, the aforementioned drug could be a possible lead compound for the development of an efficient anti-tumor molecule targeting human DNA topoisomerase IB.
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Affiliation(s)
- Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Beatrice Messina
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Giada Andreotti
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alice Romeo
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Mattia Falconi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alessandro Desideri
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
- Institute of Translational Pharmacology, National Research Council, CNR, Via del Fosso del Cavaliere 100, 00133 Rome, Italy
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5
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Bocian W, Naumczuk B, Urbanowicz M, Sitkowski J, Bierczyńska-Krzysik A, Bednarek E, Wiktorska K, Milczarek M, Kozerski L. The Mode of SN38 Derivatives Interacting with Nicked DNA Mimics Biological Targeting of Topo I Poisons. Int J Mol Sci 2021; 22:ijms22147471. [PMID: 34299090 PMCID: PMC8303725 DOI: 10.3390/ijms22147471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
The compounds 7-ethyl-9-(N-methylamino)methyl-10-hydroxycamptothecin (2) and 7-ethyl-9-(N-morpholino)methyl-10-hydroxycamptothecin (3) are potential topoisomerase I poisons. Moreover, they were shown to have favorable anti-neoplastic effects on several tumor cell lines. Due to these properties, the compounds are being considered for advancement to the preclinical development stage. To gain better insights into the molecular mechanism with the biological target, here, we conducted an investigation into their interactions with model nicked DNA (1) using different techniques. In this work, we observed the complexity of the mechanism of action of the compounds 2 and 3, in addition to their decomposition products: compound 4 and SN38. Using DOSY experiments, evidence of the formation of strongly bonded molecular complexes of SN38 derivatives with DNA duplexes was provided. The molecular modeling based on cross-peaks from the NOESY spectrum also allowed us to assign the geometry of a molecular complex of DNA with compound 2. Confirmation of the alkylation reaction of both compounds was obtained using MALDI–MS. Additionally, in the case of 3, alkylation was confirmed in the recording of cross-peaks in the 1H/13C HSQC spectrum of 13C-enriched compound 3. In this work, we showed that the studied compounds—parent compounds 2 and 3, and their potential metabolite 4 and SN38—interact inside the nick of 1, either forming the molecular complex or alkylating the DNA nitrogen bases. In order to confirm the influence of the studied compounds on the topoisomerase I relaxation activity of supercoiled DNA, the test was performed based upon the measurement of the fluorescence of DNA stain which can differentiate between supercoiled and relaxed DNA. The presented results confirmed that studied SN38 derivatives effectively block DNA relaxation mediated by Topo I, which means that they stop the machinery of Topo I activity.
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Affiliation(s)
- Wojciech Bocian
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Beata Naumczuk
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Correspondence: ; Tel.: +48-22-8514371 (ext. 318)
| | - Magdalena Urbanowicz
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Jerzy Sitkowski
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | | | - Elżbieta Bednarek
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Katarzyna Wiktorska
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Małgorzata Milczarek
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Lech Kozerski
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
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6
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Ottaviani A, Iacovelli F, Fiorani P, Desideri A. Natural Compounds as Therapeutic Agents: The Case of Human Topoisomerase IB. Int J Mol Sci 2021; 22:4138. [PMID: 33923641 PMCID: PMC8073192 DOI: 10.3390/ijms22084138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/25/2022] Open
Abstract
Natural products are widely used as source for drugs development. An interesting example is represented by natural drugs developed against human topoisomerase IB, a ubiquitous enzyme involved in many cellular processes where several topological problems occur due the formation of supercoiled DNA. Human topoisomerase IB, involved in the solution of such problems relaxing the DNA cleaving and religating a single DNA strand, represents an important target in anticancer therapy. Several natural compounds inhibiting or poisoning this enzyme are under investigation as possible new drugs. This review summarizes the natural products that target human topoisomerase IB that may be used as the lead compounds to develop new anticancer drugs. Moreover, the natural compounds and their derivatives that are in clinical trial are also commented on.
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Affiliation(s)
- Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
- Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Alessandro Desideri
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
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7
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Iacopetta D, Lappano R, Mariconda A, Ceramella J, Sinicropi MS, Saturnino C, Talia M, Cirillo F, Martinelli F, Puoci F, Rosano C, Longo P, Maggiolini M. Newly Synthesized Imino-Derivatives Analogues of Resveratrol Exert Inhibitory Effects in Breast Tumor Cells. Int J Mol Sci 2020; 21:ijms21207797. [PMID: 33096835 PMCID: PMC7589783 DOI: 10.3390/ijms21207797] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Abstract
Breast cancer represents the most frequently diagnosed malignancy in women worldwide. Various therapeutics are currently used in order to halt the progression of breast tumor, even though certain side effects may limit the beneficial effects. In recent years, many efforts have been addressed to the usefulness of natural compounds as anticancer agents due to their low toxicity. Resveratrol, a stilbene found in grapes, berries, peanuts and soybeans, has raised a notable interest for its antioxidant, anti-inflammatory, and antitumor properties. Here, we report the design, the synthesis and the characterization of the anticancer activity of a small series of imino N-aryl-substituted compounds that are analogues of resveratrol. In particular, the most active compound, named 3, exhibited anti-tumor activity in diverse types of breast cancer cells through the inhibition of the human topoisomerase II and the induction of apoptotic cell death. Therefore, the abovementioned compound maybe considered as a promising agent in more comprehensive treatments of breast cancer.
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Affiliation(s)
- Domenico Iacopetta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Italy; (D.I.); (R.L.); (J.C.); (M.T.); (F.C.); (F.P.); (M.M.)
| | - Rosamaria Lappano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Italy; (D.I.); (R.L.); (J.C.); (M.T.); (F.C.); (F.P.); (M.M.)
| | - Annaluisa Mariconda
- Department of Science, University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (A.M.); (F.M.)
| | - Jessica Ceramella
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Italy; (D.I.); (R.L.); (J.C.); (M.T.); (F.C.); (F.P.); (M.M.)
- Department of Biology and Chemistry, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy;
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Italy; (D.I.); (R.L.); (J.C.); (M.T.); (F.C.); (F.P.); (M.M.)
- Correspondence: (M.S.S.); (C.S.); Tel.: +39-0984-493200 (M.S.S.); Tel.: +39-0971-26442 (C.S.)
| | - Carmela Saturnino
- Department of Science, University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (A.M.); (F.M.)
- Correspondence: (M.S.S.); (C.S.); Tel.: +39-0984-493200 (M.S.S.); Tel.: +39-0971-26442 (C.S.)
| | - Marianna Talia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Italy; (D.I.); (R.L.); (J.C.); (M.T.); (F.C.); (F.P.); (M.M.)
| | - Francesca Cirillo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Italy; (D.I.); (R.L.); (J.C.); (M.T.); (F.C.); (F.P.); (M.M.)
| | - Fabio Martinelli
- Department of Science, University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (A.M.); (F.M.)
| | - Francesco Puoci
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Italy; (D.I.); (R.L.); (J.C.); (M.T.); (F.C.); (F.P.); (M.M.)
| | - Camillo Rosano
- Biopolymers and Proteomics IRCCS, Ospedale Policlinico San Martino–IST, Largo R. Benzi 10, 16132 Genova, Italy;
| | - Pasquale Longo
- Department of Biology and Chemistry, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy;
| | - Marcello Maggiolini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Italy; (D.I.); (R.L.); (J.C.); (M.T.); (F.C.); (F.P.); (M.M.)
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8
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Abstract
Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand(s) through a break on a single DNA or RNA strand. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 5'-phosphotyrosine linkage to the cleaved nucleic acid. A divalent ion interaction helps to position the 3'-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates.
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Affiliation(s)
- Tumpa Dasgupta
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA
| | - Shomita Ferdous
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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9
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Zagnoli-Vieira G, Caldecott KW. Untangling trapped topoisomerases with tyrosyl-DNA phosphodiesterases. DNA Repair (Amst) 2020; 94:102900. [PMID: 32653827 DOI: 10.1016/j.dnarep.2020.102900] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/14/2020] [Accepted: 06/14/2020] [Indexed: 02/08/2023]
Abstract
DNA topoisomerases alleviate the torsional stress that is generated by processes that are central to genome metabolism such as transcription and DNA replication. To do so, these enzymes generate an enzyme intermediate known as the cleavage complex in which the topoisomerase is covalently linked to the termini of a DNA single- or double-strand break. Whilst cleavage complexes are normally transient they can occasionally become abortive, creating protein-linked DNA breaks that threaten genome stability and cell survival; a process promoted and exploited in the cancer clinic by the use of topoisomerase 'poisons'. Here, we review the consequences to genome stability and human health of abortive topoisomerase-induced DNA breakage and the cellular pathways that cells have adopted to mitigate them, with particular focus on an important class of enzymes known as tyrosyl-DNA phosphodiesterases.
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Affiliation(s)
- Guido Zagnoli-Vieira
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK.
| | - Keith W Caldecott
- Genome Damage Stability Centre, University of Sussex, Falmer Road, Brighton, BN1 9RQ, UK.
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10
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Kondekar SM, Gunjal GV, Pablo Radicella J, Rao DN. Molecular dissection of Helicobacter pylori Topoisomerase I reveals an additional active site in the carboxyl terminus of the enzyme. DNA Repair (Amst) 2020; 91-92:102853. [PMID: 32447233 DOI: 10.1016/j.dnarep.2020.102853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/07/2020] [Accepted: 04/05/2020] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases play a crucial role in maintaining DNA superhelicity, thereby regulating various cellular processes. Unlike most other species, the human pathogen Helicobacter pylori has only two topoisomerases, Topoisomerase I and DNA gyrase, the physiological roles of which remain to be explored. Interestingly, there is enormous variability among the C-terminal domains (CTDs) of Topoisomerase I across bacteria. H. pylori Topoisomerase I (HpTopoI) CTD harbors four zinc finger motifs (ZFs). We show here that sequential deletion of the third and/or fourth ZFs had only a marginal effect on the HpTopoI activity, while deletion of the second, third and fourth ZFs severely reduced DNA relaxation activity. Deletion of all ZFs drastically hampered DNA binding and thus abolished DNA relaxation. Surprisingly, mutagenesis of the annotated active site tyrosine residue (Y297 F) did not abrogate the enzyme activity and HpTopoI CTD alone (spanning the four ZFs) showed DNA relaxation activity. Additionally, a covalent linkage between the DNA and HpTopoI CTD was identified. The capacity of HpTopoI CTD to complement Escherichia coli topA mutant strains further supported the in vitro observations. Collectively these results imply that not all ZFs are dispensable for HpTopoI activity and unveil the presence of additional non-canonical catalytic site(s) within the enzyme.
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Affiliation(s)
- Sumedha M Kondekar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Gaurav V Gunjal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Juan Pablo Radicella
- Institute of Cellular and Molecular Radiobiology, Institut de Biologie François Jacob, CEA, F-92265 Fontenay aux Roses, France; Université de Paris and Université Paris-Saclay, F-92265 Fontenay aux Roses, France
| | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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11
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Cao N, Tan K, Zuo X, Annamalai T, Tse-Dinh YC. Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains. Nucleic Acids Res 2020; 48:4448-4462. [PMID: 32232337 PMCID: PMC7192597 DOI: 10.1093/nar/gkaa201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/20/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Type IA topoisomerases interact with G-strand and T-strand ssDNA to regulate DNA topology. However, simultaneous binding of two ssDNA segments to a type IA topoisomerase has not been observed previously. We report here the crystal structure of a type IA topoisomerase with ssDNA segments bound in opposite polarity to the N- and C-terminal domains. Titration of small ssDNA oligonucleotides to Mycobacterium smegmatis topoisomerase I with progressive C-terminal deletions showed that the C-terminal region has higher affinity for ssDNA than the N-terminal active site. This allows the C-terminal domains to capture one strand of underwound negatively supercoiled DNA substrate first and position the N-terminal domains to bind and cleave the opposite strand in the relaxation reaction. Efficiency of negative supercoiling relaxation increases with the number of domains that bind ssDNA primarily with conserved aromatic residues and possibly with assistance from polar/basic residues. A comparison of bacterial topoisomerase I structures showed that a conserved transesterification unit (N-terminal toroid structure) for cutting and rejoining of a ssDNA strand can be combined with two different types of C-terminal ssDNA binding domains to form diverse bacterial topoisomerase I enzymes that are highly efficient in their physiological role of preventing excess negative supercoiling in the genome.
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Affiliation(s)
- Nan Cao
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Xiaobing Zuo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
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12
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Wang X, Yu J, Lan W, Yang S, Wang S, Mi Y, Ye Q, Li Y, Liu Y. Novel Stable DNA Nanoscale Material and Its Application on Specific Enrichment of DNA. ACS Appl Mater Interfaces 2020; 12:19834-19839. [PMID: 32250112 DOI: 10.1021/acsami.0c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA nanostructures are a new type of technology for constructing nanomaterials that has been developed in recent years. By relying on the complementary pairing of DNA molecules to form a double-stranded property, DNA molecules can construct a variety of nanoscale structures of 2D and 3D shapes. However, most of the previously reported DNA nanostructures rely solely on hydrogen bonds to maintain structural stability, resulting in DNA structures that can be maintained only at low temperature and in the presence of Mg2+, which greatly limits the application of DNA nanostructures. This study designed a DNA nanonetwork structure (nanonet) and changed its topological structure to DNA nanomesh by using DNA topoisomerase to make it thermally stable, while escaping the dependence on Mg2+, and the stability of the structure can be maintained in a nonsolution state. Moreover, the nanomesh also has a large amount of ssDNA (about 50%), providing active sites capable of exerting biological functions. Using the above characteristics, we prepared the nanomesh into a device capable of adsorbing specific DNA molecules, and used the device to enrich DNA. We also tried to mount antibodies using DNA probes. Preliminary results show that the DNA nanomesh also has the ability to enrich specific proteins.
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Affiliation(s)
- Xueting Wang
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Jia Yu
- College of Life Sciences, Qingdao University, Qingdao 266071, P. R. China
| | - Wenjie Lan
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shuo Yang
- Department of Medicine, Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Shiqing Wang
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Yue Mi
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Qing Ye
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, P. R. China
| | - Yuan Li
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Yin Liu
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
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13
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Beebe SJ, Celestine MJ, Bullock JL, Sandhaus S, Arca JF, Cropek DM, Ludvig TA, Foster SR, Clark JS, Beckford FA, Tano CM, Tonsel-White EA, Gurung RK, Stankavich CE, Tse-Dinh YC, Jarrett WL, Holder AA. Synthesis, characterization, DNA binding, topoisomerase inhibition, and apoptosis induction studies of a novel cobalt(III) complex with a thiosemicarbazone ligand. J Inorg Biochem 2020; 203:110907. [PMID: 31715377 PMCID: PMC7053658 DOI: 10.1016/j.jinorgbio.2019.110907] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 10/24/2019] [Accepted: 10/27/2019] [Indexed: 01/09/2023]
Abstract
In this study, 9-anthraldehyde-N(4)-methylthiosemicarbazone (MeATSC) 1 and [Co(phen)2(O2CO)]Cl·6H2O 2 (where phen = 1,10-phenanthroline) were synthesized. [Co(phen)2(O2CO)]Cl·6H2O 2 was used to produce anhydrous [Co(phen)2(H2O)2](NO3)33. Subsequently, anhydrous [Co(phen)2(H2O)2](NO3)33 was reacted with MeATSC 1 to produce [Co(phen)2(MeATSC)](NO3)3·1.5H2O·C2H5OH 4. The ligand, MeATSC 1 and all complexes were characterized by elemental analysis, FT IR, UV-visible, and multinuclear NMR (1H, 13C, and 59Co) spectroscopy, along with HRMS, and conductivity measurements, where appropriate. Interactions of MeATSC 1 and complex 4 with calf thymus DNA (ctDNA) were investigated by carrying out UV-visible spectrophotometric studies. UV-visible spectrophotometric studies revealed weak interactions between ctDNA and the analytes, MeATSC 1 and complex 4 (Kb = 8.1 × 105 and 1.6 × 104 M-1, respectively). Topoisomerase inhibition assays and cleavage studies proved that complex 4 was an efficient catalytic inhibitor of human topoisomerases I and IIα. Based upon the results obtained from the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay on 4T1-luc metastatic mammary breast cancer cells (IC50 = 34.4 ± 5.2 μM when compared to IC50 = 13.75 ± 1.08 μM for the control, cisplatin), further investigations into the molecular events initiated by exposure to complex 4 were investigated. Studies have shown that complex 4 activated both the apoptotic and autophagic signaling pathways in addition to causing dissipation of the mitochondrial membrane potential (ΔΨm). Furthermore, activation of cysteine-aspartic proteases3 (caspase 3) in a time- and concentration-dependent manner coupled with the ΔΨm, studies implicated the intrinsic apoptotic pathway as the major regulator of cell death mechanism.
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Affiliation(s)
- Stephen J Beebe
- The Frank Reidy Center for Bioelectrics, 4211 Monarch Way, Suite 300, Norfolk, VA 23529, USA
| | - Michael J Celestine
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Jimmie L Bullock
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Shayna Sandhaus
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Jessa Faye Arca
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, 118 College Drive, Hattiesburg, MS 39406, USA
| | - Donald M Cropek
- U.S. Army Corps of Engineers, Construction Engineering Research Laboratory, Champaign, IL 61822, USA
| | - Tekettay A Ludvig
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Sydney R Foster
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Jasmine S Clark
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Floyd A Beckford
- The University of Virginia's College at Wise, 1 College Avenue, Wise, VA 24293, USA
| | - Criszcele M Tano
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Elizabeth A Tonsel-White
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Raj K Gurung
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Courtney E Stankavich
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - William L Jarrett
- School of Polymers and High-Performance Materials, The University of Southern Mississippi, 118 College Drive, #5050, Hattiesburg, MS 39406, USA
| | - Alvin A Holder
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Boulevard, Norfolk, VA 23529, USA.
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14
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Bartas М, Bažantová P, Brázda V, Liao JС, Červeň J, Pečinka P. [Identification of Distinct Amino Acid Composition of Human Cruciform Binding Proteins]. Mol Biol (Mosk) 2019; 53:120-131. [PMID: 30895959 DOI: 10.1134/s0026898419010026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/20/2018] [Indexed: 11/22/2022]
Abstract
Cruciform structures are preferential targets for many architectural and regulatory proteins, as well as a number of DNA binding proteins with weak sequence specificity. Some of these proteins are also capable of inducing the formation of cruciform structures upon DNA binding. In this paper we analyzed the amino acid composition of eighteen cruciform binding proteins of Homo sapiens. Comparison with general amino acid frequencies in all human proteins revealed unique differences, with notable enrichment for lysine and serine and/or depletion for alanine, glycine, glutamine, arginine, tyrosine and tryptophan residues. Based on bootstrap resampling and fuzzy cluster analysis, multiple molecular mechanisms of interaction with cruciform DNA structures could be suggested, including those involved in DNA repair, transcription and chromatin regulation. The proteins DEK, HMGB1 and TOP1 in particular formed a very distinctive group. Nonetheless, a strong interaction network connecting nearly all the cruciform binding proteins studied was demonstrated. Data reported here will be very useful for future prediction of new cruciform binding proteins or even construction of predictive tool/web-based application.
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Affiliation(s)
- М Bartas
- Department of Biology and Ecology / Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 71000 Czech Republic
| | - P Bažantová
- Department of Biology and Ecology / Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 71000 Czech Republic
| | - V Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Brno, 61265 Czech Republic
| | - J С Liao
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Brno, 61265 Czech Republic
- School of Medicine, The University of Queensland, Greenslopes Private Hospital, Greenslopes, 4120 Australia
| | - J Červeň
- Department of Biology and Ecology / Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 71000 Czech Republic
| | - P Pečinka
- Department of Biology and Ecology / Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 71000 Czech Republic
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15
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Abstract
Type IA topoisomerases cleave single-stranded DNA and relieve negative supercoils in discrete steps corresponding to the passage of the intact DNA strand through the cleaved strand. Although type IA topoisomerases are assumed to accomplish this strand passage via a protein-mediated DNA gate, opening of this gate has never been observed. We developed a single-molecule assay to directly measure gate opening of the Escherichia coli type IA topoisomerases I and III. We found that after cleavage of single-stranded DNA, the protein gate opens by as much as 6.6 nm and can close against forces in excess of 16 pN. Key differences in the cleavage, ligation, and gate dynamics of these two enzymes provide insights into their different cellular functions. The single-molecule results are broadly consistent with conformational changes obtained from molecular dynamics simulations. These results allowed us to develop a mechanistic model of interactions between type IA topoisomerases and single-stranded DNA.
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Affiliation(s)
- Maria Mills
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuk-Ching Tse-Dinh
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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16
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Cincinelli R, Musso L, Artali R, Guglielmi MB, La Porta I, Melito C, Colelli F, Cardile F, Signorino G, Fucci A, Frusciante M, Pisano C, Dallavalle S. Hybrid topoisomerase I and HDAC inhibitors as dual action anticancer agents. PLoS One 2018; 13:e0205018. [PMID: 30300374 PMCID: PMC6177136 DOI: 10.1371/journal.pone.0205018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/18/2018] [Indexed: 12/29/2022] Open
Abstract
Recent studies have shown that HDAC inhibitors act synergistically with camptothecin derivatives in combination therapies. To exploit this synergy, new hybrid molecules targeting simultaneously topoisomerase I and HDAC were designed. In particular, a selected multivalent agent containing a camptothecin and a SAHA-like template showed a broad spectrum of antiproliferative activity, with IC50 values in the nanomolar range. Preliminary in vivo results indicated a strong antitumor activity on human mesothelioma primary cell line MM473 orthotopically xenografted in CD-1 nude mice and very high tolerability.
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Affiliation(s)
- Raffaella Cincinelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano, Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano, Italy
| | | | | | | | - Carmela Melito
- Biogem, Research Institute, Ariano Irpino, Avellino, Italy
| | | | | | | | | | | | - Claudio Pisano
- Biogem, Research Institute, Ariano Irpino, Avellino, Italy
- * E-mail: (SD); (CP)
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano, Italy
- * E-mail: (SD); (CP)
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17
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Zhou Q, Gomez Hernandez ME, Fernandez-Lima F, Tse-Dinh YC. Biochemical Basis of E. coli Topoisomerase I Relaxation Activity Reduction by Nonenzymatic Lysine Acetylation. Int J Mol Sci 2018; 19:ijms19051439. [PMID: 29751635 PMCID: PMC5983628 DOI: 10.3390/ijms19051439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 01/06/2023] Open
Abstract
The relaxation activity of E. coli topoisomerase I is required for regulation of global and local DNA supercoiling. The in vivo topoisomerase I enzyme activity is sensitive to lysine acetylation⁻deacetylation and can affect DNA supercoiling and growth as a result. Nonenzymatic lysine acetylation by acetyl phosphate has been shown to reduce the relaxation activity of E. coli topoisomerase I. In this work, the biochemical consequence of topoisomerase I modification by acetyl phosphate with enzymatic assays was studied. Results showed that noncovalent binding to DNA and DNA cleavage by the enzyme were reduced as a result of the acetylation, with greater effect on DNA cleavage. Four lysine acetylation sites were identified using bottom-up proteomics: Lys13, Lys45, Lys346, and Lys488. The Lys13 residue modified by acetyl phosphate has not been reported previously as a lysine acetylation site for E. coli topoisomerase I. We discuss the potential biochemical consequence of lysine acetylation at this strictly conserved lysine and other lysine residues on the enzyme based on available genetic and structural information.
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Affiliation(s)
- Qingxuan Zhou
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Mario E Gomez Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Francisco Fernandez-Lima
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Yuk-Ching Tse-Dinh
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
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18
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Li D, Lv B, Wang Q, Liu Y, Zhuge Q. Direct observation of positive supercoils introduced by reverse gyrase through atomic force microscopy. Bioorg Med Chem Lett 2017; 27:4086-4090. [PMID: 28756025 DOI: 10.1016/j.bmcl.2017.07.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 11/18/2022]
Abstract
Reverse gyrase is a hyperthermophilic enzyme that can introduce positive supercoiling in substrate DNA. It is showed in our studies that positive DNA supercoils were induced in both pBR322 vector and an artificially synthesized mini-plasmid DNA by reverse gyrase. The left-handed structures adopted by positively supercoiled DNA molecules could be identified from their right-handed topoisomers through atomic force microscopic examination. Additional structural comparisons revealed that positively supercoiled DNA molecule AFM images exhibited increased contour lengths. Moreover, enzymatic assays showed that the positively supercoiled DNA could not be cleaved by T7 endonuclease. Together, this suggests that the overwound structure of positive supercoils could prevent genomic duplex DNA from randomly forming single-stranded DNA regions and intra-stranded secondary structures.
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Affiliation(s)
- Dawei Li
- Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China.
| | - Bei Lv
- Jiangsu Key Laboratory for Biofunctional Molecules, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing 210037, China
| | - Qiang Wang
- Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Yun Liu
- Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
| | - Qiang Zhuge
- Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
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19
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Zhang P, Zhang L, Zhang Y, Mao L, Jiang H. Substitutions in Spodoptera exigua topoisomerase I modulate its relaxation activity and camptothecin sensitivity. Pest Manag Sci 2017; 73:1179-1186. [PMID: 27643798 DOI: 10.1002/ps.4440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/25/2016] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Topoisomerase I (Top I) is referred as the cellular target of the camptothecins (CPTs) which are now being explored as potential pesticides for insect control. Three amino acid substitutions, including L530P, A653T and S729T, in Top Is of insects were found in our previous studies. In order to investigate the effect of these three substitutions, a comparative analysis was conducted between the wild-type and mutant Top Is in Spodoptera exigua Hübner. RESULTS The optimal salt concentration of A653T and S729T was 150 mm, which is consistent with that of the wild-type Top I, while the mutant L530P showed maximum relaxation activity at a lower KCl concentration (100 mm). The mutated L530P and A653T Top Is showed a higher relaxation efficiency owing to an increased relaxation velocity toward the negatively supercoiled plasmid pBR322 DNA, which rendered L530P and A653T resistant to CPTs, whereas mutant S729T exhibited sensitivity to CPTs as a result of a decreased relaxation activity toward plasmid pBR322 DNA. CONCLUSIONS These results suggested that the polymorphism in Top I of insects was related to the biological activity of CPTs, which provided the basic information for reasonable usage of CPTs to control insect pests. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Pei Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanning Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liangang Mao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyun Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Andersen MB, Tesauro C, Gonzalez M, Kristoffersen EL, Alonso C, Rubiales G, Coletta A, Frøhlich R, Stougaard M, Ho YP, Palacios F, Knudsen BR. Advantages of an optical nanosensor system for the mechanistic analysis of a novel topoisomerase I targeting drug: a case study. Nanoscale 2017; 9:1886-1895. [PMID: 28094391 DOI: 10.1039/c6nr06848k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The continuous need for the development of new small molecule anti-cancer drugs calls for easily accessible sensor systems for measuring the effect of vast numbers of new drugs on their potential cellular targets. Here we demonstrate the use of an optical DNA biosensor to unravel the inhibitory mechanism of a member of a new family of small molecule human topoisomerase I inhibitors, the so-called indeno-1,5-naphthyridines. By analysing human topoisomerase I catalysis on the biosensor in the absence or presence of added drug complemented with a few traditional assays, we demonstrate that the investigated member of the indeno-1,5-naphthyridine family inhibited human topoisomerase I activity by blocking enzyme-DNA dissociation. To our knowledge, this represents the first characterized example of a small molecule drug that inhibits a post-ligation step of catalysis. The elucidation of a completely new and rather surprising drug mechanism-of-action using an optical real time sensor highlights the value of this assay system in the search for new topoisomerase I targeting small molecule drugs.
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Affiliation(s)
- Marie B Andersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - María Gonzalez
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Emil L Kristoffersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Andrea Coletta
- Department of Chemistry, Langelandsgade 140, Aarhus University, 8000 Aarhus C, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Nørrebrogade 44 building 18B, Aarhus University, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark. and Interdisciplinary Nanoscience Center, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark and Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
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Rajan R, Osterman A, Mondragón A. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site. Nucleic Acids Res 2016; 44:3464-74. [PMID: 26908655 PMCID: PMC4838376 DOI: 10.1093/nar/gkw122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 01/08/2023] Open
Abstract
Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide.
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Affiliation(s)
- Rakhi Rajan
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Amy Osterman
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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22
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Marinello J, Bertoncini S, Aloisi I, Cristini A, Malagoli Tagliazucchi G, Forcato M, Sordet O, Capranico G. Dynamic Effects of Topoisomerase I Inhibition on R-Loops and Short Transcripts at Active Promoters. PLoS One 2016; 11:e0147053. [PMID: 26784695 PMCID: PMC4718701 DOI: 10.1371/journal.pone.0147053] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022] Open
Abstract
Topoisomerase I-DNA-cleavage complexes (Top1cc) stabilized by camptothecin (CPT) have specific effects at transcriptional levels. We recently reported that Top1cc increase antisense transcript (aRNAs) levels at divergent CpG-island promoters and, transiently, DNA/RNA hybrids (R-loop) in nuclear and mitochondrial genomes of colon cancer HCT116 cells. However, the relationship between R-loops and aRNAs was not established. Here, we show that aRNAs can form R-loops in N-TERA-2 cells under physiological conditions, and that promoter-associated R-loops are somewhat increased and extended in length immediately upon cell exposure to CPT. In contrast, persistent Top1ccs reduce the majority of R-loops suggesting that CPT-accumulated aRNAs are not commonly involved in R-loops. The enhancement of aRNAs by Top1ccs is present both in human colon cancer HCT116 cells and WI38 fibroblasts suggesting a common response of cancer and normal cells. Although Top1ccs lead to DSB and DDR kinases activation, we do not detect a dependence of aRNA accumulation on ATM or DNA-PK activation. However, we showed that the cell response to persistent Top1ccs can involve an impairment of aRNA turnover rather than a higher synthesis rate. Finally, a genome-wide analysis shows that persistent Top1ccs also determine an accumulation of sense transcripts at 5’-end gene regions suggesting an increased occurrence of truncated transcripts. Taken together, the results indicate that Top1 may regulate transcription initiation by modulating RNA polymerase-generated negative supercoils, which can in turn favor R-loop formation at promoters, and that transcript accumulation at TSS is a response to persistent transcriptional stress by Top1 poisoning.
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Affiliation(s)
- Jessica Marinello
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefania Bertoncini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Iris Aloisi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Agnese Cristini
- Cancer Research Center of Toulouse, INSERM UMR1037, Toulouse, France
| | | | - Mattia Forcato
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Olivier Sordet
- Cancer Research Center of Toulouse, INSERM UMR1037, Toulouse, France
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- * E-mail:
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23
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Weijer R, Broekgaarden M, Krekorian M, Alles LK, van Wijk AC, Mackaaij C, Verheij J, van der Wal AC, van Gulik TM, Storm G, Heger M. Inhibition of hypoxia inducible factor 1 and topoisomerase with acriflavine sensitizes perihilar cholangiocarcinomas to photodynamic therapy. Oncotarget 2016; 7:3341-56. [PMID: 26657503 PMCID: PMC4823110 DOI: 10.18632/oncotarget.6490] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/16/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Photodynamic therapy (PDT) induces tumor cell death by oxidative stress and hypoxia but also survival signaling through activation of hypoxia-inducible factor 1 (HIF-1). Since perihilar cholangiocarcinomas are relatively recalcitrant to PDT, the aims were to (1) determine the expression levels of HIF-1-associated proteins in human perihilar cholangiocarcinomas, (2) investigate the role of HIF-1 in PDT-treated human perihilar cholangiocarcinoma cells, and (3) determine whether HIF-1 inhibition reduces survival signaling and enhances PDT efficacy. RESULTS Increased expression of VEGF, CD105, CD31/Ki-67, and GLUT-1 was confirmed in human perihilar cholangiocarcinomas. PDT with liposome-delivered zinc phthalocyanine caused HIF-1α stabilization in SK-ChA-1 cells and increased transcription of HIF-1α downstream genes. Acriflavine was taken up by SK-ChA-1 cells and translocated to the nucleus under hypoxic conditions. Importantly, pretreatment of SK-ChA-1 cells with acriflavine enhanced PDT efficacy via inhibition of HIF-1 and topoisomerases I and II. METHODS The expression of VEGF, CD105, CD31/Ki-67, and GLUT-1 was determined by immunohistochemistry in human perihilar cholangiocarcinomas. In addition, the response of human perihilar cholangiocarcinoma (SK-ChA-1) cells to PDT with liposome-delivered zinc phthalocyanine was investigated under both normoxic and hypoxic conditions. Acriflavine, a HIF-1α/HIF-1β dimerization inhibitor and a potential dual topoisomerase I/II inhibitor, was evaluated for its adjuvant effect on PDT efficacy. CONCLUSIONS HIF-1, which is activated in human hilar cholangiocarcinomas, contributes to tumor cell survival following PDT in vitro. Combining PDT with acriflavine pretreatment improves PDT efficacy in cultured cells and therefore warrants further preclinical validation for therapy-recalcitrant perihilar cholangiocarcinomas.
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MESH Headings
- Acriflavine/pharmacology
- Anti-Infective Agents, Local/pharmacology
- Apoptosis
- Bile Duct Neoplasms/metabolism
- Bile Duct Neoplasms/pathology
- Bile Duct Neoplasms/therapy
- Blotting, Western
- Cell Proliferation
- DNA Topoisomerases, Type I/chemistry
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/metabolism
- Flow Cytometry
- Humans
- Hypoxia
- Hypoxia-Inducible Factor 1, alpha Subunit/antagonists & inhibitors
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Klatskin Tumor/metabolism
- Klatskin Tumor/pathology
- Klatskin Tumor/therapy
- Photochemotherapy
- RNA, Messenger/genetics
- Radiation-Sensitizing Agents/pharmacology
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Signal Transduction
- Tumor Cells, Cultured
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Affiliation(s)
- Ruud Weijer
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Controlled Drug Delivery, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Mans Broekgaarden
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Massis Krekorian
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Lindy K. Alles
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Albert C. van Wijk
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Claire Mackaaij
- Department of Pathology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Allard C. van der Wal
- Department of Pathology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Thomas M. van Gulik
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Gert Storm
- Department of Controlled Drug Delivery, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CG Utrecht, The Netherlands
| | - Michal Heger
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CG Utrecht, The Netherlands
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24
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Jepsen ML, Harmsen C, Godbole AA, Nagaraja V, Knudsen BR, Ho YP. Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor. Nanoscale 2016; 8:358-364. [PMID: 26616006 DOI: 10.1039/c5nr06326d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.
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Affiliation(s)
- Morten Leth Jepsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus 8000 C, Denmark. and Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Charlotte Harmsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Adwait Anand Godbole
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Birgitta R Knudsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus 8000 C, Denmark. and Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus 8000 C, Denmark. and Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
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25
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Tan K, Cao N, Cheng B, Joachimiak A, Tse-Dinh YC. Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold. J Mol Biol 2015; 428:182-193. [PMID: 26655023 DOI: 10.1016/j.jmb.2015.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 01/17/2023]
Abstract
The DNA topoisomerase I enzyme of Mycobacterium tuberculosis (MtTOP1) is essential for the viability of the organism and survival in a murine model. This topoisomerase is being pursued as a novel target for the discovery of new therapeutic agents for the treatment of drug-resistant tuberculosis. In this study, we succeeded in obtaining a structure of MtTOP1 by first predicting that the C-terminal region of MtTOP1 contains four repeated domains that do not involve the Zn-binding tetracysteine motifs seen in the C-terminal domains of Escherichia coli topoisomerase I. A construct (amino acids A2-T704), MtTOP1-704t, that includes the N-terminal domains (D1-D4) and the first predicted C-terminal domain (D5) of MtTOP1 was expressed and found to retain DNA cleavage-religation activity and catalyze single-stranded DNA catenation. MtTOP1-704t was crystallized, and a structure of 2.52Å resolution limit was obtained. The structure of the MtTOP1 N-terminal domains has features that have not been observed in other previously available bacterial topoisomerase I crystal structures. The first C-terminal domain D5 forms a novel protein fold of a four-stranded antiparallel β-sheet stabilized by a crossing-over α-helix. Since there is only one type IA topoisomerase present in Mycobacteriaceae and related Actinobacteria, this subfamily of type IA topoisomerase may be required for multiple functions in DNA replication, transcription, recombination, and repair. The unique structural features observed for MtTOP1 may allow these topoisomerase I enzymes to carry out physiological functions associated with topoisomerase III enzyme in other bacteria.
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Affiliation(s)
- Kemin Tan
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.
| | - Nan Cao
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
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26
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D'yakonov VA, Dzhemileva LU, Tuktarova RA, Makarov AA, Islamov II, Mulyukova AR, Dzhemilev UM. Catalytic cyclometallation in steroid chemistry III: Synthesis of steroidal derivatives of 5Z,9Z-dienoic acid and investigation of its human topoisomerase I inhibitory activity. Steroids 2015; 102:110-7. [PMID: 26276106 DOI: 10.1016/j.steroids.2015.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 08/03/2015] [Accepted: 08/08/2015] [Indexed: 11/20/2022]
Abstract
Two approaches to stereoselective synthesis of steroid 5Z,9Z-dienoic acids were developed, the first one being based on the cross-cyclomagnesiation of 2-(hepta-5,6-dien-1-yloxy)tetrahydro-2H-pyran and 1,2-diene cholesterol derivatives on treatment with EtMgBr catalyzed by Cp2TiCl2, while the other involving the synthesis of esters of hydroxy steroids with (5Z,9Z)-tetradeca-5,9-dienedioic acid, prepared in two steps using homo-cyclomagnesiation of 2-(hepta-5,6-dien-1-yloxy)tetrahydro-2H-pyran as the key step. High inhibitory activity of the synthesized acids against human topoisomerase I (hTop1) was found.
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Affiliation(s)
- Vladimir A D'yakonov
- Institute of Petrochemistry and Catalysis, Russian Academy of Science, 141 Prospekt Oktyabrya, 450075 Ufa, Russian Federation.
| | - Lilya U Dzhemileva
- Department of Immunology and Human Reproductive Health, Bashkir State Medical University, 3 Lenin Street, Ufa, Bashkortostan 450003, Russian Federation.
| | - Regina A Tuktarova
- Institute of Petrochemistry and Catalysis, Russian Academy of Science, 141 Prospekt Oktyabrya, 450075 Ufa, Russian Federation
| | - Aleksey A Makarov
- Institute of Petrochemistry and Catalysis, Russian Academy of Science, 141 Prospekt Oktyabrya, 450075 Ufa, Russian Federation
| | - Ilgiz I Islamov
- Institute of Petrochemistry and Catalysis, Russian Academy of Science, 141 Prospekt Oktyabrya, 450075 Ufa, Russian Federation
| | - Alfiya R Mulyukova
- Institute of Petrochemistry and Catalysis, Russian Academy of Science, 141 Prospekt Oktyabrya, 450075 Ufa, Russian Federation
| | - Usein M Dzhemilev
- Institute of Petrochemistry and Catalysis, Russian Academy of Science, 141 Prospekt Oktyabrya, 450075 Ufa, Russian Federation
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Kristoffersen EL, Jørgensen LA, Franch O, Etzerodt M, Frøhlich R, Bjergbæk L, Stougaard M, Ho YP, Knudsen BR. Real-time investigation of human topoisomerase I reaction kinetics using an optical sensor: a fast method for drug screening and determination of active enzyme concentrations. Nanoscale 2015; 7:9825-9834. [PMID: 25963854 DOI: 10.1039/c5nr01474c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Human DNA topoisomerase I (hTopI) is a nuclear enzyme that catalyzes relaxation of super helical tension that arises in the genome during essential DNA metabolic processes. This is accomplished through a common reaction mechanism shared among the type IB topoisomerase enzymes, including eukaryotic and poxvirus topoisomerase I. The mechanism of hTopI is specifically targeted in cancer treatment using camptothecin derivatives. These drugs convert the hTopI activity into a cellular poison, and hence the cytotoxic effects of camptothecin derivatives correlate with the hTopI activity. Therefore, fast and reliable techniques for high throughput measurements of hTopI activity are of high clinical interest. Here we demonstrate potential applications of a fluorophore-quencher based DNA sensor designed for measurement of hTopI cleavage-ligation activities, which are the catalytic steps affected by camptothecin. The kinetic analysis of the hTopI reaction with the DNA sensor exhibits a characteristic burst profile. This is the result of a two-step ping-pong reaction mechanism, where a fast first reaction, the one creating the signal, is followed by a slower second reaction necessary for completion of the catalytic cycle. Hence, the burst profile holds information about two reactions in the enzymatic mechanism. Moreover, it allows the amount of active enzyme in the reaction to be determined. The presented results pave the way for future high throughput drug screening and the potential of measuring active hTopI concentrations in clinical samples for individualized treatment.
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28
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Juul S, Obliosca JM, Liu C, Liu YL, Chen YA, Imphean DM, Knudsen BR, Ho YP, Leong KW, Yeh HC. NanoCluster Beacons as reporter probes in rolling circle enhanced enzyme activity detection. Nanoscale 2015; 7:8332-7. [PMID: 25901841 PMCID: PMC4441223 DOI: 10.1039/c5nr01705j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
As a newly developed assay for the detection of endogenous enzyme activity at the single-catalytic-event level, Rolling Circle Enhanced Enzyme Activity Detection (REEAD) has been used to measure enzyme activity in both single human cells and malaria-causing parasites, Plasmodium sp. Current REEAD assays rely on organic dye-tagged linear DNA probes to report the rolling circle amplification products (RCPs), the cost of which may hinder the widespread use of REEAD. Here we show that a new class of activatable probes, NanoCluster Beacons (NCBs), can simplify the REEAD assays. Easily prepared without any need for purification and capable of large fluorescence enhancement upon hybridization, NCBs are cost-effective and sensitive. Compared to conventional fluorescent probes, NCBs are also more photostable. As demonstrated in reporting the human topoisomerases I (hTopI) cleavage-ligation reaction, the proposed NCBs suggest a read-out format attractive for future REEAD-based diagnostics.
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Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Judy M. Obliosca
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Cong Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Yen-Liang Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu-An Chen
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Darren M. Imphean
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
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29
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Cheng B, Annamalai T, Sandhaus S, Bansod P, Tse-Dinh YC. Inhibition of Zn(II) binding type IA topoisomerases by organomercury compounds and Hg(II). PLoS One 2015; 10:e0120022. [PMID: 25798600 PMCID: PMC4370478 DOI: 10.1371/journal.pone.0120022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022] Open
Abstract
Type IA topoisomerase activities are essential for resolving DNA topological barriers via an enzyme-mediated transient single strand DNA break. Accumulation of topoisomerase DNA cleavage product can lead to cell death or genomic rearrangement. Many antibacterial and anticancer drugs act as topoisomerase poison inhibitors that form stabilized ternary complexes with the topoisomerase covalent intermediate, so it is desirable to identify such inhibitors for type IA topoisomerases. Here we report that organomercury compounds were identified during a fluorescence based screening of the NIH diversity set of small molecules for topoisomerase inhibitors that can increase the DNA cleavage product of Yersinia pestis topoisomerase I. Inhibition of relaxation activity and accumulation of DNA cleavage product were confirmed for these organomercury compounds in gel based assays of Escherichia coli topoisomerase I. Hg(II), but not As(III), could also target the cysteines that form the multiple Zn(II) binding tetra-cysteine motifs found in the C-terminal domains of these bacterial topoisomerase I for relaxation activity inhibition. Mycobacterium tuberculosis topoisomerase I activity is not sensitive to Hg(II) or the organomercury compounds due to the absence of the Zn(II) binding cysteines. It is significant that the type IA topoisomerases with Zn(II) binding domains can still cleave DNA when interfered by Hg(II) or organomercury compounds. The Zn(II) binding domains found in human Top3α and Top3β may be potential targets of toxic metals and organometallic complexes, with potential consequence on genomic stability and development.
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Affiliation(s)
- Bokun Cheng
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Shayna Sandhaus
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Priyanka Bansod
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- * E-mail:
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30
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Abstract
DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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31
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Liu X, Sun ZL, Jia AR, Shi YP, Li RH, Yang PM. Extraction, preliminary characterization and evaluation of in vitro antitumor and antioxidant activities of polysaccharides from Mentha piperita. Int J Mol Sci 2014; 15:16302-19. [PMID: 25226538 PMCID: PMC4200825 DOI: 10.3390/ijms150916302] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/25/2014] [Accepted: 09/03/2014] [Indexed: 11/26/2022] Open
Abstract
This study describes the extraction, preliminary characterization and evaluation of the in vitro antitumor and antioxidant activities of polysaccharides extracted from Mentha piperita (MPP). The optimal parameters for the extraction of MPP were obtained by Box-Behnken experimental design and response surface methodology (RSM) at the ratio of water to raw material of 20, extraction time of 1.5 h and extraction temperature at 80 °C. Chemical composition analysis showed that MPP was mainly composed of glucuronic acid, galacturonic acid, glucose, galactose and arabinose, and the molecular weight of its two major fractions were estimated to be about 2.843 and 1.139 kDa, respectively. In vitro bioactivity experiments showed that MPP not only inhibited the growth of A549 cells but possessed potent inhibitory action against DNA topoisomerase I (topo I), and an appreciative antioxidant action as well. These results indicate that MPP may be useful for developing safe natural health products.
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Affiliation(s)
- Xin Liu
- Biology Institute of Shandong Academy of Sciences/Key Laboratory for Applied Microbiology of Shandong Province, Jinan 250014, China.
| | - Zhen-Liang Sun
- State Key Laboratory of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai 200040, China.
| | - Ai-Rong Jia
- Biology Institute of Shandong Academy of Sciences/Key Laboratory for Applied Microbiology of Shandong Province, Jinan 250014, China.
| | - Ya-Ping Shi
- Biology Institute of Shandong Academy of Sciences/Key Laboratory for Applied Microbiology of Shandong Province, Jinan 250014, China.
| | - Rui-Hong Li
- Fengxian Hospital Affiliated to Southern Medical University, 6600 NanFeng Road, Shanghai 201499, China.
| | - Pei-Ming Yang
- State Key Laboratory of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai 200040, China.
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32
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Del Toro Duany Y, Ganguly A, Klostermeier D. Differential contributions of the latch in Thermotoga maritima reverse gyrase to the binding of single-stranded DNA before and after ATP hydrolysis. Biol Chem 2014; 395:83-93. [PMID: 23959663 DOI: 10.1515/hsz-2013-0177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/14/2013] [Indexed: 11/15/2022]
Abstract
Reverse gyrase catalyzes the ATP-dependent introduction of positive supercoils into DNA. Supercoiling requires the functional cooperation of its N-terminal helicase domain with the C-terminal topoisomerase domain. The helicase domain contains a superfamily 2 helicase core formed by two RecA domains, H1 and H2. We show here that a helicase domain lacking the latch, an insertion in H2, fails to close the cleft in the helicase core in response to nucleotide and DNA binding at the beginning of the catalytic cycle. In the presence of the pre-hydrolysis ATP analog ADP·BeFx, however, the closed conformer can still be formed in the absence of the latch. The helicase domain lacking the latch exhibits reduced DNA affinities. The energetic difference between the two nucleotide states involved in duplex separation is diminished, rationalizing the unwinding deficiency of reverse gyrase lacking the latch. The latch most strongly contributes to binding of single-stranded DNA in the post-hydrolysis state, before phosphate release. Our results are in line with contributions of the latch in determining the direction of strand passage, and in orienting the cleaved single-stranded DNA for re-ligation. At the same time, the latch may coordinate the re-ligation reaction with strand passage and with the nucleotide cycle.
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33
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Dellafiora L, Mena P, Del Rio D, Cozzini P. Modeling the effect of phase II conjugations on topoisomerase I poisoning: pilot study with luteolin and quercetin. J Agric Food Chem 2014; 62:5881-5886. [PMID: 24869916 DOI: 10.1021/jf501548g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Topoisomerases are targeted by several drugs in cancer chemotherapy acting as key enzymes in cell viability. Some flavonoids and their glycosides may exert health protective effects through the poisoning of topoisomerases. However, previous studies did not consider the substantial modifications taking place after ingestion neglecting that only metabolites can interact with the internal compartments of the human body. Since the high number of possible metabolites hinders their systematic analysis, an in silico approach can be a valuable tool to prioritize compounds by identifying candidates for further characterization. Specifically focusing on luteolin and quercetin, among the most ubiquitous flavonoids in the human diet, this work reports a computational procedure to model the effect of hepatic phase II conjugative metabolism on poisoning of human Topoisomerase I. As a general effect, glucuronidation and sulphation might enhance and quench poisoning activity, respectively. Among all, quercetin-3-O-glucuronide represents a promising candidate to be analyzed more thoroughly.
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Affiliation(s)
- Luca Dellafiora
- Molecular Modeling Laboratory, Department of Food Science, ‡The Laboratory of Phytochemicals in Physiology, Human Nutrition Unit, Department of Food Science, and §LS9 Bioactives and Health, Interlaboratory Group, Department of Food Science, University of Parma , 43125 Parma, Italy
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34
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Castelli S, Coletta A, D'Annessa I, Fiorani P, Tesauro C, Desideri A. Interaction between natural compounds and human topoisomerase I. Biol Chem 2014; 393:1327-40. [PMID: 23109546 DOI: 10.1515/hsz-2012-0240] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/22/2012] [Indexed: 11/15/2022]
Abstract
Eukaryotic topoisomerase I (Top1) is a monomeric enzyme that catalyzes the relaxation of supercoiled DNA during important processes including DNA replication, transcription, recombination and chromosome condensation. Human Top1 I is of significant medical interest since it is the unique cellular target of camptothecin (CPT), a plant alkaloid that rapidly blocks both DNA and RNA synthesis. In this review, together with CPT, we point out the interaction between human Top1 and some natural compounds, such us terpenoids, flavonoids, stilbenes and fatty acids. The drugs can interact with the enzyme at different levels perturbing the binding, cleavage, rotation or religation processes. Here we focus on different assays that can be used to identify the catalytic step of the enzyme inhibited by different natural compounds.
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Affiliation(s)
- Silvia Castelli
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, I-00133 Rome, Italy
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35
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Cheng Z, Tan G, Wang W, Su X, Landry AP, Lu J, Ding H. Iron and zinc binding activity of Escherichia coli topoisomerase I homolog YrdD. Biometals 2014; 27:229-36. [PMID: 24469504 DOI: 10.1007/s10534-013-9698-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/27/2013] [Indexed: 11/26/2022]
Abstract
YrdD, a homolog of the C-terminal zinc-binding region of Escherichia coli topoisomerase I, is highly conserved among proteobacteria and enterobacteria. However, the function of YrdD remains elusive. Here we report that YrdD purified from E. coli cells grown in LB media contains both zinc and iron. Supplement of exogenous zinc in the medium abolishes the iron binding of YrdD in E. coli cells, indicating that iron and zinc may compete for the same metal binding sites in the protein. While the zinc-bound YrdD is able to bind single-stranded (ss) DNA and protect ssDNA from the DNase I digestion in vitro, the iron-bound YrdD has very little or no binding activity for ssDNA, suggesting that the zinc-bound YrdD may have an important role in DNA repair by interacting with ssDNA in cells.
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Affiliation(s)
- Zishuo Cheng
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
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36
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Drwal MN, Agama K, Pommier Y, Griffith R. Development of purely structure-based pharmacophores for the topoisomerase I-DNA-ligand binding pocket. J Comput Aided Mol Des 2013; 27:1037-49. [PMID: 24293134 PMCID: PMC7578780 DOI: 10.1007/s10822-013-9695-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/26/2013] [Indexed: 12/30/2022]
Abstract
Purely structure-based pharmacophores (SBPs) are an alternative method to ligand-based approaches and have the advantage of describing the entire interaction capability of a binding pocket. Here, we present the development of SBPs for topoisomerase I, an anticancer target with an unusual ligand binding pocket consisting of protein and DNA atoms. Different approaches to cluster and select pharmacophore features are investigated, including hierarchical clustering and energy calculations. In addition, the performance of SBPs is evaluated retrospectively and compared to the performance of ligand- and complex-based pharmacophores. SBPs emerge as a valid method in virtual screening and a complementary approach to ligand-focussed methods. The study further reveals that the choice of pharmacophore feature clustering and selection methods has a large impact on the virtual screening hit lists. A prospective application of the SBPs in virtual screening reveals that they can be used successfully to identify novel topoisomerase inhibitors.
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Affiliation(s)
- Malgorzata N Drwal
- Department of Pharmacology, School of Medical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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37
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Prada CF, Álvarez-Velilla R, Díaz-Gozález R, Pérez-Pertejo Y, Balaña-Fouce R, Reguera RM. Identification and characterization of the regions involved in the nuclear translocation of the heterodimeric leishmanial DNA topoisomerase IB. PLoS One 2013; 8:e73565. [PMID: 24023887 PMCID: PMC3759442 DOI: 10.1371/journal.pone.0073565] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/16/2013] [Indexed: 01/09/2023] Open
Abstract
Leishmania donovani, the causative organism for visceral leishmaniasis, contains a unique heterodimeric DNA-topoisomerase IB (LdTopIB). LdTopIB is a heterodimer made up of a large subunit and a small subunit that must interact with each other to build an active enzyme able to solve the topological tensions on the DNA. As LdTopIB is located within the nucleus, one or more nuclear localization signals (NLS) should exist to ensure its nuclear translocation. In this report three novel NLS have been identified through a sequential deletion study of the genes encoding of both subunits fused to that encoding the green fluorescent protein (GFP). NLS1 is a highly basic sequence of 43 amino acids in the C-terminal extension of the large protomer. We found two well-defined sequences in the small protomer: NLS2 is a 10-amino acid motif located in the N-terminal extension of the protein; NLS3 consists of a complex region of 28 amino acids placed in the vicinity of the catalytic Tyr-222 included at the conserved SKINY signature within the C-terminal. Furthermore, by means of yeast cell viability assays, conducted with several LdTopIB chimeras lacking any of the NLS motives, we have revealed that both subunits are transported independently to the nucleus. There was no evidence of LdTopIB accumulation in mitochondria or association to the kinetoplast DNA network. The results rule out the former hypothesis, which attributes nucleocytoplasmic transport of LdTopIB entirely to the large subunit. The LdTopIB is localized to the nucleus only.
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Affiliation(s)
- Christopher F. Prada
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana, León, Spain
| | - Raquel Álvarez-Velilla
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana, León, Spain
| | - Rosario Díaz-Gozález
- Instituto de Parasitología y Biomedicina "López-Neyra", Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana, León, Spain
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana, León, Spain
- * E-mail:
| | - Rosa M. Reguera
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana, León, Spain
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38
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Ohniwa RL, Muchaku H, Saito S, Wada C, Morikawa K. Atomic force microscopy analysis of the role of major DNA-binding proteins in organization of the nucleoid in Escherichia coli. PLoS One 2013; 8:e72954. [PMID: 23951337 PMCID: PMC3741201 DOI: 10.1371/journal.pone.0072954] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 07/19/2013] [Indexed: 01/07/2023] Open
Abstract
Bacterial genomic DNA is packed within the nucleoid of the cell along with various proteins and RNAs. We previously showed that the nucleoid in log phase cells consist of fibrous structures with diameters ranging from 30 to 80 nm, and that these structures, upon RNase A treatment, are converted into homogeneous thinner fibers with diameter of 10 nm. In this study, we investigated the role of major DNA-binding proteins in nucleoid organization by analyzing the nucleoid of mutant Escherichia coli strains lacking HU, IHF, H–NS, StpA, Fis, or Hfq using atomic force microscopy. Deletion of particular DNA-binding protein genes altered the nucleoid structure in different ways, but did not release the naked DNA even after the treatment with RNase A. This suggests that major DNA-binding proteins are involved in the formation of higher order structure once 10-nm fiber structure is built up from naked DNA.
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Affiliation(s)
- Ryosuke L Ohniwa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tennoh-dai, Tsukuba, Ibaraki, Japan.
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39
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Arnò B, D’Annessa I, Tesauro C, Zuccaro L, Ottaviani A, Knudsen B, Fiorani P, Desideri A. Replacement of the human topoisomerase linker domain with the plasmodial counterpart renders the enzyme camptothecin resistant. PLoS One 2013; 8:e68404. [PMID: 23844196 PMCID: PMC3699648 DOI: 10.1371/journal.pone.0068404] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/29/2013] [Indexed: 12/17/2022] Open
Abstract
A human/plasmodial hybrid enzyme, generated by swapping the human topoisomerase IB linker domain with the corresponding domain of the Plasmodium falciparum enzyme, has been produced and characterized. The hybrid enzyme displays a relaxation activity comparable to the human enzyme, but it is characterized by a much faster religation rate. The hybrid enzyme is also camptothecin resistant. A 3D structure of the hybrid enzyme has been built and its structural-dynamical properties have been analyzed by molecular dynamics simulation. The analysis indicates that the swapped plasmodial linker samples a conformational space much larger than the corresponding domain in the human enzyme. The large linker conformational variability is then linked to important functional properties such as an increased religation rate and a low drug reactivity, demonstrating that the linker domain has a crucial role in the modulation of the topoisomerase IB activity.
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Affiliation(s)
- Barbara Arnò
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Ilda D’Annessa
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Cinzia Tesauro
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Laura Zuccaro
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Alessio Ottaviani
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Birgitta Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Rome, Italy
| | - Alessandro Desideri
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
- * E-mail:
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40
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Guerrant W, Patil V, Canzoneri JC, Yao LP, Hood R, Oyelere AK. Dual-acting histone deacetylase-topoisomerase I inhibitors. Bioorg Med Chem Lett 2013; 23:3283-7. [PMID: 23622981 PMCID: PMC3657756 DOI: 10.1016/j.bmcl.2013.03.108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/25/2013] [Accepted: 03/27/2013] [Indexed: 12/20/2022]
Abstract
Current chemotherapy regimens are comprised mostly of single-target drugs which are often plagued by toxic side effects and resistance development. A pharmacological strategy for circumventing these drawbacks could involve designing multivalent ligands that can modulate multiple targets while avoiding the toxicity of a single-targeted agent. Two attractive targets, histone deacetylase (HDAC) and topoisomerase I (Topo I), are cellular modulators that can broadly arrest cancer proliferation through a range of downstream effects. Both are clinically validated targets with multiple inhibitors in therapeutic use. We describe herein the design and synthesis of dual-acting histone deacetylase-topoisomerase I inhibitors. We also show that these dual-acting agents retain activity against HDAC and Topo I, and potently arrest cancer proliferation.
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Affiliation(s)
- William Guerrant
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
| | - Vishal Patil
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
| | - Joshua C. Canzoneri
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
| | - Li-Pan Yao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
| | - Rebecca Hood
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
| | - Adegboyega K. Oyelere
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400 USA
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Bandyopadhyay K, Li P, Gjerset RA. The p14ARF alternate reading frame protein enhances DNA binding of topoisomerase I by interacting with the serine 506-phosphorylated core domain. PLoS One 2013; 8:e58835. [PMID: 23555599 PMCID: PMC3608632 DOI: 10.1371/journal.pone.0058835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/07/2013] [Indexed: 12/27/2022] Open
Abstract
In addition to its well-characterized function as a tumor suppressor, p14ARF (ARF) is a positive regulator of topoisomerase I (topo I), a central enzyme in DNA metabolism and a target for cancer therapy. We previously showed that topo I hyperphosphorylation, a cancer-associated event mediated by elevated levels of the protein kinase CK2, increases topo I activity and the cellular sensitivity to topo I-targeted drugs. Topo I hyperphosphorylation also increases its interaction with ARF. Because the ARF−topo I interaction could be highly relevant to DNA metabolism and cancer treatment, we identified the regions of topo I involved in ARF binding and characterized the effects of ARF binding on topo I function. Using a series of topo I deletion constructs, we found that ARF interacted with the topo I core domain, which encompasses most of the catalytic and DNA-interacting residues. ARF binding increased the DNA relaxation activity of hyperphosphorylated topo I by enhancing its association with DNA, but did not affect the topo I catalytic rate. In cells, ARF promoted the chromatin association of hyperphosphorylated, but not basal phosphorylated, topo I, and increased topo I-mediated DNA nicking under conditions of oxidative stress. The aberrant nicking was found to correlate with increased formation of DNA double-strand breaks, which are precursors of many genome destabilizing events. The results suggest that the convergent actions of oxidative stress and elevated CK2 and ARF levels, which are common features of cancer cells, lead to a dysregulation of topo I that may contribute both to the cellular response to topo I-targeted drugs and to genome instability.
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Affiliation(s)
- Keya Bandyopadhyay
- Torrey Pines Institute for Molecular Studies San Diego, California, United States of America
| | - Pingchuan Li
- Torrey Pines Institute for Molecular Studies San Diego, California, United States of America
| | - Ruth A. Gjerset
- Torrey Pines Institute for Molecular Studies San Diego, California, United States of America
- * E-mail:
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42
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Zhang L, Ma D, Zhang Y, He W, Yang J, Li C, Jiang H. Characterization of DNA topoisomerase-1 in Spodoptera exigua for toxicity evaluation of camptothecin and hydoxy-camptothecin. PLoS One 2013; 8:e56458. [PMID: 23451051 PMCID: PMC3579855 DOI: 10.1371/journal.pone.0056458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 01/14/2013] [Indexed: 11/20/2022] Open
Abstract
Camptothecin (CPT), a plant alkaloid originally isolated from the native Chinese tree, Camptotheca acuminate, exerts the toxic effect by targeting eukaryotic DNA topoisomerase 1 (DNA Topo1). Besides as potent anti-cancer agents, CPT and its derivatives are now being explored as potential pesticides for insect control. In this study, we assessed their toxicity to an insect homolog, the Topo1 protein from beet armyworms (Spodoptera exigua Hübner), a worldwide pest of many important crops. The S. exigua Topo1 gene contains an ORF of 2790 base pairs that is predicted to encode a polypeptide of 930 amino acids. The deduced polypeptide exhibits polymorphism at residue sites V420, L530, A653 and T729 (numbered according to human Topo1) among insect species, which are predicted to confer sensitivity to CPT. The DNA relaxation activity of this protein was subsequently examined using a truncated form that contained the residues 337–930 and was expressed in bacteria BL21 cells. The purified protein retained the ability to relax double-stranded DNA and was susceptible to CPT and its derivative hydroxy-camptothecin (HCPT) in a dose-dependent manner. The same inhibitory effect was also found on the native Topo1 extracted from IOZCAS-Spex-II cells, a cell line established from beet armyworms. Additionally, CPT and HCPT treatment reduced the steady accumulation of Topo1 protein despite the increased mRNA expression in response to the treatment. Our studies provide information of the S. exigua Topo1 gene and its amino acid polymorphism in insects and uncover some clues about potential mechanisms of CPT toxicity against insect pests. These results also are useful for development of more effective Topo1-targeted CPT insecticides in the future.
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Affiliation(s)
- Lan Zhang
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dejun Ma
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yanning Zhang
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weizhi He
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingjing Yang
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Chuanren Li
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Hongyun Jiang
- Key Laboratory of Integrated Pest Management in Crops, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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Thai KM, Bui QH, Tran TD, Huynh TNP. QSAR modeling on benzo[c]phenanthridine analogues as topoisomerase I inhibitors and anti-cancer agents. Molecules 2012; 17:5690-712. [PMID: 22580401 PMCID: PMC6268722 DOI: 10.3390/molecules17055690] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 04/25/2012] [Accepted: 05/04/2012] [Indexed: 12/28/2022] Open
Abstract
Benzo[c]phenanthridine (BCP) derivatives were identified as topoisomerase I (TOP-I) targeting agents with pronounced antitumor activity. In this study, hologram-QSAR, 2D-QSAR and 3D-QSAR models were developed for BCPs on topoisomerase I inbibitory activity and cytotoxicity against seven tumor cell lines including RPMI8402, CPT-K5, P388, CPT45, KB3-1, KBV-1and KBH5.0. The hologram, 2D, and 3D-QSAR models were obtained with the square of correlation coefficient R² = 0.58-0.77, the square of the crossvalidation coefficient q² = 0.41-0.60 as well as the external set's square of predictive correlation coefficient r² = 0.5-0.80. Moreover, the assessment method based on reliability test with confidence level of 95% was used to validate the predictive power of QSAR models and to prevent over-fitting phenomenon of classical QSAR models. Our QSAR model could be applied to design new analogues of BCPs with higher antitumor and topoisomerase I inhibitory activity.
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Affiliation(s)
- Khac-Minh Thai
- Department of Medicinal Chemistry, School of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang St., Dist. 1, Ho Chi Minh City, Vietnam.
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Jain S, Zweig M, Peeters E, Siewering K, Hackett KT, Dillard JP, van der Does C. Characterization of the single stranded DNA binding protein SsbB encoded in the Gonoccocal Genetic Island. PLoS One 2012; 7:e35285. [PMID: 22536367 PMCID: PMC3334931 DOI: 10.1371/journal.pone.0035285] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 03/14/2012] [Indexed: 11/18/2022] Open
Abstract
Background Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in genetic islands of different proteobacteria. This cluster encodes DNA-processing enzymes such as the ParA and ParB partitioning proteins, the TopB topoisomerase, and four conserved hypothetical proteins. The SsbB homologs found in these clusters form a family separated from other ssDNA binding proteins. Methodology/Principal Findings In contrast to most other SSBs, SsbB did not complement the Escherichia coli ssb deletion mutant. Purified SsbB forms a stable tetramer. Electrophoretic mobility shift assays and fluorescence titration assays, as well as atomic force microscopy demonstrate that SsbB binds ssDNA specifically with high affinity. SsbB binds single-stranded DNA with minimal binding frames for one or two SsbB tetramers of 15 and 70 nucleotides. The binding mode was independent of increasing Mg2+ or NaCl concentrations. No role of SsbB in ssDNA secretion or DNA uptake could be identified, but SsbB strongly stimulated Topoisomerase I activity. Conclusions/Significance We propose that these novel SsbBs play an unknown role in the maintenance of genetic islands.
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Affiliation(s)
- Samta Jain
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Maria Zweig
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Katja Siewering
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kathleen T. Hackett
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Joseph P. Dillard
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Chris van der Does
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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Morales R, Sriratana P, Zhang J, Cann IKO. Methanosarcina acetivorans C2A topoisomerase IIIα, an archaeal enzyme with promiscuity in divalent cation dependence. PLoS One 2011; 6:e26903. [PMID: 22046402 PMCID: PMC3202574 DOI: 10.1371/journal.pone.0026903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 10/06/2011] [Indexed: 11/21/2022] Open
Abstract
Topoisomerases play a fundamental role in genome stability, DNA replication and repair. As a result, topoisomerases have served as therapeutic targets of interest in Eukarya and Bacteria, two of the three domains of life. Since members of Archaea, the third domain of life, have not been implicated in any diseased state to-date, there is a paucity of data on archaeal topoisomerases. Here we report Methanosarcina acetivorans TopoIIIα (MacTopoIIIα) as the first biochemically characterized mesophilic archaeal topoisomerase. Maximal activity for MacTopoIIIα was elicited at 30-35°C and 100 mM NaCl. As little as 10 fmol of the enzyme initiated DNA relaxation, and NaCl concentrations above 250 mM inhibited this activity. The present study also provides the first evidence that a type IA Topoisomerase has activity in the presence of all divalent cations tested (Mg(2+), Ca(2+), Sr(2+), Ba(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+) and Cd(2+)). Activity profiles were, however, specific to each metal. Known type I (ssDNA and camptothecin) and type II (etoposide, novobiocin and nalidixic acid) inhibitors with different mechanisms of action were used to demonstrate that MacTopoIIIα is a type IA topoisomerase. Alignment of MacTopoIIIα with characterized topoisomerases identified Y317 as the putative catalytic residue, and a Y317F mutation ablated DNA relaxation activity, demonstrating that Y317 is essential for catalysis. As the role of Domain V (C-terminal domain) is unclear, MacTopoIIIα was aligned with the canonical E. coli TopoI 67 kDa fragment in order to construct an N-terminal (1-586) and a C-terminal (587-752) fragment for analysis. Activity could neither be elicited from the fragments individually nor reconstituted from a mixture of the fragments, suggesting that native folding is impaired when the two fragments are expressed separately. Evidence that each of the split domains plays a role in Zn(2+) binding of the enzyme is also provided.
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Affiliation(s)
- Raymond Morales
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Palita Sriratana
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Jing Zhang
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Isaac K. O. Cann
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
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García MT, Blázquez MA, Ferrándiz MJ, Sanz MJ, Silva-Martín N, Hermoso JA, de la Campa AG. New alkaloid antibiotics that target the DNA topoisomerase I of Streptococcus pneumoniae. J Biol Chem 2011; 286:6402-13. [PMID: 21169356 PMCID: PMC3057782 DOI: 10.1074/jbc.m110.148148] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 12/15/2010] [Indexed: 11/06/2022] Open
Abstract
Streptococcus pneumoniae has two type II DNA-topoisomerases (DNA-gyrase and DNA topoisomerase IV) and a single type I enzyme (DNA-topoisomerase I, TopA), as demonstrated here. Although fluoroquinolones target type II enzymes, antibiotics efficiently targeting TopA have not yet been reported. Eighteen alkaloids (seven aporphine and 11 phenanthrenes) were semisynthesized from boldine and used to test inhibition both of TopA activity and of cell growth. Two phenanthrenes (seconeolitsine and N-methyl-seconeolitsine) effectively inhibited both TopA activity and cell growth at equivalent concentrations (∼17 μM). Evidence for in vivo TopA targeting by seconeolitsine was provided by the protection of growth inhibition in a S. pneumoniae culture in which the enzyme was overproduced. Additionally, hypernegative supercoiling was observed in an internal plasmid after drug treatment. Furthermore, a model of pneumococcal TopA was made based on the crystal structure of Escherichia coli TopA. Docking calculations indicated strong interactions of the alkaloids with the nucleotide-binding site in the closed protein conformation, which correlated with their inhibitory effect. Finally, although seconeolitsine and N-methyl-seconeolitsine inhibited TopA and bacterial growth, they did not affect human cell viability. Therefore, these new alkaloids can be envisaged as new therapeutic candidates for the treatment of S. pneumoniae infections resistant to other antibiotics.
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Affiliation(s)
- María Teresa García
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
| | - María Amparo Blázquez
- the Departamento de Farmacología, Facultat de Farmàcia, Universitat de València, Vicent Andrés Estellés s/n. 46100 Burjasot, Valencia, and
| | - María José Ferrándiz
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
| | - María Jesús Sanz
- the Departamento de Farmacología, Facultat de Farmàcia, Universitat de València, Vicent Andrés Estellés s/n. 46100 Burjasot, Valencia, and
| | - Noella Silva-Martín
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan A. Hermoso
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano”, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Adela G. de la Campa
- From the Unidad de Genética Bacteriana, Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid
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Wang F, Yang Y, Singh TR, Busygina V, Guo R, Wan K, Wang W, Sung P, Meetei AR, Lei M. Crystal structures of RMI1 and RMI2, two OB-fold regulatory subunits of the BLM complex. Structure 2011; 18:1159-70. [PMID: 20826342 PMCID: PMC5955610 DOI: 10.1016/j.str.2010.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/03/2010] [Accepted: 06/07/2010] [Indexed: 11/17/2022]
Abstract
Mutations in BLM, a RecQ-like helicase, are linked to the autosomal recessive cancer-prone disorder Bloom's syndrome. BLM associates with topoisomerase (Topo) IIIα, RMI1, and RMI2 to form the BLM complex that is essential for genome stability. The RMI1-RMI2 heterodimer stimulates the dissolution of double Holliday junction into non-crossover recombinants mediated by BLM-Topo IIIα and is essential for stabilizing the BLM complex. However, the molecular basis of these functions of RMI1 and RMI2 remains unclear. Here we report the crystal structures of multiple domains of RMI1-RMI2, providing direct confirmation of the existence of three oligonucleotide/oligosaccharide binding (OB)-folds in RMI1-RMI2. Our structural and biochemical analyses revealed an unexpected insertion motif in RMI1N-OB, which is important for stimulating the dHJ dissolution. We also revealed the structural basis of the interaction between RMI1C-OB and RMI2-OB and demonstrated the functional importance of the RMI1-RMI2 interaction in genome stability maintenance.
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Affiliation(s)
- Feng Wang
- Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Winnicka K, Bielawska A, Bielawski K. Inhibition of DNA topoisomerases I and II by G3 PAMAM-NH2 dendrimer-modified digoxin and proscillaridin A conjugates in a cell free system. Acta Pol Pharm 2010; 67:630-634. [PMID: 21229879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Two modified glycosides--digoxin and proscillaridin A conjugated to a generation 3 of polyamidoamine dendrimer (G3 PAMAM-NH2) were evaluated as DNA topoisomerase II inhibitors. The ability of these compounds (PAMAM-Dig and PAMAM-Prosc) to inhibit topoisomerase I and II activity was quantified by measuring the action on supercoiled DNA substrate as a function of increasing concentration of the test compounds by the use of agarose gel electrophoresis. The obtained results suggest that a conjugation of the modified glycosides with G3 PAMAM-NH2 significantly improved the ability of the parent compounds to an inhibition of DNA topoisomerases.
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Affiliation(s)
- Katarzyna Winnicka
- Department of Pharmaceutical Technology, Medical University of Białystok, Kilińskiego 1, 15-089 Białystok, Poland.
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49
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Subramani R, Juul S, Rotaru A, Andersen FF, Gothelf KV, Mamdouh W, Besenbacher F, Dong M, Knudsen BR. A novel secondary DNA binding site in human topoisomerase I unravelled by using a 2D DNA origami platform. ACS Nano 2010; 4:5969-5977. [PMID: 20828215 DOI: 10.1021/nn101662a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The biologically and clinically important nuclear enzyme human topoisomerase I relaxes both positively and negatively supercoiled DNA and binds consequently DNA with supercoils of positive or negative sign with a strong preference over relaxed DNA. One scheme to explain this preference relies on the existence of a secondary DNA binding site in the enzyme facilitating binding to DNA nodes characteristic for plectonemic DNA. Here we demonstrate the ability of human topoisomerase I to induce formation of DNA synapses at protein containing nodes or filaments using atomic force microscopy imaging. By means of a two-dimensional (2D) DNA origami platform, we monitor the interactions between a single human topoisomerase I covalently bound to one DNA fragment and a second DNA fragment protruding from the DNA origami. This novel single molecule origami-based detection scheme provides direct evidence for the existence of a secondary DNA interaction site in human topoisomerase I and lends further credence to the theory of two distinct DNA interaction sites in human topoisomerase I, possibly facilitating binding to DNA nodes characteristic for plectonemic supercoils.
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Affiliation(s)
- Ramesh Subramani
- Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark
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50
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Hoadley KA, Xu D, Xue Y, Satyshur KA, Wang W, Keck JL. Structure and cellular roles of the RMI core complex from the bloom syndrome dissolvasome. Structure 2010; 18:1149-58. [PMID: 20826341 PMCID: PMC2937010 DOI: 10.1016/j.str.2010.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Revised: 06/07/2010] [Accepted: 06/07/2010] [Indexed: 01/07/2023]
Abstract
BLM, the protein product of the gene mutated in Bloom syndrome, is one of five human RecQ helicases. It functions to separate double Holliday junction DNA without genetic exchange as a component of the "dissolvasome," which also includes topoisomerase IIIα and the RMI (RecQ-mediated genome instability) subcomplex (RMI1 and RMI2). We describe the crystal structure of the RMI core complex, comprising RMI2 and the C-terminal OB domain of RMI1. The overall RMI core structure strongly resembles two-thirds of the trimerization core of the eukaryotic single-stranded DNA-binding protein, Replication Protein A. Immunoprecipitation experiments with RMI2 variants confirm key interactions that stabilize the RMI core interface. Disruption of this interface leads to a dramatic increase in cellular sister chromatid exchange events similar to that seen in BLM-deficient cells. The RMI core interface is therefore crucial for BLM dissolvasome assembly and may have additional cellular roles as a docking hub for other proteins.
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Affiliation(s)
- Kelly A. Hoadley
- Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706-1532
| | - Dongyi Xu
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Boulevard 10B113, Baltimore, MD 21224-6825
| | - Yutong Xue
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Boulevard 10B113, Baltimore, MD 21224-6825
| | - Kenneth A. Satyshur
- Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706-1532
| | - Weidong Wang
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Boulevard 10B113, Baltimore, MD 21224-6825
- To whom correspondence should be addressed. WW: Telephone (410) 558-8334, FAX (410) 558-8331, JLK: Telephone (608) 263-1815, FAX (608) 262-5253,
| | - James L. Keck
- Department of Biomolecular Chemistry, 550 Medical Science Center, 1300 University Avenue, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706-1532
- To whom correspondence should be addressed. WW: Telephone (410) 558-8334, FAX (410) 558-8331, JLK: Telephone (608) 263-1815, FAX (608) 262-5253,
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