1
|
Olszewski M, Maciejewska N, Kallingal A, Chylewska A, Dąbrowska AM, Biedulska M, Makowski M, Padrón JM, Baginski M. Palindromic carbazole derivatives: unveiling their antiproliferative effect via topoisomerase II catalytic inhibition and apoptosis induction. J Enzyme Inhib Med Chem 2024; 39:2302920. [PMID: 38221785 PMCID: PMC10791108 DOI: 10.1080/14756366.2024.2302920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/24/2023] [Indexed: 01/16/2024] Open
Abstract
Human DNA topoisomerases are essential for crucial cellular processes, including DNA replication, transcription, chromatin condensation, and maintenance of its structure. One of the significant strategies employed in cancer treatment involves the inhibition of a specific type of topoisomerase, known as topoisomerase II (Topo II). Carbazole derivatives, recognised for their varied biological activities, have recently become a significant focus in oncological research. This study assesses the efficacy of three symmetrically substituted carbazole derivatives: 2,7-Di(2-furyl)-9H-carbazole (27a), 3,6-Di(2-furyl)-9H-carbazole (36a), and 3,6-Di(2-thienyl)-9H-carbazole (36b) - as anticancer agents. Among investigated carbazole derivatives, compound 3,6-di(2-furyl)-9H-carbazole bearing two furan moieties emerged as a novel catalytic inhibitor of Topo II. Notably, 3,6-di(2-furyl)-9H-carbazole effectively selectively inhibited the relaxation and decatenation activities of Topo IIα, with minimal effects on the IIβ isoform. These findings underscore the potential of compound 3,6-Di(2-furyl)-9H-carbazole as a promising lead candidate warranting further investigation in the realm of anticancer drug development.
Collapse
Affiliation(s)
- Mateusz Olszewski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Natalia Maciejewska
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Anoop Kallingal
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Agnieszka Chylewska
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Aleksandra M. Dąbrowska
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Małgorzata Biedulska
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Mariusz Makowski
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - José M. Padrón
- BioLab, Instituto Universitario de Bio-Orgánica “Antonio González”, Universidad de La Laguna, La Laguna, Spain
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| |
Collapse
|
2
|
Royzenblat SK, Freddolino L. Spatio-temporal organization of the E. coli chromosome from base to cellular length scales. EcoSal Plus 2024:eesp00012022. [PMID: 38864557 DOI: 10.1128/ecosalplus.esp-0001-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
Abstract
Escherichia coli has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the E. coli nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of E. coli chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.
Collapse
Affiliation(s)
- Sonya K Royzenblat
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lydia Freddolino
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| |
Collapse
|
3
|
Sutormin D, Galivondzhyan A, Gafurov A, Severinov K. Single-nucleotide resolution detection of Topo IV cleavage activity in the Escherichia coli genome with Topo-Seq. Front Microbiol 2023; 14:1160736. [PMID: 37089538 PMCID: PMC10117906 DOI: 10.3389/fmicb.2023.1160736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/16/2023] [Indexed: 04/08/2023] Open
Abstract
Topoisomerase IV (Topo IV) is the main decatenation enzyme in Escherichia coli; it removes catenation links that are formed during DNA replication. Topo IV binding and cleavage sites were previously identified in the E. coli genome with ChIP-Seq and NorfIP. Here, we used a more sensitive, single-nucleotide resolution Topo-Seq procedure to identify Topo IV cleavage sites (TCSs) genome-wide. We detected thousands of TCSs scattered in the bacterial genome. The determined cleavage motif of Topo IV contained previously known cleavage determinants (−4G/+8C, −2A/+6 T, −1 T/+5A) and additional, not observed previously, positions −7C/+11G and −6C/+10G. TCSs were depleted in the Ter macrodomain except for two exceptionally strong non-canonical cleavage sites located in 33 and 38 bp from the XerC-box of the dif-site. Topo IV cleavage activity was increased in Left and Right macrodomains flanking the Ter macrodomain and was especially high in the 50–60 kb region containing the oriC origin of replication. Topo IV enrichment was also increased downstream of highly active transcription units, indicating that the enzyme is involved in relaxation of transcription-induced positive supercoiling.
Collapse
Affiliation(s)
- Dmitry Sutormin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- *Correspondence: Dmitry Sutormin,
| | | | - Azamat Gafurov
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Konstantin Severinov,
| |
Collapse
|
4
|
Jeong J, Lee JH, Carcamo CC, Parker MW, Berger JM. DNA-Stimulated Liquid-Liquid phase separation by eukaryotic topoisomerase ii modulates catalytic function. eLife 2022; 11:e81786. [PMID: 36342377 PMCID: PMC9674351 DOI: 10.7554/elife.81786] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Type II topoisomerases modulate chromosome supercoiling, condensation, and catenation by moving one double-stranded DNA segment through a transient break in a second duplex. How DNA strands are chosen and selectively passed to yield appropriate topological outcomes - for example, decatenation vs. catenation - is poorly understood. Here, we show that at physiological enzyme concentrations, eukaryotic type IIA topoisomerases (topo IIs) readily coalesce into condensed bodies. DNA stimulates condensation and fluidizes these assemblies to impart liquid-like behavior. Condensation induces both budding yeast and human topo IIs to switch from DNA unlinking to active DNA catenation, and depends on an unstructured C-terminal region, the loss of which leads to high levels of knotting and reduced catenation. Our findings establish that local protein concentration and phase separation can regulate how topo II creates or dissolves DNA links, behaviors that can account for the varied roles of the enzyme in supporting transcription, replication, and chromosome compaction.
Collapse
Affiliation(s)
- Joshua Jeong
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Joyce H Lee
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Claudia C Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Matthew W Parker
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| |
Collapse
|
5
|
Menger KE, Chapman J, Díaz-Maldonado H, Khazeem M, Deen D, Erdinc D, Casement JW, Di Leo V, Pyle A, Rodríguez-Luis A, Cowell I, Falkenberg M, Austin C, Nicholls T. Two type I topoisomerases maintain DNA topology in human mitochondria. Nucleic Acids Res 2022; 50:11154-11174. [PMID: 36215039 PMCID: PMC9638942 DOI: 10.1093/nar/gkac857] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/03/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Genetic processes require the activity of multiple topoisomerases, essential enzymes that remove topological tension and intermolecular linkages in DNA. We have investigated the subcellular localisation and activity of the six human topoisomerases with a view to understanding the topological maintenance of human mitochondrial DNA. Our results indicate that mitochondria contain two topoisomerases, TOP1MT and TOP3A. Using molecular, genomic and biochemical methods we find that both proteins contribute to mtDNA replication, in addition to the decatenation role of TOP3A, and that TOP1MT is stimulated by mtSSB. Loss of TOP3A or TOP1MT also dysregulates mitochondrial gene expression, and both proteins promote transcription elongation in vitro. We find no evidence for TOP2 localisation to mitochondria, and TOP2B knockout does not affect mtDNA maintenance or expression. Our results suggest a division of labour between TOP3A and TOP1MT in mtDNA topology control that is required for the proper maintenance and expression of human mtDNA.
Collapse
Affiliation(s)
- Katja E Menger
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - James Chapman
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Héctor Díaz-Maldonado
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Mushtaq M Khazeem
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dasha Deen
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Direnis Erdinc
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - John W Casement
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Valeria Di Leo
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alejandro Rodríguez-Luis
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ian G Cowell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Caroline A Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| |
Collapse
|
6
|
Wang K, Chen YF, Yang YCSH, Huang HM, Lee SY, Shih YJ, Li ZL, Whang-Peng J, Lin HY, Davis PJ. The power of heteronemin in cancers. J Biomed Sci 2022; 29:41. [PMID: 35705962 PMCID: PMC9202199 DOI: 10.1186/s12929-022-00816-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Heteronemin (Haimian jing) is a sesterterpenoid-type natural marine product that is isolated from sponges and has anticancer properties. It inhibits cancer cell proliferation via different mechanisms, such as reactive oxygen species (ROS) production, cell cycle arrest, apoptosis as well as proliferative gene changes in various types of cancers. Recently, the novel structure and bioactivity evaluation of heteronemin has received extensive attention. Hormones control physiological activities regularly, however, they may also affect several abnormalities such as cancer. L-Thyroxine (T4), steroid hormones, and epidermal growth factor (EGF) up-regulate the accumulation of checkpoint programmed death-ligand 1 (PD-L1) and promote inflammation in cancer cells. Heteronemin suppresses PD-L1 expression and reduces the PD-L1-induced proliferative effect. In the current review, we evaluated research and evidence regarding the antitumor effects of heteronemin and the antagonizing effects of non-peptide hormones and growth factors on heteronemin-induced anti-cancer properties and utilized computational molecular modeling to explain how these ligands interacted with the integrin αvβ3 receptors. On the other hand, thyroid hormone deaminated analogue, tetraiodothyroacetic acid (tetrac), modulates signal pathways and inhibits cancer growth and metastasis. The combination of heteronemin and tetrac derivatives has been demonstrated to compensate for anti-proliferation in cancer cells under different circumstances. Overall, this review outlines the potential of heteronemin in managing different types of cancers that may lead to its clinical development as an anticancer agent.
Collapse
Affiliation(s)
- Kuan Wang
- Graduate Institute of Nanomedicine and Medical Engineering, College of Medical Engineering, Taipei Medical University, 250 Wuxing Street, Taipei 110, Taipei, 11031, Taiwan
| | - Yi-Fong Chen
- Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Yu-Chen S H Yang
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, 11031, Taiwan
| | - Haw-Ming Huang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, 11031, Taiwan
| | - Sheng-Yang Lee
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, 11031, Taiwan.,Dentistry, Wan-Fang Medical Center, Taipei Medical University, Taipei, 11031, Taiwan
| | - Ya-Jung Shih
- Graduate Institute of Nanomedicine and Medical Engineering, College of Medical Engineering, Taipei Medical University, 250 Wuxing Street, Taipei 110, Taipei, 11031, Taiwan.,Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Zi-Lin Li
- Graduate Institute of Nanomedicine and Medical Engineering, College of Medical Engineering, Taipei Medical University, 250 Wuxing Street, Taipei 110, Taipei, 11031, Taiwan.,Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Jacqueline Whang-Peng
- Cancer Center, Wan Fang Hospital, Taipei Medical University, No. 111, Section 3, Xinglong Road, Wenshan District, Taipei City, 116, Taipei, 11031, Taiwan.
| | - Hung-Yun Lin
- Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan. .,Cancer Center, Wan Fang Hospital, Taipei Medical University, No. 111, Section 3, Xinglong Road, Wenshan District, Taipei City, 116, Taipei, 11031, Taiwan. .,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, 11031, Taiwan. .,Traditional Herbal Medicine Research Center of Taipei Medical University Hospital, Taipei Medical University, Taipei, 11031, Taiwan. .,Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, 12144, USA.
| | - Paul J Davis
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, 12144, USA.,Department of Medicine, Albany Medical College, Albany, NY12144, USA
| |
Collapse
|
7
|
Van Ravenstein SX, Mehta KP, Kavlashvili T, Byl JAW, Zhao R, Osheroff N, Cortez D, Dewar JM. Topoisomerase II poisons inhibit vertebrate DNA replication through distinct mechanisms. EMBO J 2022; 41:e110632. [PMID: 35578785 PMCID: PMC9194788 DOI: 10.15252/embj.2022110632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/09/2022] Open
Abstract
Topoisomerase II (TOP2) unlinks chromosomes during vertebrate DNA replication. TOP2 "poisons" are widely used chemotherapeutics that stabilize TOP2 complexes on DNA, leading to cytotoxic DNA breaks. However, it is unclear how these drugs affect DNA replication, which is a major target of TOP2 poisons. Using Xenopus egg extracts, we show that the TOP2 poisons etoposide and doxorubicin both inhibit DNA replication through different mechanisms. Etoposide induces TOP2-dependent DNA breaks and TOP2-dependent fork stalling by trapping TOP2 behind replication forks. In contrast, doxorubicin does not lead to appreciable break formation and instead intercalates into parental DNA to stall replication forks independently of TOP2. In human cells, etoposide stalls forks in a TOP2-dependent manner, while doxorubicin stalls forks independently of TOP2. However, both drugs exhibit TOP2-dependent cytotoxicity. Thus, etoposide and doxorubicin inhibit DNA replication through distinct mechanisms despite shared genetic requirements for cytotoxicity.
Collapse
Affiliation(s)
| | - Kavi P Mehta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Runxiang Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| |
Collapse
|
8
|
Lee JH, Mosher EP, Lee YS, Bumpus NN, Berger JM. Control of topoisomerase II activity and chemotherapeutic inhibition by TCA cycle metabolites. Cell Chem Biol 2022; 29:476-489.e6. [PMID: 34529934 PMCID: PMC8913808 DOI: 10.1016/j.chembiol.2021.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/16/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022]
Abstract
Topoisomerase II (topo II) is essential for disentangling newly replicated chromosomes. DNA unlinking involves the physical passage of one duplex through another and depends on the transient formation of double-stranded DNA breaks, a step exploited by frontline chemotherapeutics to kill cancer cells. Although anti-topo II drugs are efficacious, they also elicit cytotoxic side effects in normal cells; insights into how topo II is regulated in different cellular contexts is essential to improve their targeted use. Using chemical fractionation and mass spectrometry, we have discovered that topo II is subject to metabolic control through the TCA cycle. We show that TCA metabolites stimulate topo II activity in vitro and that levels of TCA flux modulate cellular sensitivity to anti-topo II drugs in vivo. Our work reveals an unanticipated connection between the control of DNA topology and cellular metabolism, a finding with ramifications for the clinical use of anti-topo II therapies.
Collapse
Affiliation(s)
- Joyce H Lee
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric P Mosher
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Young-Sam Lee
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Namandjé N Bumpus
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
9
|
Cebrián J, Martínez V, Hernández P, Krimer DB, Fernández-Nestosa MJ, Schvartzman JB. Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates. BIOLOGY 2021; 10:biology10111195. [PMID: 34827187 PMCID: PMC8615216 DOI: 10.3390/biology10111195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 11/28/2022]
Abstract
Simple Summary During replication, DNA molecules undergo topological changes that affect supercoiling, catenation and knotting. To better understand this process and the role of topoisomerases, the enzymes that control DNA topology in in vivo, two-dimensional agarose gel electrophoresis were used to investigate the efficiency of three type II DNA topoisomerases, the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α, on partially replicated bacterial plasmids containing replication forks stalled at specific sites. The results obtained revealed that despite the fact these DNA topoisomerases may have evolved to accomplish specific tasks, they share abilities. To our knowledge, this is the first time two-dimensional agarose gel electrophoresis have been used to examine the ability of these topoisomerases to relax supercoiling in the un-replicated region and unlink pre-catenanes in the replicated one of partially replicated molecules in vitro. The methodology described here can be used to study the role of different topoisomerases in partially replicated molecules. Abstract DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined. However, their ability to relax supercoiling and unlink the pre-catenanes of partially replicated molecules has received little attention. Here, we used two-dimensional agarose gel electrophoresis to test the function of three type II DNA topoisomerases in vitro: the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α. We examined the proficiency of these topoisomerases on a partially replicated bacterial plasmid: pBR-TerE@AatII, with an unidirectional replicating fork, stalled when approximately half of the plasmid had been replicated in vivo. DNA was isolated from two strains of Escherichia coli: DH5αF’ and parE10. These experiments allowed us to assess, for the first time, the efficiency of the topoisomerases examined to resolve supercoiling and pre-catenanes in partially replicated molecules and fully replicated catenanes formed in vivo. The results obtained revealed the preferential functions and also some redundancy in the abilities of these DNA topoisomerases in vitro.
Collapse
Affiliation(s)
- Jorge Cebrián
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón, CIBERCV, 28040 Madrid, Spain
| | - Victor Martínez
- Bioinformatics Laboratory, Polytechnic School, National University of Asunción, San Lorenzo P.O. Box 2111, Paraguay;
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
| | - Dora B. Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
| | - María-José Fernández-Nestosa
- Bioinformatics Laboratory, Polytechnic School, National University of Asunción, San Lorenzo P.O. Box 2111, Paraguay;
- Correspondence:
| | - Jorge B. Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
| |
Collapse
|
10
|
Coordinating DNA Replication and Mitosis through Ubiquitin/SUMO and CDK1. Int J Mol Sci 2021; 22:ijms22168796. [PMID: 34445496 PMCID: PMC8395760 DOI: 10.3390/ijms22168796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022] Open
Abstract
Post-translational modification of the DNA replication machinery by ubiquitin and SUMO plays key roles in the faithful duplication of the genetic information. Among other functions, ubiquitination and SUMOylation serve as signals for the extraction of factors from chromatin by the AAA ATPase VCP. In addition to the regulation of DNA replication initiation and elongation, we now know that ubiquitination mediates the disassembly of the replisome after DNA replication termination, a process that is essential to preserve genomic stability. Here, we review the recent evidence showing how active DNA replication restricts replisome ubiquitination to prevent the premature disassembly of the DNA replication machinery. Ubiquitination also mediates the removal of the replisome to allow DNA repair. Further, we discuss the interplay between ubiquitin-mediated replisome disassembly and the activation of CDK1 that is required to set up the transition from the S phase to mitosis. We propose the existence of a ubiquitin–CDK1 relay, where the disassembly of terminated replisomes increases CDK1 activity that, in turn, favors the ubiquitination and disassembly of more replisomes. This model has important implications for the mechanism of action of cancer therapies that induce the untimely activation of CDK1, thereby triggering premature replisome disassembly and DNA damage.
Collapse
|
11
|
Chang WT, Bow YD, Fu PJ, Li CY, Wu CY, Chang YH, Teng YN, Li RN, Lu MC, Liu YC, Chiu CC. A Marine Terpenoid, Heteronemin, Induces Both the Apoptosis and Ferroptosis of Hepatocellular Carcinoma Cells and Involves the ROS and MAPK Pathways. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:7689045. [PMID: 33488943 PMCID: PMC7803406 DOI: 10.1155/2021/7689045] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/27/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of death, resulting in over 700 thousand deaths annually worldwide. Chemotherapy is the primary therapeutic strategy for patients with late-stage HCC. Heteronemin is a marine natural product isolated from Hippospongia sp. that has been found to protect against carcinogenesis in cholangiocarcinoma, prostate cancer, and acute myeloid leukemia. In this study, heteronemin was found to inhibit the proliferation of the HCC cell lines HA22T and HA59T and induce apoptosis via the caspase pathway. Heteronemin treatment also induced the formation of reactive oxygen species (ROS), which are associated with heteronemin-induced cell death, and to trigger ROS removal by mitochondrial SOD2 rather than cytosolic SOD1. The mitogen-activated protein kinase (MAPK) signaling pathway was associated with ROS-induced cell death, and heteronemin downregulated the expression of ERK, a MAPK that is associated with cell proliferation. Inhibitors of JNK and p38, which are MAPKs associated with apoptosis, restored heteronemin-induced cell death. In addition, heteronemin treatment reduced the expression of GPX4, a protein that inhibits ferroptosis, which is a novel form of nonapoptotic programmed cell death. Ferroptosis inhibitor treatment also restored heteronemin-induced cell death. Thus, with appropriate structural modification, heteronemin can act as a potent therapeutic against HCC.
Collapse
Affiliation(s)
- Wen-Tsan Chang
- Division of General and Digestive Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Surgery, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Digestive Disease Center, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yung-Ding Bow
- Ph.D. Program in Life Sciences, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Pei-Jung Fu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chang-Yi Wu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Yi-Hua Chang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yen-Ni Teng
- Department of Biological Sciences and Technology, National University of Tainan, Tainan 700, Taiwan
| | - Ruei-Nian Li
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Mei-Chin Lu
- Graduate Institute of Marine Biotechnology, National Dong Hwa University, Pingtung 944, Taiwan
| | - Yi-Chang Liu
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Internal Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chien-Chih Chiu
- Center for Cancer Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
- The Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| |
Collapse
|
12
|
Heintzman DR, Campos LV, Byl JAW, Osheroff N, Dewar JM. Topoisomerase II Is Crucial for Fork Convergence during Vertebrate Replication Termination. Cell Rep 2020; 29:422-436.e5. [PMID: 31597101 PMCID: PMC6919565 DOI: 10.1016/j.celrep.2019.08.097] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/27/2019] [Accepted: 08/28/2019] [Indexed: 11/28/2022] Open
Abstract
Termination of DNA replication occurs when two replication forks converge upon the same stretch of DNA. Resolution of topological stress by topoisomerases is crucial for fork convergence in bacteria and viruses, but it is unclear whether similar mechanisms operate during vertebrate termination. Using Xenopus egg extracts, we show that topoisomerase II (Top2) resolves topological stress to prevent converging forks from stalling during termination. Under these conditions, stalling arises due to an inability to unwind the final stretch of DNA ahead of each fork. By promoting fork convergence, Top2 facilitates all downstream events of termination. Converging forks ultimately overcome stalling independently of Top2, indicating that additional mechanisms support fork convergence. Top2 acts throughout replication to prevent the accumulation of topological stress that would otherwise stall converging forks. Thus, termination poses evolutionarily conserved topological problems that can be mitigated by careful execution of the earlier stages of replication.
Collapse
Affiliation(s)
- Darren R Heintzman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lillian V Campos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Medicine (Hematology, Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| |
Collapse
|
13
|
Schvartzman JB, Hernández P, Krimer DB. Replication Fork Barriers and Topological Barriers: Progression of DNA Replication Relies on DNA Topology Ahead of Forks. Bioessays 2020; 42:e1900204. [PMID: 32115727 DOI: 10.1002/bies.201900204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/05/2020] [Indexed: 11/09/2022]
Abstract
During replication, the topology of DNA changes continuously in response to well-known activities of DNA helicases, polymerases, and topoisomerases. However, replisomes do not always progress at a constant speed and can slow-down and even stall at precise sites. The way these changes in the rate of replisome progression affect DNA topology is not yet well understood. The interplay of DNA topology and replication in several cases where progression of replication forks reacts differently to changes in DNA topology ahead is discussed here. It is proposed, there are at least two types of replication fork barriers: those that behave also as topological barriers and those that do not. Two-Dimensional (2D) agarose gel electrophoresis is the method of choice to distinguish between these two different types of replication fork barriers.
Collapse
Affiliation(s)
- Jorge B Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Dora B Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| |
Collapse
|
14
|
Schvartzman JB, Hernández P, Krimer DB, Dorier J, Stasiak A. Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes. Nucleic Acids Res 2019; 47:7182-7198. [PMID: 31276584 PMCID: PMC6698734 DOI: 10.1093/nar/gkz586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/20/2019] [Accepted: 07/02/2019] [Indexed: 01/28/2023] Open
Abstract
Due to helical structure of DNA, massive amounts of positive supercoils are constantly introduced ahead of each replication fork. Positive supercoiling inhibits progression of replication forks but various mechanisms evolved that permit very efficient relaxation of that positive supercoiling. Some of these mechanisms lead to interesting topological situations where DNA supercoiling, catenation and knotting coexist and influence each other in DNA molecules being replicated. Here, we first review fundamental aspects of DNA supercoiling, catenation and knotting when these qualitatively different topological states do not coexist in the same circular DNA but also when they are present at the same time in replicating DNA molecules. We also review differences between eukaryotic and prokaryotic cellular strategies that permit relaxation of positive supercoiling arising ahead of the replication forks. We end our review by discussing very recent studies giving a long-sought answer to the question of how slow DNA topoisomerases capable of relaxing just a few positive supercoils per second can counteract the introduction of hundreds of positive supercoils per second ahead of advancing replication forks.
Collapse
Affiliation(s)
- Jorge B Schvartzman
- Department of Cell and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Hernández
- Department of Cell and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Dora B Krimer
- Department of Cell and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Julien Dorier
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrzej Stasiak
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
15
|
Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint. PLoS One 2019; 14:e0224936. [PMID: 31747397 PMCID: PMC6867626 DOI: 10.1371/journal.pone.0224936] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/30/2019] [Indexed: 12/22/2022] Open
Abstract
The restricted access of regulatory factors to their binding sites on DNA wrapped around the nucleosomes is generally interpreted in terms of molecular shielding exerted by nucleosomal structure and internucleosomal interactions. Binding of proteins to DNA often includes intercalation of hydrophobic amino acids into the DNA. To assess the role of constrained superhelicity in limiting these interactions, we studied the binding of small molecule intercalators to chromatin in close to native conditions by laser scanning cytometry. We demonstrate that the nucleosome-constrained superhelical configuration of DNA is the main barrier to intercalation. As a result, intercalating compounds are virtually excluded from the nucleosome-occupied regions of the chromatin. Binding of intercalators to extranucleosomal regions is limited to a smaller degree, in line with the existence of net supercoiling in the regions comprising linker and nucleosome free DNA. Its relaxation by inducing as few as a single nick per ~50 kb increases intercalation in the entire chromatin loop, demonstrating the possibility for long-distance effects of regulatory potential.
Collapse
|
16
|
Cell Cycle-Dependent Control and Roles of DNA Topoisomerase II. Genes (Basel) 2019; 10:genes10110859. [PMID: 31671531 PMCID: PMC6896119 DOI: 10.3390/genes10110859] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes in all branches of life that can alter DNA superhelicity and unlink double-stranded DNA segments during processes such as replication and transcription. In cells, type II topoisomerases are particularly useful for their ability to disentangle newly-replicated sister chromosomes. Growing lines of evidence indicate that eukaryotic topoisomerase II (topo II) activity is monitored and regulated throughout the cell cycle. Here, we discuss the various roles of topo II throughout the cell cycle, as well as mechanisms that have been found to govern and/or respond to topo II function and dysfunction. Knowledge of how topo II activity is controlled during cell cycle progression is important for understanding how its misregulation can contribute to genetic instability and how modulatory pathways may be exploited to advance chemotherapeutic development.
Collapse
|
17
|
Atkin ND, Raimer HM, Wang YH. Broken by the Cut: A Journey into the Role of Topoisomerase II in DNA Fragility. Genes (Basel) 2019; 10:E791. [PMID: 31614754 PMCID: PMC6826763 DOI: 10.3390/genes10100791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023] Open
Abstract
DNA topoisomerase II (TOP2) plays a critical role in many processes such as replication and transcription, where it resolves DNA structures and relieves torsional stress. Recent evidence demonstrated the association of TOP2 with topologically associated domains (TAD) boundaries and CCCTC-binding factor (CTCF) binding sites. At these sites, TOP2 promotes interactions between enhancers and gene promoters, and relieves torsional stress that accumulates at these physical barriers. Interestingly, in executing its enzymatic function, TOP2 contributes to DNA fragility through re-ligation failure, which results in persistent DNA breaks when unrepaired or illegitimately repaired. Here, we discuss the biological processes for which TOP2 is required and the steps at which it can introduce DNA breaks. We describe the repair processes that follow removal of TOP2 adducts and the resultant broken DNA ends, and present how these processes can contribute to disease-associated mutations. Furthermore, we examine the involvement of TOP2-induced breaks in the formation of oncogenic translocations of leukemia and papillary thyroid cancer, as well as the role of TOP2 and proteins which repair TOP2 adducts in other diseases. The participation of TOP2 in generating persistent DNA breaks and leading to diseases such as cancer, could have an impact on disease treatment and prevention.
Collapse
Affiliation(s)
- Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
| | - Heather M Raimer
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
| |
Collapse
|
18
|
Abstract
Genome replication involves dealing with obstacles that can result from DNA damage but also from chromatin alterations, topological stress, tightly bound proteins or non-B DNA structures such as R loops. Experimental evidence reveals that an engaged transcription machinery at the DNA can either enhance such obstacles or be an obstacle itself. Thus, transcription can become a potentially hazardous process promoting localized replication fork hindrance and stress, which would ultimately cause genome instability, a hallmark of cancer cells. Understanding the causes behind transcription-replication conflicts as well as how the cell resolves them to sustain genome integrity is the aim of this review.
Collapse
|
19
|
Deegan TD, Baxter J, Ortiz Bazán MÁ, Yeeles JTP, Labib KPM. Pif1-Family Helicases Support Fork Convergence during DNA Replication Termination in Eukaryotes. Mol Cell 2019; 74:231-244.e9. [PMID: 30850330 PMCID: PMC6477153 DOI: 10.1016/j.molcel.2019.01.040] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/26/2018] [Accepted: 01/29/2019] [Indexed: 01/21/2023]
Abstract
The convergence of two DNA replication forks creates unique problems during DNA replication termination. In E. coli and SV40, the release of torsional strain by type II topoisomerases is critical for converging replisomes to complete DNA synthesis, but the pathways that mediate fork convergence in eukaryotes are unknown. We studied the convergence of reconstituted yeast replication forks that include all core replisome components and both type I and type II topoisomerases. We found that most converging forks stall at a very late stage, indicating a role for additional factors. We showed that the Pif1 and Rrm3 DNA helicases promote efficient fork convergence and completion of DNA synthesis, even in the absence of type II topoisomerase. Furthermore, Rrm3 and Pif1 are also important for termination of plasmid DNA replication in vivo. These findings identify a eukaryotic pathway for DNA replication termination that is distinct from previously characterized prokaryotic mechanisms.
Collapse
Affiliation(s)
- Tom D Deegan
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Jonathan Baxter
- Genome Damage and Stability Centre, Department of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - María Ángeles Ortiz Bazán
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Joseph T P Yeeles
- The MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Karim P M Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| |
Collapse
|
20
|
Nelson WG, Haffner MC, Yegnasubramanian S. The structure of the nucleus in normal and neoplastic prostate cells: untangling the role of type 2 DNA topoisomerases. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2018; 6:107-113. [PMID: 29666839 PMCID: PMC5902729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Donald S. Coffey, a pioneer in the study of the structural basis of mammalian genome organization, was fascinated by DNA topoisomerases, chemo-mechanical enzymes that could catalyze changes in DNA structure. Work initiated in his laboratory and carried on with his influence and inspiration has led to the elucidation of specific roles for each of the two type 2 topoisomerases in DNA replication, RNA transcription, and androgen action in prostate cells. TOP2A principally acts in DNA synthesis elongation to prevent tangling of daughter DNA molecules during genome replication and mitotic segregation; TOP2B is required for androgen-stimulation of target gene transcription. DNA double-strand breaks inflicted by TOP2B upon androgen exposure appear responsible for the generation of TMPRSS2-ERG and other gene fusions, often found in complex chained rearrangements termed chromoplexy, in prostate cancer cells. TOP2B-mediated genome damage may also provide an avenue for improving prostate cancer treatment via timed androgen administration in conjunction with ionizing radiation, with TOP2-targeted drugs, or with DNA repair inhibitors.
Collapse
Affiliation(s)
- William G Nelson
- Sidney Kimmel Comprehensive Cancer Center and Brady Urological Institute, Johns Hopkins University School of MedicineBaltimore, MD 21218, USA
| | - Michael C Haffner
- Sidney Kimmel Comprehensive Cancer Center and Brady Urological Institute, Johns Hopkins University School of MedicineBaltimore, MD 21218, USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center and Brady Urological Institute, Johns Hopkins University School of MedicineBaltimore, MD 21218, USA
| |
Collapse
|
21
|
Abstract
DNA topoisomerases are proven therapeutic targets of antibacterial agents. Quinolones, especially fluoroquinolones, are the most successful topoisomerase-targeting antibacterial drugs. These drugs target type IIA topoisomerases in bacteria. Recent structural and biochemical studies on fluoroquinolones have provided the molecular basis for both their mechanism of action, as well as the molecular basis of bacterial resistance. Due to the development of drug resistance, including fluoroquinolone resistance, among bacterial pathogens, there is an urgent need to discover novel antibacterial agents. Recent advances in topoisomerase inhibitors may lead to the development of novel antibacterial drugs that are effective against fluoroquinolone-resistant pathogens. They include type IIA topoisomerase inhibitors that either interact with the GyrB/ParE subunit or form nick-containing ternary complexes. In addition, several topoisomerase I inhibitors have recently been identified. Thus, DNA topoisomerases remain important targets of antibacterial agents.
Collapse
|
22
|
Mariezcurrena A, Uhlmann F. Observation of DNA intertwining along authentic budding yeast chromosomes. Genes Dev 2017; 31:2151-2161. [PMID: 29208645 PMCID: PMC5749163 DOI: 10.1101/gad.305557.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022]
Abstract
DNA replication of circular genomes generates physically interlinked or catenated sister DNAs. These are resolved through transient DNA fracture by type II topoisomerases to permit chromosome segregation during cell division. Topoisomerase II is similarly required for linear chromosome segregation, suggesting that linear chromosomes also remain intertwined following DNA replication. Indeed, chromosome resolution defects are a frequent cause of chromosome segregation failure and consequent aneuploidies. When and where intertwines arise and persist along linear chromosomes are not known, owing to the difficulty of demonstrating intertwining of linear DNAs. Here, we used excision of chromosomal regions as circular "loop outs" to convert sister chromatid intertwines into catenated circles. This revealed intertwining at replication termination and cohesin-binding sites, where intertwines are thought to arise and persist but not to a greater extent than elsewhere in the genome. Intertwining appears to spread evenly along chromosomes but is excluded from heterochromatin. We found that intertwines arise before replication termination, suggesting that replication forks rotate during replication elongation to dissipate torsion ahead of the forks. Our approach provides previously inaccessible insight into the topology of eukaryotic chromosomes and illuminates a process critical for successful chromosome segregation.
Collapse
Affiliation(s)
- Ainhoa Mariezcurrena
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| |
Collapse
|
23
|
Khan FA, Ali SO. Physiological Roles of DNA Double-Strand Breaks. J Nucleic Acids 2017; 2017:6439169. [PMID: 29181194 PMCID: PMC5664317 DOI: 10.1155/2017/6439169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/24/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic integrity is constantly threatened by sources of DNA damage, internal and external alike. Among the most cytotoxic lesions is the DNA double-strand break (DSB) which arises from the cleavage of both strands of the double helix. Cells boast a considerable set of defences to both prevent and repair these breaks and drugs which derail these processes represent an important category of anticancer therapeutics. And yet, bizarrely, cells deploy this very machinery for the intentional and calculated disruption of genomic integrity, harnessing potentially destructive DSBs in delicate genetic transactions. Under tight spatiotemporal regulation, DSBs serve as a tool for genetic modification, widely used across cellular biology to generate diverse functionalities, ranging from the fundamental upkeep of DNA replication, transcription, and the chromatin landscape to the diversification of immunity and the germline. Growing evidence points to a role of aberrant DSB physiology in human disease and an understanding of these processes may both inform the design of new therapeutic strategies and reduce off-target effects of existing drugs. Here, we review the wide-ranging roles of physiological DSBs and the emerging network of their multilateral regulation to consider how the cell is able to harness DNA breaks as a critical biochemical tool.
Collapse
Affiliation(s)
- Farhaan A. Khan
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
| | - Syed O. Ali
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
| |
Collapse
|
24
|
Zilio N, Eifler-Olivi K, Ulrich HD. Functions of SUMO in the Maintenance of Genome Stability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:51-87. [PMID: 28197906 DOI: 10.1007/978-3-319-50044-7_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like in most other areas of cellular metabolism, the functions of the ubiquitin-like modifier SUMO in the maintenance of genome stability are manifold and varied. Perturbations of global sumoylation causes a wide spectrum of phenotypes associated with defects in DNA maintenance, such as hypersensitivity to DNA-damaging agents, gross chromosomal rearrangements and loss of entire chromosomes. Consistent with these observations, many key factors involved in various DNA repair pathways have been identified as SUMO substrates. However, establishing a functional connection between a given SUMO target, the cognate SUMO ligase and a relevant phenotype has remained a challenge, mainly because of the difficulties involved in identifying important modification sites and downstream effectors that specifically recognize the target in its sumoylated state. This review will give an overview over the major pathways of DNA repair and genome maintenance influenced by the SUMO system and discuss selected examples of SUMO's actions in these pathways where the biological consequences of the modification have been elucidated.
Collapse
Affiliation(s)
- Nicola Zilio
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | | | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.
| |
Collapse
|
25
|
Puddu F, Salguero I, Herzog M, Geisler NJ, Costanzo V, Jackson SP. Chromatin determinants impart camptothecin sensitivity. EMBO Rep 2017; 18:1000-1012. [PMID: 28389464 PMCID: PMC5452016 DOI: 10.15252/embr.201643560] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 11/09/2022] Open
Abstract
Camptothecin-induced locking of topoisomerase 1 on DNA generates a physical barrier to replication fork progression and creates topological stress. By allowing replisome rotation, absence of the Tof1/Csm3 complex promotes the conversion of impending topological stress to DNA catenation and causes camptothecin hypersensitivity. Through synthetic viability screening, we discovered that histone H4 K16 deacetylation drives the sensitivity of yeast cells to camptothecin and that inactivation of this pathway by mutating H4 K16 or the genes SIR1-4 suppresses much of the hypersensitivity of tof1∆ strains towards this agent. We show that disruption of rDNA or telomeric silencing does not mediate camptothecin resistance but that disruption of Sir1-dependent chromatin domains is sufficient to suppress camptothecin sensitivity in wild-type and tof1∆ cells. We suggest that topoisomerase 1 inhibition in proximity of these domains causes topological stress that leads to DNA hypercatenation, especially in the absence of the Tof1/Csm3 complex. Finally, we provide evidence of the evolutionarily conservation of this mechanism.
Collapse
Affiliation(s)
- Fabio Puddu
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Israel Salguero
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mareike Herzog
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton Cambridge, UK
| | - Nicola J Geisler
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vincenzo Costanzo
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy
| | - Stephen P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
26
|
Chan PF, Germe T, Bax BD, Huang J, Thalji RK, Bacqué E, Checchia A, Chen D, Cui H, Ding X, Ingraham K, McCloskey L, Raha K, Srikannathasan V, Maxwell A, Stavenger RA. Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase. Proc Natl Acad Sci U S A 2017; 114:E4492-E4500. [PMID: 28507124 PMCID: PMC5465892 DOI: 10.1073/pnas.1700721114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones. Although fluoroquinolones stabilize double-stranded DNA breaks, the antibacterial thiophenes stabilize gyrase-mediated DNA-cleavage complexes in either one DNA strand or both DNA strands. X-ray crystallography of DNA gyrase-DNA complexes shows the compounds binding to a protein pocket between the winged helix domain and topoisomerase-primase domain, remote from the DNA. Mutations of conserved residues around this pocket affect activity of the thiophene inhibitors, consistent with allosteric inhibition of DNA gyrase. This druggable pocket provides potentially complementary opportunities for targeting bacterial topoisomerases for antibiotic development.
Collapse
Affiliation(s)
- Pan F Chan
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426;
| | - Thomas Germe
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Benjamin D Bax
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Jianzhong Huang
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Reema K Thalji
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Eric Bacqué
- Therapeutic Strategic Unit Infectious Diseases, Sanofi Research & Development, 69280, Marcy L'Etoile, France
| | - Anna Checchia
- Aptuit Center of Drug Discovery and Development, 37135, Verona, Italy
| | - Dongzhao Chen
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Haifeng Cui
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Xiao Ding
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Karen Ingraham
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Lynn McCloskey
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Kaushik Raha
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Velupillai Srikannathasan
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert A Stavenger
- Antibacterial Discovery Performance Unit, Infectious Diseases Therapy Area Unit, GlaxoSmithKline, Collegeville, PA 19426;
| |
Collapse
|
27
|
Abstract
Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation. We briefly review the mechanism of termination in the bacterium Escherichia coli and in simian virus 40 (SV40) and also focus on recent advances in eukaryotic replication termination. In particular, we discuss the recently discovered E3 ubiquitin ligases that control replisome disassembly in yeast and higher eukaryotes, and how their activity is regulated to avoid genome instability.
Collapse
|
28
|
Gambus A. Termination of Eukaryotic Replication Forks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:163-187. [DOI: 10.1007/978-981-10-6955-0_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
29
|
Kelly T. Historical Perspective of Eukaryotic DNA Replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:1-41. [PMID: 29357051 DOI: 10.1007/978-981-10-6955-0_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The replication of the genome of a eukaryotic cell is a complex process requiring the ordered assembly of multiprotein replisomes at many chromosomal sites. The process is strictly controlled during the cell cycle to ensure the complete and faithful transmission of genetic information to progeny cells. Our current understanding of the mechanisms of eukaryotic DNA replication has evolved over a period of more than 30 years through the efforts of many investigators. The aim of this perspective is to provide a brief history of the major advances during this period.
Collapse
Affiliation(s)
- Thomas Kelly
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
30
|
Pommier Y, Sun Y, Huang SYN, Nitiss JL. Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat Rev Mol Cell Biol 2016; 17:703-721. [DOI: 10.1038/nrm.2016.111] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
31
|
Bates D, Pettitt BM, Buck GR, Zechiedrich L. Importance of disentanglement and entanglement during DNA replication and segregation: Comment on: "Disentangling DNA molecules" by Alexander Vologodskii. Phys Life Rev 2016; 18:160-164. [PMID: 27666770 DOI: 10.1016/j.plrev.2016.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/08/2016] [Indexed: 10/21/2022]
Affiliation(s)
- David Bates
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gregory R Buck
- Department of Mathematics, St. Anselm College, Manchester, NH, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
32
|
MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation. Nat Commun 2016; 7:10466. [PMID: 26818444 PMCID: PMC4738335 DOI: 10.1038/ncomms10466] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/11/2015] [Indexed: 01/08/2023] Open
Abstract
The Escherichia coli SMC complex, MukBEF, forms clusters of molecules that interact with the decatenase topisomerase IV and which are normally associated with the chromosome replication origin region (ori). Here we demonstrate an additional ATP-hydrolysis-dependent association of MukBEF with the replication termination region (ter). Consistent with this, MukBEF interacts with MatP, which binds matS sites in ter. MatP displaces wild-type MukBEF complexes from ter, thereby facilitating their association with ori, and limiting the availability of topoisomerase IV (TopoIV) at ter. Displacement of MukBEF is impaired when MukB ATP hydrolysis is compromised and when MatP is absent, leading to a stable association of ter and MukBEF. Impairing the TopoIV-MukBEF interaction delays sister ter segregation in cells lacking MatP. We propose that the interplay between MukBEF and MatP directs chromosome organization in relation to MukBEF clusters and associated topisomerase IV, thereby ensuring timely chromosome unlinking and segregation. MukBEF, the bacterial structural maintenance of chromosomes complex, is known to associate with origins of replication and topoisomerase IV. Here the authors show an association of MukBEF with MatP and replication termination regions, important for proper sister chromatid decatenation and segregation.
Collapse
|
33
|
Dewar JM, Budzowska M, Walter JC. The mechanism of DNA replication termination in vertebrates. Nature 2015; 525:345-50. [PMID: 26322582 PMCID: PMC4575634 DOI: 10.1038/nature14887] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 07/01/2015] [Indexed: 12/18/2022]
Abstract
Eukaryotic DNA replication terminates when replisomes from adjacent replication origins converge. Termination involves local completion of DNA synthesis, decatenation of daughter molecules, and replisome disassembly. Termination has been difficult to study because termination events are generally asynchronous and sequence non-specific. To overcome these challenges, we paused converging replisomes with a site-specific barrier in Xenopus egg extracts. Upon removal of the barrier, forks underwent synchronous and site-specific termination, allowing mechanistic dissection of this process. We show that DNA synthesis does not slow detectably as forks approach each other and that leading strands pass each other unhindered before undergoing ligation to downstream lagging strands. Dissociation of CMG helicases occurs only after the final ligation step, and is not required for completion of DNA synthesis, strongly suggesting that converging CMGs pass one another and dissociate from double-stranded DNA. This termination mechanism allows rapid completion of DNA synthesis while avoiding premature replisome disassembly
Collapse
Affiliation(s)
- James M Dewar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Magda Budzowska
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
34
|
Schalbetter SA, Mansoubi S, Chambers AL, Downs JA, Baxter J. Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proc Natl Acad Sci U S A 2015; 112:E4565-70. [PMID: 26240319 PMCID: PMC4547287 DOI: 10.1073/pnas.1505356112] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Faithful genome duplication and inheritance require the complete resolution of all intertwines within the parental DNA duplex. This is achieved by topoisomerase action ahead of the replication fork or by fork rotation and subsequent resolution of the DNA precatenation formed. Although fork rotation predominates at replication termination, in vitro studies have suggested that it also occurs frequently during elongation. However, the factors that influence fork rotation and how rotation and precatenation may influence other replication-associated processes are unknown. Here we analyze the causes and consequences of fork rotation in budding yeast. We find that fork rotation and precatenation preferentially occur in contexts that inhibit topoisomerase action ahead of the fork, including stable protein-DNA fragile sites and termination. However, generally, fork rotation and precatenation are actively inhibited by Timeless/Tof1 and Tipin/Csm3. In the absence of Tof1/Timeless, excessive fork rotation and precatenation cause extensive DNA damage following DNA replication. With Tof1, damage related to precatenation is focused on the fragile protein-DNA sites where fork rotation is induced. We conclude that although fork rotation and precatenation facilitate unwinding in hard-to-replicate contexts, they intrinsically disrupt normal chromosome duplication and are therefore restricted by Timeless/Tipin.
Collapse
Affiliation(s)
- Stephanie A Schalbetter
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Sahar Mansoubi
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Anna L Chambers
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom; School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Jessica A Downs
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Jonathan Baxter
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom;
| |
Collapse
|
35
|
Cebrián J, Castán A, Martínez V, Kadomatsu-Hermosa MJ, Parra C, Fernández-Nestosa MJ, Schaerer C, Hernández P, Krimer DB, Schvartzman JB. Direct Evidence for the Formation of Precatenanes during DNA Replication. J Biol Chem 2015; 290:13725-35. [PMID: 25829493 PMCID: PMC4447951 DOI: 10.1074/jbc.m115.642272] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/30/2015] [Indexed: 11/06/2022] Open
Abstract
The dynamics of DNA topology during replication are still poorly understood. Bacterial plasmids are negatively supercoiled. This underwinding facilitates strand separation of the DNA duplex during replication. Leading the replisome, a DNA helicase separates the parental strands that are to be used as templates. This strand separation causes overwinding of the duplex ahead. If this overwinding persists, it would eventually impede fork progression. In bacteria, DNA gyrase and topoisomerase IV act ahead of the fork to keep DNA underwound. However, the processivity of the DNA helicase might overcome DNA gyrase and topoisomerase IV. It was proposed that the overwinding that builds up ahead of the fork could force it to swivel and diffuse this positive supercoiling behind the fork where topoisomerase IV would also act to maintain replicating the DNA underwound. Putative intertwining of sister duplexes in the replicated region are called precatenanes. Fork swiveling and the formation of precatenanes, however, are still questioned. Here, we used classical genetics and high resolution two-dimensional agarose gel electrophoresis to examine the torsional tension of replication intermediates of three bacterial plasmids with the fork stalled at different sites before termination. The results obtained indicated that precatenanes do form as replication progresses before termination.
Collapse
Affiliation(s)
- Jorge Cebrián
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| | - Alicia Castán
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| | - Víctor Martínez
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - Maridian J Kadomatsu-Hermosa
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - Cristina Parra
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - María José Fernández-Nestosa
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - Christian Schaerer
- the Scientific and Applied Computing Laboratory, Polytechnic School, National University of Asunción. P.O. Box 2111 SL. San Lorenzo, Paraguay
| | - Pablo Hernández
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| | - Dora B Krimer
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| | - Jorge B Schvartzman
- From the Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040, Madrid, Spain and
| |
Collapse
|
36
|
Abstract
To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component – Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.
Collapse
Key Words
- CMG, Cdc45, Mcm2–7, GINS complex
- CRL, cullin-RING ligase
- D loop, displacement loop
- DDR, DNA damage response
- DNA replication
- DSB, double strand break
- DUB, deubiquitylating enzyme
- ER, endoplasmic reticulum
- ERAD, endoplasmic reticulum associated protein degradation
- GINS, Go-Ichi-Ni-San, complex made of Sld5, Psf1, Psf2, Psf3
- ICL, intra-strand crosslink
- MCM, Minichromosome maintenance
- Mcm2–7
- OriC, chromosomal replication origin
- R loop, RNA:DNA hybrid
- RING, really interesting gene
- RPC, Replisome Progression Complex
- Ter, termination site
- Tus-Ter, terminus utilisation substance - termination
- Xenopus
- p97 segregase
- replication termination
- replicative helicase
- replisome
- ubiquitin
Collapse
Affiliation(s)
- Rachael Bailey
- a School of Cancer Sciences; University of Birmingham ; Birmingham , UK
| | | | | |
Collapse
|
37
|
Baxter J. “Breaking Up Is Hard to Do”: The Formation and Resolution of Sister Chromatid Intertwines. J Mol Biol 2015; 427:590-607. [DOI: 10.1016/j.jmb.2014.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/08/2014] [Accepted: 08/20/2014] [Indexed: 10/24/2022]
|
38
|
Sowd GA, Mody D, Eggold J, Cortez D, Friedman KL, Fanning E. SV40 utilizes ATM kinase activity to prevent non-homologous end joining of broken viral DNA replication products. PLoS Pathog 2014; 10:e1004536. [PMID: 25474690 PMCID: PMC4256475 DOI: 10.1371/journal.ppat.1004536] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/23/2014] [Indexed: 11/18/2022] Open
Abstract
Simian virus 40 (SV40) and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PKcs kinase activity, facilitates some aspects of double strand break (DSB) repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR) and do not colocalize with non-homologous end joining (NHEJ) factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PKcs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5′ to 3′ end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication. Viruses from both Polyomaviridae and Papillomaviridae families share several characteristics. These include common modes of DNA replication and an accumulation of DNA damage signaling and repair proteins at replicating viral DNA. Several DNA repair proteins, with unknown functions during viral DNA replication, associate with the viral replication centers of the polyomavirus simian virus 40 (SV40). In this study we examined the mechanisms that regulate and recruit DNA repair machinery to replicating viral DNA during permissive SV40 infection. We found that the virus deploys DNA repair to broken viral DNA using cellular DNA damage signaling pathways. Our results shed light on why both Polyomaviridae and Papillomaviridae DNA replication elicits DNA damage signaling and repair. As no effective treatments currently exist for the Polyomaviridae family, our data identify pathways that might be therapeutically targeted to inhibit productive viral replication. Additionally, we categorize distinct functions for DNA repair and damage signaling pathways during viral replication. The results provide insights into how viruses exploit cellular processes to overwhelm the cell and propagate.
Collapse
Affiliation(s)
- Gregory A. Sowd
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (GAS); (KLF)
| | - Dviti Mody
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Joshua Eggold
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Katherine L. Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (GAS); (KLF)
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| |
Collapse
|
39
|
Abstract
DNA topology changes dynamically during DNA replication. Supercoiling, precatenation, catenation and knotting interplay throughout the process that is finely regulated by DNA topoisomerases. In the present article, we provide an overview of theoretical and experimental approaches to understand the interplay between various manifestations of topological constraints acting on replicating DNA molecules. Data discussed reveal that DNA entanglements (supercoils and catenanes) play an active role in preventing the formation of deleterious knots.
Collapse
|
40
|
Gaggioli V, Le Viet B, Germe T, Hyrien O. DNA topoisomerase IIα controls replication origin cluster licensing and firing time in Xenopus egg extracts. Nucleic Acids Res 2013; 41:7313-31. [PMID: 23757188 PMCID: PMC3753627 DOI: 10.1093/nar/gkt494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sperm chromatin incubated in Xenopus egg extracts undergoes origin licensing and nuclear assembly before DNA replication. We found that depletion of DNA topoisomerase IIα (topo IIα), the sole topo II isozyme of eggs and its inhibition by ICRF-193, which clamps topo IIα around DNA have opposite effects on these processes. ICRF-193 slowed down replication origin cluster activation and fork progression in a checkpoint-independent manner, without altering replicon size. In contrast, topo IIα depletion accelerated origin cluster activation, and topo IIα add-back negated overinitiation. Therefore, topo IIα is not required for DNA replication, but topo IIα clamps slow replication, probably by forming roadblocks. ICRF-193 had no effect on DNA synthesis when added after nuclear assembly, confirming that topo IIα activity is dispensable for replication and revealing that topo IIα clamps formed on replicating DNA do not block replication, presumably because topo IIα acts behind and not in front of forks. Topo IIα depletion increased, and topo IIα addition reduced, chromatin loading of MCM2-7 replicative helicase, whereas ICRF-193 did not affect MCM2-7 loading. Therefore, topo IIα restrains MCM2-7 loading in an ICRF-193-resistant manner during origin licensing, suggesting a model for establishing the sequential firing of origin clusters.
Collapse
Affiliation(s)
- Vincent Gaggioli
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), S2-Génomique Fonctionnelle, CNRS UMR8197, Inserm U1024, 46 rue d'Ulm, 75005 Paris, France
| | | | | | | |
Collapse
|
41
|
Yang H, Liu C, Jamsen J, Wu Z, Wang Y, Chen J, Zheng L, Shen B. The DNase domain-containing protein TATDN1 plays an important role in chromosomal segregation and cell cycle progression during zebrafish eye development. Cell Cycle 2012. [PMID: 23187801 DOI: 10.4161/cc.22886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The DNase domain-containing protein TATDN1 is a conserved nuclease in both prokaryotes and eukaryotes. It was previously implicated to play a role in apoptotic DNA fragmentation in yeast and C. elegans. However, its biological function in higher organisms, such as vertebrates, is unknown. Here, we report that zebrafish TATDN1 (zTATDN1) possesses a novel endonuclease activity, which first makes a nick at the DNA duplex and subsequently converts the nick into a DNA double-strand break in vitro. This biochemical property allows zTATDN1 to catalyze decatenation of catenated kinetoplast DNA to produce separated linear DNA in vitro. We further determine that zTATDN1 is predominantly expressed in eye cells during embryonic development. Knockdown of TATDN1 in zebrafish embryos results in an abnormal cell cycle progression, formation of polyploidy and aberrant chromatin structures. Consequently, the TATDN1-deficient morphants have disordered eye cell layers and significantly smaller eyes compared with the WT control. Altogether, our current studies suggest that zTATDN1 plays an important role in chromosome segregation and eye development in zebrafish.
Collapse
Affiliation(s)
- Hui Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Bulgar AD, Weeks LD, Miao Y, Yang S, Xu Y, Guo C, Markowitz S, Oleinick N, Gerson SL, Liu L. Removal of uracil by uracil DNA glycosylase limits pemetrexed cytotoxicity: overriding the limit with methoxyamine to inhibit base excision repair. Cell Death Dis 2012; 3:e252. [PMID: 22237209 PMCID: PMC3270269 DOI: 10.1038/cddis.2011.135] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/09/2011] [Accepted: 11/09/2011] [Indexed: 01/03/2023]
Abstract
Uracil DNA glycosylase (UDG) specifically removes uracil bases from DNA, and its repair activity determines the sensitivity of the cell to anticancer agents that are capable of introducing uracil into DNA. In the present study, the participation of UDG in the response to pemetrexed-induced incorporation of uracil into DNA was studied using isogenic human tumor cell lines with or without UDG (UDG(+/+)/UDG(-/-)). UDG(-/-) cells were very sensitive to pemetrexed. Cell killing by pemetrexed was associated with genomic uracil accumulation, stalled DNA replication, and catastrophic DNA strand breaks. By contrast, UDG(+/+) cells were >10 times more resistant to pemetrexed due to the rapid removal of uracil from DNA by UDG and subsequent repair of the resultant AP sites (abasic sites) via the base excision repair (BER). The resistance to pemetrexed in UDG(+/+) cells could be reversed by the addition of methoxyamine (MX), which binds to AP sites and interrupts BER pathway. Furthermore, MX-bound AP sites induced cell death was related to their cytotoxic effect of dual inactivation of UDG and topoisomerase IIα, two genes that are highly expressed in lung cancer cells in comparison with normal cells. Thus, targeting BER-based therapy exhibits more selective cytotoxicity on cancer cells through a synthetic lethal mechanism.
Collapse
Affiliation(s)
- A D Bulgar
- Department of Medicine, Division of Hematology/Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - L D Weeks
- Department of Medicine, Division of Hematology/Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - Y Miao
- Department of Medicine, Division of Hematology/Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - S Yang
- Case Comprehensive Cancer Center, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Y Xu
- Case Comprehensive Cancer Center, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - C Guo
- Department of Medicine, Division of Hematology/Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - S Markowitz
- Department of Medicine, Division of Hematology/Oncology, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
- Department of Genetics, Case Western Reserve University, Cleveland, OH, USA
| | - N Oleinick
- Case Comprehensive Cancer Center, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
- Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - S L Gerson
- Department of Medicine, Division of Hematology/Oncology, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - L Liu
- Department of Medicine, Division of Hematology/Oncology, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| |
Collapse
|
43
|
López V, Martínez-Robles ML, Hernández P, Krimer DB, Schvartzman JB. Topo IV is the topoisomerase that knots and unknots sister duplexes during DNA replication. Nucleic Acids Res 2011; 40:3563-73. [PMID: 22187153 PMCID: PMC3333868 DOI: 10.1093/nar/gkr1237] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA topology plays a crucial role in all living cells. In prokaryotes, negative supercoiling is required to initiate replication and either negative or positive supercoiling assists decatenation. The role of DNA knots, however, remains a mystery. Knots are very harmful for cells if not removed efficiently, but DNA molecules become knotted in vivo. If knots are deleterious, why then does DNA become knotted? Here, we used classical genetics, high-resolution 2D agarose gel electrophoresis and atomic force microscopy to show that topoisomerase IV (Topo IV), one of the two type-II DNA topoisomerases in bacteria, is responsible for the knotting and unknotting of sister duplexes during DNA replication. We propose that when progression of the replication forks is impaired, sister duplexes become loosely intertwined. Under these conditions, Topo IV inadvertently makes the strand passages that lead to the formation of knots and removes them later on to allow their correct segregation.
Collapse
Affiliation(s)
| | | | | | | | - Jorge B. Schvartzman
- *To whom correspondence should be addressed. Tel: +34 91 837 3112 (ext. 4232); Fax: +34 91 536 0432;
| |
Collapse
|
44
|
Timsit Y. Local sensing of global DNA topology: from crossover geometry to type II topoisomerase processivity. Nucleic Acids Res 2011; 39:8665-76. [PMID: 21764774 PMCID: PMC3203592 DOI: 10.1093/nar/gkr556] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes that control the topology and higher order structures of DNA. Type IIA enzymes have the remarkable property to sense locally the global DNA topology. Although many theoretical models have been proposed, the molecular mechanism of chiral discrimination is still unclear. While experimental studies have established that topoisomerases IIA discriminate topology on the basis of crossover geometry, a recent single-molecule experiment has shown that the enzyme has a different processivity on supercoiled DNA of opposite sign. Understanding how cross-over geometry influences enzyme processivity is, therefore, the key to elucidate the mechanism of chiral discrimination. Analysing this question from the DNA side reveals first, that the different stability of chiral DNA cross-overs provides a way to locally sense the global DNA topology. Second, it shows that these enzymes have evolved to recognize the G- and T-segments stably assembled into a right-handed cross-over. Third, it demonstrates how binding right-handed cross-overs across their large angle imposes a different topological link between the topoIIA rings and the plectonemes of opposite sign thus directly affecting the enzyme freedom of motion and processivity. In bridging geometry and kinetic data, this study brings a simple solution for type IIA topoisomerase chiral discrimination.
Collapse
Affiliation(s)
- Youri Timsit
- Information Génomique et Structurale, CNRS - UPR2589, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, Parc Scientifique de Luminy, Marseille, France
| |
Collapse
|
45
|
Gardner L, Malik R, Shimizu Y, Mullins N, ElShamy WM. Geminin overexpression prevents the completion of topoisomerase IIα chromosome decatenation, leading to aneuploidy in human mammary epithelial cells. Breast Cancer Res 2011; 13:R53. [PMID: 21595939 PMCID: PMC3218940 DOI: 10.1186/bcr2884] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 04/16/2011] [Accepted: 05/19/2011] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION The nuclear enzyme topoisomerase IIα (TopoIIα) is able to cleave DNA in a reversible manner, making it a valuable target for agents such as etoposide that trap the enzyme in a covalent bond with the 5' DNA end to which it cleaves. This prevents DNA religation and triggers cell death in cancer cells. However, development of resistance to these agents limits their therapeutic use. In this study, we examined the therapeutic targeting of geminin for improving the therapeutic potential of TopoIIα agents. METHODS Human mammary epithelial (HME) cells and several breast cancer cell lines were used in this study. Geminin, TopoIIα and cell division cycle 7 (Cdc7) silencing were done using specific small interfering RNA. Transit or stable inducible overexpression of these proteins and casein kinase Iε (CKIε) were also used, as well as several pharmacological inhibitors that target TopoIIα, Cdc7 or CKIε. We manipulated HME cells that expressed H2B-GFP, or did not, to detect chromosome bridges. Immunoprecipitation and direct Western blot analysis were used to detect interactions between these proteins and their total expression, respectively, whereas interactions on chromosomal arms were detected using a trapped in agarose DNA immunostaining assay. TopoIIα phosphorylation by Cdc7 or CKIε was done using an in vitro kinase assay. The TopoGen decatenation kit was used to measure TopoIIα decatenation activity. Finally, a comet assay and metaphase chromosome spread were used to detect chromosome breakage and changes in chromosome condensation or numbers, respectively. RESULTS We found that geminin and TopoIIα interact primarily in G2/M/early G1 cells on chromosomes, that geminin recruits TopoIIα to chromosomal decatenation sites or vice versa and that geminin silencing in HME cells triggers the formation of chromosome bridges by suppressing TopoIIα access to chromosomal arms. CKIε kinase phosphorylates and positively regulates TopoIIα chromosome localization and function. CKIε kinase overexpression or Cdc7 kinase silencing, which we show phosphorylates TopoIIα in vitro, restored DNA decatenation and chromosome segregation in geminin-silenced cells before triggering cell death. In vivo, at normal concentration, geminin recruits the deSUMOylating sentrin-specific proteases SENP1 and SENP2 enzymes to deSUMOylate chromosome-bound TopoIIα and promote its release from chromosomes following completion of DNA decatenation. In cells overexpressing geminin, premature departure of TopoIIα from chromosomes is thought to be due to the fact that geminin recruits more of these deSUMOylating enzymes, or recruits them earlier, to bound TopoIIα. This triggers premature release of TopoIIα from chromosomes, which we propose induces aneuploidy in HME cells, since chromosome breakage generated through this mechanism were not sensed and/or repaired and the cell cycle was not arrested. Expression of mitosis-inducing proteins such as cyclin A and cell division kinase 1 was also increased in these cells because of the overexpression of geminin. CONCLUSIONS TopoIIα recruitment and its chromosome decatenation function require a normal level of geminin. Geminin silencing induces a cytokinetic checkpoint in which Cdc7 phosphorylates TopoIIα and inhibits its chromosomal recruitment and decatenation and/or segregation function. Geminin overexpression prematurely deSUMOylates TopoIIα, triggering its premature departure from chromosomes and leading to chromosomal abnormalities and the formation of aneuploid, drug-resistant cancer cells. On the basis of our findings, we propose that therapeutic targeting of geminin is essential for improving the therapeutic potential of TopoIIα agents.
Collapse
Affiliation(s)
- Lauren Gardner
- Cancer Institute, Department of Biochemistry, University of Mississippi Medical Center, Jackson, 39216, USA
| | | | | | | | | |
Collapse
|
46
|
Fachinetti D, Bermejo R, Cocito A, Minardi S, Katou Y, Kanoh Y, Shirahige K, Azvolinsky A, Zakian VA, Foiani M. Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol Cell 2010; 39:595-605. [PMID: 20797631 DOI: 10.1016/j.molcel.2010.07.024] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 05/05/2010] [Accepted: 06/08/2010] [Indexed: 01/19/2023]
Abstract
Chromosome replication initiates at multiple replicons and terminates when forks converge. In E. coli, the Tus-TER complex mediates polar fork converging at the terminator region, and aberrant termination events challenge chromosome integrity and segregation. Since in eukaryotes, termination is less characterized, we used budding yeast to identify the factors assisting fork fusion at replicating chromosomes. Using genomic and mechanistic studies, we have identified and characterized 71 chromosomal termination regions (TERs). TERs contain fork pausing elements that influence fork progression and merging. The Rrm3 DNA helicase assists fork progression across TERs, counteracting the accumulation of X-shaped structures. The Top2 DNA topoisomerase associates at TERs in S phase, and G2/M facilitates fork fusion and prevents DNA breaks and genome rearrangements at TERs. We propose that in eukaryotes, replication fork barriers, Rrm3, and Top2 coordinate replication fork progression and fusion at TERs, thus counteracting abnormal genomic transitions.
Collapse
Affiliation(s)
- Daniele Fachinetti
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare (IFOM-IEO Campus), Via Adamello 16, 20139 Milan, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Schvartzman JB, Martínez-Robles ML, Hernández P, Krimer DB. Plasmid DNA replication and topology as visualized by two-dimensional agarose gel electrophoresis. Plasmid 2009; 63:1-10. [PMID: 19925824 DOI: 10.1016/j.plasmid.2009.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 11/10/2009] [Accepted: 11/12/2009] [Indexed: 11/25/2022]
Abstract
During the last 20 years, two-dimensional agarose gel electrophoresis combined with other techniques such as Polymerase Chain Reaction, helicase assay and electron microscopy, helped to characterize plasmid DNA replication and topology. Here we describe some of the most important findings that were made using this method including the characterization of uni-directional replication, replication origin interference, DNA breakage at the forks, replication fork blockage, replication knotting, replication fork reversal, the interplay of supercoiling and catenation and other changes in DNA topology that take place as replication progresses.
Collapse
Affiliation(s)
- J B Schvartzman
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | | | | | | |
Collapse
|
48
|
Bermejo R, Capra T, Gonzalez-Huici V, Fachinetti D, Cocito A, Natoli G, Katou Y, Mori H, Kurokawa K, Shirahige K, Foiani M. Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription. Cell 2009; 138:870-84. [DOI: 10.1016/j.cell.2009.06.022] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 04/10/2009] [Accepted: 06/10/2009] [Indexed: 12/18/2022]
|
49
|
Hyrien O. Topological analysis of plasmid DNA replication intermediates using two-dimensional agarose gels. Methods Mol Biol 2009; 521:139-67. [PMID: 19563105 DOI: 10.1007/978-1-60327-815-7_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
A fundamental process in DNA replication is the disentangling of the two parental strands by DNA topoisomerases. In this chapter, I detail the topological analysis of plasmid replication intermediates using two-dimensional (2D) agarose gels. The method can resolve replication intermediates according to mass and topology, and can resolve unlinked monomeric circles from catenated dimers of varying topology. The method has been used, alone or in combination with a procedure for purifying covalent protein-DNA complexes, to analyse the effect oftopoisomerase inhibitors on the topology of replication intermediates, to map the location of drug-stabilized topoisomerase cleavage complexes with respect to replication forks and to detect the breakage and repair of replication forks following collision with cleavage complexes. Other applications include the detection of knots that form independently of, or concomitantly with, DNA replication.
Collapse
Affiliation(s)
- Olivier Hyrien
- Genetique Moleculaire, Ecole Normale Supérieure, Paris, France
| |
Collapse
|
50
|
Martínez-Robles ML, Witz G, Hernández P, Schvartzman JB, Stasiak A, Krimer DB. Interplay of DNA supercoiling and catenation during the segregation of sister duplexes. Nucleic Acids Res 2009; 37:5126-37. [PMID: 19553196 PMCID: PMC2731910 DOI: 10.1093/nar/gkp530] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The discrete regulation of supercoiling, catenation and knotting by DNA topoisomerases is well documented both in vivo and in vitro, but the interplay between them is still poorly understood. Here we studied DNA catenanes of bacterial plasmids arising as a result of DNA replication in Escherichia coli cells whose topoisomerase IV activity was inhibited. We combined high-resolution two-dimensional agarose gel electrophoresis with numerical simulations in order to better understand the relationship between the negative supercoiling of DNA generated by DNA gyrase and the DNA interlinking resulting from replication of circular DNA molecules. We showed that in those replication intermediates formed in vivo, catenation and negative supercoiling compete with each other. In interlinked molecules with high catenation numbers negative supercoiling is greatly limited. However, when interlinking decreases, as required for the segregation of newly replicated sister duplexes, their negative supercoiling increases. This observation indicates that negative supercoiling plays an active role during progressive decatenation of newly replicated DNA molecules in vivo.
Collapse
Affiliation(s)
- María Luisa Martínez-Robles
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | | | | | | | | |
Collapse
|