1
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Bainbridge LJ, Daigaku Y. Bulk synthesis and beyond: The roles of eukaryotic replicative DNA polymerases. DNA Repair (Amst) 2024; 141:103740. [PMID: 39096696 DOI: 10.1016/j.dnarep.2024.103740] [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: 05/14/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024]
Abstract
An organism's genomic DNA must be accurately duplicated during each cell cycle. DNA synthesis is catalysed by DNA polymerase enzymes, which extend nucleotide polymers in a 5' to 3' direction. This inherent directionality necessitates that one strand is synthesised forwards (leading), while the other is synthesised backwards discontinuously (lagging) to couple synthesis to the unwinding of duplex DNA. Eukaryotic cells possess many diverse polymerases that coordinate to replicate DNA, with the three main replicative polymerases being Pol α, Pol δ and Pol ε. Studies conducted in yeasts and human cells utilising mutant polymerases that incorporate molecular signatures into nascent DNA implicate Pol ε in leading strand synthesis and Pol α and Pol δ in lagging strand replication. Recent structural insights have revealed how the spatial organization of these enzymes around the core helicase facilitates their strand-specific roles. However, various challenging situations during replication require flexibility in the usage of these enzymes, such as during replication initiation or encounters with replication-blocking adducts. This review summarises the roles of the replicative polymerases in bulk DNA replication and explores their flexible and dynamic deployment to complete genome replication. We also examine how polymerase usage patterns can inform our understanding of global replication dynamics by revealing replication fork directionality to identify regions of replication initiation and termination.
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Affiliation(s)
- Lewis J Bainbridge
- Cancer Genome Dynamics Project, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yasukazu Daigaku
- Cancer Genome Dynamics Project, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
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2
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Ouyang Y, Al-Amodi A, Tehseen M, Alhudhali L, Shirbini A, Takahashi M, Raducanu VS, Yi G, Danazumi AU, De Biasio A, Hamdan SM. Single-molecule characterization of SV40 replisome and novel factors: human FPC and Mcm10. Nucleic Acids Res 2024:gkae565. [PMID: 38967018 DOI: 10.1093/nar/gkae565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
The simian virus 40 (SV40) replisome only encodes for its helicase; large T-antigen (L-Tag), while relying on the host for the remaining proteins, making it an intriguing model system. Despite being one of the earliest reconstituted eukaryotic systems, the interactions coordinating its activities and the identification of new factors remain largely unexplored. Herein, we in vitro reconstituted the SV40 replisome activities at the single-molecule level, including DNA unwinding by L-Tag and the single-stranded DNA-binding protein Replication Protein A (RPA), primer extension by DNA polymerase δ, and their concerted leading-strand synthesis. We show that RPA stimulates the processivity of L-Tag without altering its rate and that DNA polymerase δ forms a stable complex with L-Tag during leading-strand synthesis. Furthermore, similar to human and budding yeast Cdc45-MCM-GINS helicase, L-Tag uses the fork protection complex (FPC) and the mini-chromosome maintenance protein 10 (Mcm10) during synthesis. Hereby, we demonstrate that FPC increases this rate, and both FPC and Mcm10 increase the processivity by stabilizing stalled replisomes and increasing their chances of restarting synthesis. The detailed kinetics and novel factors of the SV40 replisome establish it as a closer mimic of the host replisome and expand its application as a model replication system.
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Affiliation(s)
- Yujing Ouyang
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Amani Al-Amodi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lubna Alhudhali
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Afnan Shirbini
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Masateru Takahashi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Gang Yi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Ammar Usman Danazumi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Alfredo De Biasio
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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3
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Jurkovic CM, Raisch J, Tran S, Nguyen HD, Lévesque D, Scott MS, Campos EI, Boisvert FM. Replisome Proximal Protein Associations and Dynamic Proteomic Changes at Stalled Replication Forks. Mol Cell Proteomics 2024; 23:100767. [PMID: 38615877 PMCID: PMC11101681 DOI: 10.1016/j.mcpro.2024.100767] [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: 08/16/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024] Open
Abstract
DNA replication is a fundamental cellular process that ensures the transfer of genetic information during cell division. Genome duplication takes place in S phase and requires a dynamic and highly coordinated recruitment of multiple proteins at replication forks. Various genotoxic stressors lead to fork instability and collapse, hence the need for DNA repair pathways. By identifying the multitude of protein interactions implicated in those events, we can better grasp the complex and dynamic molecular mechanisms that facilitate DNA replication and repair. Proximity-dependent biotin identification was used to identify associations with 17 proteins within four core replication components, namely the CDC45/MCM2-7/GINS helicase that unwinds DNA, the DNA polymerases, replication protein A subunits, and histone chaperones needed to disassemble and reassemble chromatin. We further investigated the impact of genotoxic stress on these interactions. This analysis revealed a vast proximity association network with 108 nuclear proteins further modulated in the presence of hydroxyurea; 45 being enriched and 63 depleted. Interestingly, hydroxyurea treatment also caused a redistribution of associations with 11 interactors, meaning that the replisome is dynamically reorganized when stressed. The analysis identified several poorly characterized proteins, thereby uncovering new putative players in the cellular response to DNA replication arrest. It also provides a new comprehensive proteomic framework to understand how cells respond to obstacles during DNA replication.
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Affiliation(s)
- Carla-Marie Jurkovic
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jennifer Raisch
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Stephanie Tran
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Hoang Dong Nguyen
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Lévesque
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
| | - François-Michel Boisvert
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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Radhakrishnan A, Gangopadhyay R, Sharma C, Kapardar RK, Sharma NK, Srivastav R. Unwinding Helicase MCM Functionality for Diagnosis and Therapeutics of Replication Abnormalities Associated with Cancer: A Review. Mol Diagn Ther 2024; 28:249-264. [PMID: 38530633 DOI: 10.1007/s40291-024-00701-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
The minichromosome maintenance (MCM) protein is a component of an active helicase that is essential for the initiation of DNA replication. Dysregulation of MCM functions contribute to abnormal cell proliferation and genomic instability. The interactions of MCM with cellular factors, including Cdc45 and GINS, determine the formation of active helicase and functioning of helicase. The functioning of MCM determines the fate of DNA replication and, thus, genomic integrity. This complex is upregulated in precancerous cells and can act as an important tool for diagnostic applications. The MCM protein complex can be an important broad-spectrum therapeutic target in various cancers. Investigations have supported the potential and applications of MCM in cancer diagnosis and its therapeutics. In this article, we discuss the physiological roles of MCM and its associated factors in DNA replication and cancer pathogenesis.
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Affiliation(s)
| | - Ritwik Gangopadhyay
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | | | | | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr. DY Patil Biotechnology and Bioinformatics Institute, Dr. DY Patil Vidyapeeth, Pune, Maharashtra, India
| | - Rajpal Srivastav
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India.
- Department of Science and Technology, Ministry of Science and Technology, New Delhi, India.
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5
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Elango R, Nilavar N, Li AG, Duffey EE, Jiang Y, Nguyen D, Abakir A, Willis NA, Houseley J, Scully R. Two-ended recombination at a Flp-nickase-broken replication fork. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588130. [PMID: 38645103 PMCID: PMC11030319 DOI: 10.1101/2024.04.10.588130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Collision of a replication fork with a DNA nick is thought to generate a one-ended break, fostering genomic instability. Collision of the opposing converging fork with the nick could, in principle, form a second DNA end, enabling conservative repair by homologous recombination (HR). To study mechanisms of nickase-induced HR, we developed the Flp recombinase "step arrest" nickase in mammalian cells. Flp-nickase-induced HR entails two-ended, BRCA2/RAD51-dependent short tract gene conversion (STGC), BRCA2/RAD51-independent long tract gene conversion, and discoordinated two-ended invasions. HR induced by a replication-independent break and by the Flp-nickase differ in their dependence on BRCA1 . To determine the origin of the second DNA end during Flp-nickase-induced STGC, we blocked the opposing fork using a site-specific Tus/ Ter replication fork barrier. Flp-nickase-induced STGC remained robust and two-ended. Thus, collision of a single replication fork with a Flp-nick can trigger two-ended HR, possibly reflecting replicative bypass of lagging strand nicks. This response may limit genomic instability during replication of a nicked DNA template.
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Jones RM, Reynolds-Winczura A, Gambus A. A Decade of Discovery-Eukaryotic Replisome Disassembly at Replication Termination. BIOLOGY 2024; 13:233. [PMID: 38666845 PMCID: PMC11048390 DOI: 10.3390/biology13040233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
The eukaryotic replicative helicase (CMG complex) is assembled during DNA replication initiation in a highly regulated manner, which is described in depth by other manuscripts in this Issue. During DNA replication, the replicative helicase moves through the chromatin, unwinding DNA and facilitating nascent DNA synthesis by polymerases. Once the duplication of a replicon is complete, the CMG helicase and the remaining components of the replisome need to be removed from the chromatin. Research carried out over the last ten years has produced a breakthrough in our understanding, revealing that replication termination, and more specifically replisome disassembly, is indeed a highly regulated process. This review brings together our current understanding of these processes and highlights elements of the mechanism that are conserved or have undergone divergence throughout evolution. Finally, we discuss events beyond the classic termination of DNA replication in S-phase and go over the known mechanisms of replicative helicase removal from chromatin in these particular situations.
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Affiliation(s)
- Rebecca M. Jones
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
- School of Biosciences, Aston University, Birmingham B4 7ET, UK
| | - Alicja Reynolds-Winczura
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
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Langston LD, Georgescu RE, O'Donnell ME. Mechanism of eukaryotic origin unwinding is a dual helicase DNA shearing process. Proc Natl Acad Sci U S A 2023; 120:e2316466120. [PMID: 38109526 PMCID: PMC10756200 DOI: 10.1073/pnas.2316466120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023] Open
Abstract
DNA replication in all cells begins with the melting of base pairs at the duplex origin to allow access to single-stranded DNA templates which are replicated by DNA polymerases. In bacteria, origin DNA is presumed to be melted by accessory proteins that allow loading of two ring-shaped replicative helicases around single-strand DNA (ssDNA) for bidirectional unwinding and DNA replication. In eukaryotes, by contrast, two replicative CMG (Cdc45-Mcm2-7-GINS) helicases are initially loaded head to head around origin double-strand DNA (dsDNA), and there does not appear to be a separate origin unwinding factor. This led us to investigate whether head-to-head CMGs use their adenosine triphosphate (ATP)-driven motors to initiate duplex DNA unwinding at the origin. Here, we show that CMG tracks on one strand of the duplex while surrounding it, and this feature allows two head-to-head CMGs to unwind dsDNA by using their respective motors to pull on opposite strands of the duplex. We further show that while CMG is capable of limited duplex unwinding on its own, the extent of unwinding is greatly and rapidly stimulated by addition of the multifunctional CMG-binding protein Mcm10 that is critical for productive initiation of DNA replication in vivo. On the basis of these findings, we propose that Mcm10 is a processivity or positioning factor that helps translate the work performed by the dual CMG motors at the origin into productive unwinding that facilitates bidirectional DNA replication.
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Affiliation(s)
- Lance D. Langston
- The Rockefeller University, New York City, NY10065
- HHMI, New York City, NY10065
| | - Roxana E. Georgescu
- The Rockefeller University, New York City, NY10065
- HHMI, New York City, NY10065
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8
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Evrin C, Alvarez V, Ainsworth J, Fujisawa R, Alabert C, Labib KPM. DONSON is required for CMG helicase assembly in the mammalian cell cycle. EMBO Rep 2023; 24:e57677. [PMID: 37781960 PMCID: PMC10626419 DOI: 10.15252/embr.202357677] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023] Open
Abstract
DONSON is one of 13 genes mutated in a form of primordial microcephalic dwarfism known as Meier-Gorlin syndrome. The other 12 encode components of the CDC45-MCM-GINS helicase, around which the eukaryotic replisome forms, or are factors required for helicase assembly during DNA replication initiation. A role for DONSON in CDC45-MCM-GINS assembly was unanticipated, since DNA replication initiation can be reconstituted in vitro with purified proteins from budding yeast, which lacks DONSON. Using mouse embryonic stem cells as a model for the mammalian helicase, we show that DONSON binds directly but transiently to CDC45-MCM-GINS during S-phase and is essential for chromosome duplication. Rapid depletion of DONSON leads to the disappearance of the CDC45-MCM-GINS helicase from S-phase cells and our data indicate that DONSON is dispensable for loading of the MCM2-7 helicase core onto chromatin during G1-phase, but instead is essential for CDC45-MCM-GINS assembly during S-phase. These data identify DONSON as a missing link in our understanding of mammalian chromosome duplication and provide a molecular explanation for why mutations in human DONSON are associated with Meier-Gorlin syndrome.
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Affiliation(s)
- Cecile Evrin
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Vanesa Alvarez
- Division of Molecular, Cell & Developmental Biology, School of Life SciencesUniversity of DundeeDundeeUK
| | - Johanna Ainsworth
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
| | - Constance Alabert
- Division of Molecular, Cell & Developmental Biology, School of Life SciencesUniversity of DundeeDundeeUK
| | - Karim PM Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUK
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Xiang S, Luo X, Welch D, Reed DR, Alexandrow MG. Identification of Selective ATP-Competitive CMG Helicase Inhibitors for Cancer Intervention that Disrupt CMG-Replisome Function. RESEARCH SQUARE 2023:rs.3.rs-3182731. [PMID: 37609279 PMCID: PMC10441460 DOI: 10.21203/rs.3.rs-3182731/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The human CMG helicase (Cdc45-MCM-GINS) is a novel target for anti-cancer therapy due to tumor-specific weaknesses in CMG function induced by oncogenic changes and the need for CMG function during recovery from replicative stresses such as chemotherapy. Here, we developed an orthogonal biochemical screening approach and identified selective CMG inhibitors (CMGi) that inhibit ATPase and helicase activities in an ATP-competitive manner at low micromolar concentrations. Structure-activity information and in silico docking indicate that CMGi occupy ATP binding sites and channels within MCM subunits leading to the ATP clefts, which are likely used for ATP/ADP ingress or egress. CMGi inhibit cell growth and DNA replication using multiple molecular mechanisms. CMGi block helicase assembly steps that require ATP binding/hydrolysis by the MCM complex, specifically MCM ring assembly on DNA and GINS recruitment to DNA-loaded MCM hexamers. During S-phase, inhibition of MCM ATP binding/hydrolysis by CMGi causes a 'reverse allosteric' dissociation of Cdc45/GINS from the CMG that destabilizes the replisome and disrupts interactions with Ctf4, Mcm10, and DNA polymerase-α, -δ, -ε, resulting in DNA damage. These novel CMGi are selectively toxic toward tumor cells and define a new class of CMG helicase-targeted anti-cancer compounds with distinct mechanisms of action.
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Affiliation(s)
- Shengyan Xiang
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Molecular Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Xingju Luo
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Molecular Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Darcy Welch
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Department of Individualized Cancer Management, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Damon R. Reed
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Department of Individualized Cancer Management, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Mark G. Alexandrow
- Cancer Biology and Evolution Program, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
- Molecular Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612
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10
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The CMG helicase and cancer: a tumor "engine" and weakness with missing mutations. Oncogene 2023; 42:473-490. [PMID: 36522488 PMCID: PMC9948756 DOI: 10.1038/s41388-022-02572-8] [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: 08/05/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
The replicative Cdc45-MCM-GINS (CMG) helicase is a large protein complex that functions in the DNA melting and unwinding steps as a component of replisomes during DNA replication in mammalian cells. Although the CMG performs this important role in cell growth, the CMG is not a simple bystander in cell cycle events. Components of the CMG, specifically the MCM precursors, are also involved in maintaining genomic stability by regulating DNA replication fork speeds, facilitating recovery from replicative stresses, and preventing consequential DNA damage. Given these important functions, MCM/CMG complexes are highly regulated by growth factors such as TGF-ß1 and by signaling factors such as Myc, Cyclin E, and the retinoblastoma protein. Mismanagement of MCM/CMG complexes when these signaling mediators are deregulated, and in the absence of the tumor suppressor protein p53, leads to increased genomic instability and is a contributor to tumorigenic transformation and tumor heterogeneity. The goal of this review is to provide insight into the mechanisms and dynamics by which the CMG is regulated during its assembly and activation in mammalian genomes, and how errors in CMG regulation due to oncogenic changes promote tumorigenesis. Finally, and most importantly, we highlight the emerging understanding of the CMG helicase as an exploitable vulnerability and novel target for therapeutic intervention in cancer.
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SV40 T-antigen uses a DNA shearing mechanism to initiate origin unwinding. Proc Natl Acad Sci U S A 2022; 119:e2216240119. [PMID: 36442086 PMCID: PMC9894130 DOI: 10.1073/pnas.2216240119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Duplication of DNA genomes requires unwinding of the double-strand (ds) DNA so that each single strand (ss) can be copied by a DNA polymerase. The genomes of eukaryotic cells are unwound by two ring-shaped hexameric helicases that initially encircle dsDNA but transition to ssDNA for function as replicative helicases. How the duplex is initially unwound, and the role of the two helicases in this process, is poorly understood. We recently described an initiation mechanism for eukaryotes in which the two helicases are directed inward toward one another and shear the duplex open by pulling on opposite strands of the duplex while encircling dsDNA [L. D. Langston, M. E. O'Donnell, eLife 8, e46515 (2019)]. Two head-to-head T-Antigen helicases are long known to be loaded at the SV40 origin. We show here that T-Antigen tracks head (N-tier) first on ssDNA, opposite the direction proposed for decades. We also find that SV40 T-Antigen tracks directionally while encircling dsDNA and mainly tracks on one strand of the duplex in the same orientation as during ssDNA translocation. Further, two inward directed T-Antigen helicases on dsDNA are able to melt a 150-bp duplex. These findings explain the "rabbit ear" DNA loops observed at the SV40 origin by electron microscopy and reconfigure how the DNA loops emerge from the double hexamer relative to earlier models. Thus, the mechanism of DNA shearing by two opposing helicases is conserved in a eukaryotic viral helicase and may be widely used to initiate origin unwinding of dsDNA genomes.
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12
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Hu H, Ye L, Liu Z. GINS2 regulates the proliferation and apoptosis of colon cancer cells through PTP4A1. Mol Med Rep 2022; 25:117. [PMID: 35137928 PMCID: PMC8855163 DOI: 10.3892/mmr.2022.12633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/24/2021] [Indexed: 12/24/2022] Open
Abstract
Colon cancer is associated with high death rates worldwide and poses a serious threat to public health. GINS complex subunit 2 (GINS2) serves a carcinogenic role in many cancers, including gastric adenocarcinoma, ovarian cancer and pancreatic cancer. However, the specific function of GINS2 in the development of colon cancer has not been described in detail. The present study aimed to clarify the role of GINS2 in colon cancer. A Cell Counting Kit‑8 assay, EdU staining, TUNEL and flow cytometry analyses were performed to determine the levels of cell viability, proliferation and apoptosis and to evaluate the cell cycle. Through the analysis of BioGrid, a Protein‑Protein Interaction database, it was hypothesized that protein tyrosine phosphatase 4A1 (PTP4A1) is a protein that might interact with GINS2, which was then validated using a co‑immunoprecipitation assay. mRNA and protein levels were measured using reverse transcription‑quantitative PCR and western blotting, respectively. The results of the present study demonstrated that GINS2 expression levels were increased in colon cancer cells. Furthermore, GINS2 knockdown inhibited the proliferation of colon cancer cells, while the levels of cell cycle arrest and apoptosis were increased. By interacting with PTP4A1, GINS2 promoted the expression of PTP4A1, a novel p53 target. GINS2 knockdown was increased, while PTP4A1 overexpression decreased the protein level of p53. Notably, PTP4A1 overexpression partly reversed the effects of GINS2 downregulation on colon cancer cells. Therefore, the present study demonstrated that GINS2 regulated the proliferation and apoptosis of colon cancer cells through PTP4A1/p53 pathway, highlighting that GINS2 may serve as a novel molecular marker for colon cancer prevention and therapy.
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Affiliation(s)
- Hao Hu
- Department of Endoscopy, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Lina Ye
- Department of Endoscopy, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Zhe Liu
- Department of Gastroenterology, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou 550001, P.R. China
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13
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CMG helicase can use ATPγS to unwind DNA: Implications for the rate-limiting step in the reaction mechanism. Proc Natl Acad Sci U S A 2022; 119:2119580119. [PMID: 35042821 PMCID: PMC8794833 DOI: 10.1073/pnas.2119580119] [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] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
The adenosine triphosphate (ATP) analog ATPγS often greatly slows or prevents enzymatic ATP hydrolysis. The eukaryotic CMG (Cdc45, Mcm2 to 7, GINS) replicative helicase is presumed unable to hydrolyze ATPγS and thus unable to perform DNA unwinding, as documented for certain other helicases. Consequently, ATPγS is often used to "preload" CMG onto forked DNA substrates without unwinding before adding ATP to initiate helicase activity. We find here that CMG does hydrolyze ATPγS and couples it to DNA unwinding. Indeed, the rate of unwinding of a 20- and 30-mer duplex fork of different sequences by CMG is only reduced 1- to 1.5-fold using ATPγS compared with ATP. These findings imply that a conformational change is the rate-limiting step during CMG unwinding, not hydrolysis. Instead of using ATPγS for loading CMG onto DNA, we demonstrate here that nonhydrolyzable adenylyl-imidodiphosphate (AMP-PNP) can be used to preload CMG onto a forked DNA substrate without unwinding.
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14
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Optimizing CMG helicase and CMG-dependent replication assays by designing DNA fork substrates and choosing nucleotide analogues for helicase preloading. Methods Enzymol 2022; 672:173-202. [DOI: 10.1016/bs.mie.2022.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Conwell SC, Cranford MT, Kavlashvili T, Dewar JM. Replication fork collapse in vitro using Xenopus egg extracts. Methods Enzymol 2022; 672:317-338. [DOI: 10.1016/bs.mie.2022.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Nottingham E, Mazzio E, Surapaneni SK, Kutlehria S, Mondal A, Badisa R, Safe S, Rishi AK, Singh M. Synergistic effects of methyl 2-cyano-3,11-dioxo-18beta-olean-1,-12-dien-30-oate and erlotinib on erlotinib-resistant non-small cell lung cancer cells. J Pharm Anal 2021; 11:799-807. [PMID: 35028186 PMCID: PMC8740161 DOI: 10.1016/j.jpha.2021.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 11/09/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is often characterized by an underlying mutation in the epidermal growth factor receptor (EGFR), contributing to aggressive metastatic disease. Methyl 2-cyano-3,11-dioxo-18beta-olean-1,12-dien-30-oate (CDODA-Me), a glycyrrhetinic acid derivative, reportedly improves the therapeutic response to erlotinib (ERL), an EGFR tyrosine kinase inhibitor. In the present study, we performed a series of studies to demonstrate the efficacy of CDODA-Me (2 μM) in sensitizing HCC827R (ERL-resistant) cells to ERL. Herein, we first established the selectivity of ERL-induced drug resistance in the HCC827R cells, which was sensitized when ERL was combined with CDODA-Me (2 μM), shifting the IC50 from 23.48 μM to 5.46 μM. Subsequently, whole transcriptomic microarray expression data demonstrated that the combination of ERL + CDODA-Me elicited 210 downregulated genes (0.44% of the whole transcriptome (WT)) and 174 upregulated genes (0.36% of the WT), of which approximately 80% were unique to the ERL + CDODA-Me group. Synergistic effects centered on losses to cell cycle progression transcripts, a reduction of minichromosome maintenance complex components (MCM2-7), all key components of the Cdc45·MCM2-7GINS (CMG) complex, and replicative helicases; these effects were tantamount to the upregulation of processes associated with the nuclear factor erythroid 2 like 2 translational response to oxidative stress, including sulfiredoxin 1, heme oxygenase 1, and stress-induced growth inhibitor 1. Collectively, these findings indicate that the synergistic therapeutic effects of ERL + CDODA-Me on resistant NSCLC cells are mediated via the inhibition of mitosis and induction of oxidative stress.
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Affiliation(s)
- Ebony Nottingham
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Elizabeth Mazzio
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Sunil Kumar Surapaneni
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Shallu Kutlehria
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Arindam Mondal
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Ramesh Badisa
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine, Texas A & M University, College Station, TX, 77843, USA
| | - Arun K. Rishi
- John D. Dingell VA medical Center and Department of Oncology, Wayne State University, Detroit, MI, 48201, USA
| | - Mandip Singh
- Department of Pharmaceutics, College of Pharmacy and Pharmaceutical Sciences, Florida A & M University, Tallahassee, FL, 32307, USA
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17
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Oki K, Nagata M, Yamagami T, Numata T, Ishino S, Oyama T, Ishino Y. Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome. Nucleic Acids Res 2021; 50:3601-3615. [PMID: 34568951 PMCID: PMC9023282 DOI: 10.1093/nar/gkab799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/29/2021] [Accepted: 09/06/2021] [Indexed: 11/12/2022] Open
Abstract
Genomic DNA replication requires replisome assembly. We show here the molecular mechanism by which CMG (GAN-MCM-GINS)-like helicase cooperates with the family D DNA polymerase (PolD) in Thermococcus kodakarensis. The archaeal GINS contains two Gins51 subunits, the C-terminal domain of which (Gins51C) interacts with GAN. We discovered that Gins51C also interacts with the N-terminal domain of PolD's DP1 subunit (DP1N) to connect two PolDs in GINS. The two replicases in the replisome should be responsible for leading- and lagging-strand synthesis, respectively. Crystal structure analysis of the DP1N-Gins51C-GAN ternary complex was provided to understand the structural basis of the connection between the helicase and DNA polymerase. Site-directed mutagenesis analysis supported the interaction mode obtained from the crystal structure. Furthermore, the assembly of helicase and replicase identified in this study is also conserved in Eukarya. PolD enhances the parental strand unwinding via stimulation of ATPase activity of the CMG-complex. This is the first evidence of the functional connection between replicase and helicase in Archaea. These results suggest that the direct interaction of PolD with CMG-helicase is critical for synchronizing strand unwinding and nascent strand synthesis and possibly provide a functional machinery for the effective progression of the replication fork.
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Affiliation(s)
- Keisuke Oki
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Mariko Nagata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi 400-8510, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
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18
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Kumar C, Batra S, Griffith JD, Remus D. The interplay of RNA:DNA hybrid structure and G-quadruplexes determines the outcome of R-loop-replisome collisions. eLife 2021; 10:72286. [PMID: 34494544 PMCID: PMC8479836 DOI: 10.7554/elife.72286] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/07/2021] [Indexed: 12/11/2022] Open
Abstract
R-loops are a major source of genome instability associated with transcription-induced replication stress. However, how R-loops inherently impact replication fork progression is not understood. Here, we characterize R-loop-replisome collisions using a fully reconstituted eukaryotic DNA replication system. We find that RNA:DNA hybrids and G-quadruplexes at both co-directional and head-on R-loops can impact fork progression by inducing fork stalling, uncoupling of leading strand synthesis from replisome progression, and nascent strand gaps. RNase H1 and Pif1 suppress replication defects by resolving RNA:DNA hybrids and G-quadruplexes, respectively. We also identify an intrinsic capacity of replisomes to maintain fork progression at certain R-loops by unwinding RNA:DNA hybrids, repriming leading strand synthesis downstream of G-quadruplexes, or utilizing R-loop transcripts to prime leading strand restart during co-directional R-loop-replisome collisions. Collectively, the data demonstrates that the outcome of R-loop-replisome collisions is modulated by R-loop structure, providing a mechanistic basis for the distinction of deleterious from non-deleterious R-loops.
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Affiliation(s)
- Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sahil Batra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center and Departments of Microbiology and Immunology, and Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
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19
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Mayle R, O'Donnell M. Expression of recombinant multi-protein complexes in Saccharomyces cerevisiae. Methods Enzymol 2021; 660:3-20. [PMID: 34742395 DOI: 10.1016/bs.mie.2021.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Baker's yeast, Saccharomyces cerevisiae, is a versatile system for expression of recombinant eukaryotic proteins. This system is simple to use and does not require extraordinary expertise nor tissue culture facilities. Proteins expressed in the yeast system provide eukaryotic post-translational modifications, making it superior to bacterial expression for factors that require post-translational modification. In addition, it is quite simple to co-express multiple genes at the same time, for recombinant production of large multi-protein complexes. In this chapter, we provide protocols for inducible expression of recombinant genes from episomal plasmid vectors, and protocols for integration of the recombinant genes into the chromosomes of yeast, which enables simple rapid growth of expression cells and induction of recombinant protein complexes in non-selectable rich media.
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Affiliation(s)
- Ryan Mayle
- Laboratory of DNA Replication, The Rockefeller University, New York, NY, United States
| | - Mike O'Donnell
- Laboratory of DNA Replication, The Rockefeller University, New York, NY, United States; Howard Hughes Medical Institute at Rockefeller University, New York, NY, United States.
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20
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Knockdown of GINS2 inhibits proliferation and promotes apoptosis through the p53/GADD45A pathway in non-small-cell lung cancer. Biosci Rep 2021; 40:222398. [PMID: 32181475 PMCID: PMC7133113 DOI: 10.1042/bsr20193949] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/25/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is a malignant tumour type with the highest morbidity and mortality, and non-small-cell lung cancer (NSCLC) is the most common pathological type. GINS complex subunit 2 (GINS2) is a member of the GINS family and is closely related to DNA replication and damage, participates in cell cycle regulation and plays a key role in cell proliferation and apoptosis. In the present study, we aimed to explore the role and underlying molecular mechanism of GINS2 in the development of NSCLC. The results showed that GINS2 is significantly increased in NSCLC tissues and cell lines. Knockdown of GINS2 significantly decreases cell proliferation, causing G2/M phase cell cycle arrest. Knockdown of GINS2 reverses the effect of nocodazole on the levels of cyclin-dependent kinase 1 (CDK1) and cyclin-B1. Meanwhile, knockdown of GINS2 significantly elevates the apoptosis rate and apoptosis-related protein Bax and decreases Bcl-2. In addition, GINS2 knockdown induces an increase in the levels of p53 and growth arrest and DNA damage 45A (GADD45A). Co-transfection with GINS2-siRNA and siRNA against p53 (p53-siRNA) or co-transfection with GINS2-siRNA and siRNA against GADD45A (GADD45A-siRNA) partially reverses the effects of GINS2 knockdown on cell proliferation and apoptosis. Taken together, these results indicate that GINS2 knockdown down-regulates cell proliferation, induces G2/M phase cell cycle arrest and increases apoptosis, possibly through the p53/GADD45A pathway.
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21
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Vrtis KB, Dewar JM, Chistol G, Wu RA, Graham TGW, Walter JC. Single-strand DNA breaks cause replisome disassembly. Mol Cell 2021; 81:1309-1318.e6. [PMID: 33484638 DOI: 10.1016/j.molcel.2020.12.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022]
Abstract
DNA damage impedes replication fork progression and threatens genome stability. Upon encounter with most DNA adducts, the replicative CMG helicase (CDC45-MCM2-7-GINS) stalls or uncouples from the point of synthesis, yet eventually resumes replication. However, little is known about the effect on replication of single-strand breaks or "nicks," which are abundant in mammalian cells. Using Xenopus egg extracts, we reveal that CMG collision with a nick in the leading strand template generates a blunt-ended double-strand break (DSB). Moreover, CMG, which encircles the leading strand template, "runs off" the end of the DSB. In contrast, CMG collision with a lagging strand nick generates a broken end with a single-stranded overhang. In this setting, CMG translocates along double-stranded DNA beyond the break and is then ubiquitylated and removed from chromatin by the same pathway used during replication termination. Our results show that nicks are uniquely dangerous DNA lesions that invariably cause replisome disassembly, and they suggest that CMG cannot be stored on dsDNA while cells resolve replication stress.
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Affiliation(s)
- Kyle B Vrtis
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - James M Dewar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - Gheorghe Chistol
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - Thomas G W Graham
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
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22
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The replicative CMG helicase: the ideal target for cancer therapy. UKRAINIAN BIOCHEMICAL JOURNAL 2020. [DOI: 10.15407/ubj92.06.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Kose HB, Xie S, Cameron G, Strycharska MS, Yardimci H. Duplex DNA engagement and RPA oppositely regulate the DNA-unwinding rate of CMG helicase. Nat Commun 2020; 11:3713. [PMID: 32709841 PMCID: PMC7382467 DOI: 10.1038/s41467-020-17443-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 07/01/2020] [Indexed: 01/09/2023] Open
Abstract
A ring-shaped helicase unwinds DNA during chromosome replication in all organisms. Replicative helicases generally unwind duplex DNA an order of magnitude slower compared to their in vivo replication fork rates. However, the origin of slow DNA unwinding rates by replicative helicases and the mechanism by which other replication components increase helicase speed are unclear. Here, we demonstrate that engagement of the eukaryotic CMG helicase with template DNA at the replication fork impairs its helicase activity, which is alleviated by binding of the single-stranded DNA binding protein, RPA, to the excluded DNA strand. Intriguingly, we found that, when stalled due to interaction with the parental duplex, DNA rezipping-induced helicase backtracking reestablishes productive helicase-fork engagement, underscoring the significance of plasticity in helicase action. Our work provides a mechanistic basis for relatively slow duplex unwinding by replicative helicases and explains how replisome components that interact with the excluded DNA strand stimulate fork rates.
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Affiliation(s)
- Hazal B Kose
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Sherry Xie
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - George Cameron
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Melania S Strycharska
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
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24
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Saito Y, Kobayashi J, Kanemaki MT, Komatsu K. RIF1 controls replication initiation and homologous recombination repair in a radiation dose-dependent manner. J Cell Sci 2020; 133:jcs240036. [PMID: 32434870 PMCID: PMC7328141 DOI: 10.1242/jcs.240036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/29/2020] [Indexed: 01/13/2023] Open
Abstract
RIF1 controls both DNA replication timing and the DNA double-strand break (DSB) repair pathway to maintain genome integrity. However, it remains unclear how RIF1 links these two processes following exposure to ionizing radiation (IR). Here, we show that inhibition of homologous recombination repair (HRR) by RIF1 occurs in a dose-dependent manner and is controlled via DNA replication. RIF1 inhibits both DNA end resection and RAD51 accumulation after exposure to high doses of IR. Contrastingly, HRR inhibition by RIF1 is antagonized by BRCA1 after a low-dose IR exposure. At high IR doses, RIF1 suppresses replication initiation by dephosphorylating MCM helicase. Notably, the dephosphorylation of MCM helicase inhibits both DNA end resection and HRR, even without RIF1. Thus, our data show the importance of active DNA replication for HRR and suggest a common suppression mechanism for DNA replication and HRR at high IR doses, both of which are controlled by RIF1.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yuichiro Saito
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Junya Kobayashi
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Kenshi Komatsu
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
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25
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Wasserman MR, Schauer GD, O'Donnell ME, Liu S. Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase. Cell 2020; 178:600-611.e16. [PMID: 31348887 DOI: 10.1016/j.cell.2019.06.032] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 04/05/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
The eukaryotic replicative helicase CMG is a closed ring around double-stranded (ds)DNA at origins yet must transition to single-stranded (ss)DNA for helicase action. CMG must also handle repair intermediates, such as reversed forks that lack ssDNA. Here, using correlative single-molecule fluorescence and force microscopy, we show that CMG harbors a ssDNA gate that enables transitions between ss and dsDNA. When coupled to DNA polymerase, CMG remains on ssDNA, but when uncoupled, CMG employs this gate to traverse forked junctions onto dsDNA. Surprisingly, CMG undergoes rapid diffusion on dsDNA and can transition back onto ssDNA to nucleate a functional replisome. The gate-distinct from that between Mcm2/5 used for origin loading-is intrinsic to CMG; however, Mcm10 promotes strand passage by enhancing the affinity of CMG to DNA. This gating process may explain the dsDNA-to-ssDNA transition of CMG at origins and help preserve CMG on dsDNA during fork repair.
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Affiliation(s)
- Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065, USA
| | - Grant D Schauer
- Laboratory of DNA Replication, The Rockefeller University, New York, NY 10065, USA
| | - Michael E O'Donnell
- Laboratory of DNA Replication, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065, USA.
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26
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Perera HM, Behrmann MS, Hoang JM, Griffin WC, Trakselis MA. Contacts and context that regulate DNA helicase unwinding and replisome progression. Enzymes 2019; 45:183-223. [PMID: 31627877 DOI: 10.1016/bs.enz.2019.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hexameric DNA helicases involved in the separation of duplex DNA at the replication fork have a universal architecture but have evolved from two separate protein families. The consequences are that the regulation, translocation polarity, strand specificity, and architectural orientation varies between phage/bacteria to that of archaea/eukaryotes. Once assembled and activated for single strand DNA translocation and unwinding, the DNA polymerase couples tightly to the helicase forming a robust replisome complex. However, this helicase-polymerase interaction can be challenged by various forms of endogenous or exogenous agents that can stall the entire replisome or decouple DNA unwinding from synthesis. The consequences of decoupling can be severe, leading to a build-up of ssDNA requiring various pathways for replication fork restart. All told, the hexameric helicase sits prominently at the front of the replisome constantly responding to a variety of obstacles that require transient unwinding/reannealing, traversal of more stable blocks, and alternations in DNA unwinding speed that regulate replisome progression.
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Affiliation(s)
- Himasha M Perera
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Megan S Behrmann
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Joy M Hoang
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Wezley C Griffin
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States.
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27
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Chojnacki M, Melendy T. The human papillomavirus DNA helicase E1 binds, stimulates, and confers processivity to cellular DNA polymerase epsilon. Nucleic Acids Res 2019; 46:229-241. [PMID: 29155954 PMCID: PMC5758917 DOI: 10.1093/nar/gkx1103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
The papillomavirus (PV) helicase protein E1 recruits components of the cellular DNA replication machinery to the PV replication fork, such as Replication Protein A (RPA), DNA polymerase α-primase (pol α) and topoisomerase I (topo I). Here we show that E1 binds to DNA polymerase ϵ (pol ϵ) and dramatically stimulates the DNA synthesis activity of pol ϵ. This stimulation of pol ϵ by E1 is highly specific and occurs even in the absence of the known pol ϵ cofactors Replication Factor C (RFC), Proliferating Cell Nuclear Antigen (PCNA) and RPA. This stimulation is due to an increase in the processivity of pol ϵ and occurs independently of pol ϵ’s replication cofactors. This increase in processivity is dependent on the ability of the E1 helicase to hydrolyze ATP, suggesting it is dependent on E1’s helicase action. In addition, RPA, thought to be vital for processive DNA synthesis by both pol ϵ and pol δ, was found to be dispensable for processive synthesis by pol ϵ in the presence of E1. Overall, E1 appears to be conferring processivity to pol ϵ by directly tethering pol ϵ to the DNA parental strand and towing ϵ behind the E1 helicase as the replication fork progresses; and thereby apparently obviating the need for RPA for leading strand synthesis. Thus far only pol α and pol δ have been implicated in the DNA replication of mammalian viruses; this is the first reported example of a virus recruiting pol ϵ. Furthermore, this demonstrates a unique capacity of a viral helicase having evolved to stimulate a cellular replicative DNA polymerase.
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Affiliation(s)
- Michaelle Chojnacki
- Departments of Microbiology & Immunology and Biochemistry, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Thomas Melendy
- Departments of Microbiology & Immunology and Biochemistry, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA
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28
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Langston LD, O'Donnell ME. An explanation for origin unwinding in eukaryotes. eLife 2019; 8:e46515. [PMID: 31282859 PMCID: PMC6634965 DOI: 10.7554/elife.46515] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/06/2019] [Indexed: 12/14/2022] Open
Abstract
Twin CMG complexes are assembled head-to-head around duplex DNA at eukaryotic origins of replication. Mcm10 activates CMGs to form helicases that encircle single-strand (ss) DNA and initiate bidirectional forks. How the CMGs melt duplex DNA while encircling it is unknown. Here we show that S. cerevisiae CMG tracks with force while encircling double-stranded (ds) DNA and that in the presence of Mcm10 the CMG melts long blocks of dsDNA while it encircles dsDNA. We demonstrate that CMG tracks mainly on the 3'-5' strand during duplex translocation, predicting that head-to-head CMGs at an origin exert force on opposite strands. Accordingly, we show that CMGs that encircle double strand DNA in a head-to-head orientation melt the duplex in an Mcm10-dependent reaction.
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Affiliation(s)
- Lance D Langston
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Michael E O'Donnell
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
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29
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Motahari Z, Moody SA, Maynard TM, LaMantia AS. In the line-up: deleted genes associated with DiGeorge/22q11.2 deletion syndrome: are they all suspects? J Neurodev Disord 2019; 11:7. [PMID: 31174463 PMCID: PMC6554986 DOI: 10.1186/s11689-019-9267-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND 22q11.2 deletion syndrome (22q11DS), a copy number variation (CNV) disorder, occurs in approximately 1:4000 live births due to a heterozygous microdeletion at position 11.2 (proximal) on the q arm of human chromosome 22 (hChr22) (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011). This disorder was known as DiGeorge syndrome, Velo-cardio-facial syndrome (VCFS) or conotruncal anomaly face syndrome (CTAF) based upon diagnostic cardiovascular, pharyngeal, and craniofacial anomalies (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011; Burn et al., J Med Genet 30:822-4, 1993) before this phenotypic spectrum was associated with 22q11.2 CNVs. Subsequently, 22q11.2 deletion emerged as a major genomic lesion associated with vulnerability for several clinically defined behavioral deficits common to a number of neurodevelopmental disorders (Fernandez et al., Principles of Developmental Genetics, 2015; Robin and Shprintzen, J Pediatr 147:90-6, 2005; Schneider et al., Am J Psychiatry 171:627-39, 2014). RESULTS The mechanistic relationships between heterozygously deleted 22q11.2 genes and 22q11DS phenotypes are still unknown. We assembled a comprehensive "line-up" of the 36 protein coding loci in the 1.5 Mb minimal critical deleted region on hChr22q11.2, plus 20 protein coding loci in the distal 1.5 Mb that defines the 3 Mb typical 22q11DS deletion. We categorized candidates based upon apparent primary cell biological functions. We analyzed 41 of these genes that encode known proteins to determine whether haploinsufficiency of any single 22q11.2 gene-a one gene to one phenotype correspondence due to heterozygous deletion restricted to that locus-versus complex multigenic interactions can account for single or multiple 22q11DS phenotypes. CONCLUSIONS Our 22q11.2 functional genomic assessment does not support current theories of single gene haploinsufficiency for one or all 22q11DS phenotypes. Shared molecular functions, convergence on fundamental cell biological processes, and related consequences of individual 22q11.2 genes point to a matrix of multigenic interactions due to diminished 22q11.2 gene dosage. These interactions target fundamental cellular mechanisms essential for development, maturation, or homeostasis at subsets of 22q11DS phenotypic sites.
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Affiliation(s)
- Zahra Motahari
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Sally Ann Moody
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Thomas Michael Maynard
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Anthony-Samuel LaMantia
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
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Burnham DR, Kose HB, Hoyle RB, Yardimci H. The mechanism of DNA unwinding by the eukaryotic replicative helicase. Nat Commun 2019; 10:2159. [PMID: 31089141 PMCID: PMC6517413 DOI: 10.1038/s41467-019-09896-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 04/05/2019] [Indexed: 12/18/2022] Open
Abstract
Accurate DNA replication is tightly regulated in eukaryotes to ensure genome stability during cell division and is performed by the multi-protein replisome. At the core an AAA+ hetero-hexameric complex, Mcm2-7, together with GINS and Cdc45 form the active replicative helicase Cdc45/Mcm2-7/GINS (CMG). It is not clear how this replicative ring helicase translocates on, and unwinds, DNA. We measure real-time dynamics of purified recombinant Drosophila melanogaster CMG unwinding DNA with single-molecule magnetic tweezers. Our data demonstrates that CMG exhibits a biased random walk, not the expected unidirectional motion. Through building a kinetic model we find CMG may enter up to three paused states rather than unwinding, and should these be prevented, in vivo fork rates would be recovered in vitro. We propose a mechanism in which CMG couples ATP hydrolysis to unwinding by acting as a lazy Brownian ratchet, thus providing quantitative understanding of the central process in eukaryotic DNA replication.
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Affiliation(s)
- Daniel R Burnham
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Hazal B Kose
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Rebecca B Hoyle
- School of Mathematical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Hasan Yardimci
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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Kose HB, Larsen NB, Duxin JP, Yardimci H. Dynamics of the Eukaryotic Replicative Helicase at Lagging-Strand Protein Barriers Support the Steric Exclusion Model. Cell Rep 2019; 26:2113-2125.e6. [PMID: 30784593 PMCID: PMC6381796 DOI: 10.1016/j.celrep.2019.01.086] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 12/19/2018] [Accepted: 01/24/2019] [Indexed: 12/01/2022] Open
Abstract
Progression of DNA replication depends on the ability of the replisome complex to overcome nucleoprotein barriers. During eukaryotic replication, the CMG helicase translocates along the leading-strand template and unwinds the DNA double helix. While proteins bound to the leading-strand template efficiently block the helicase, the impact of lagging-strand protein obstacles on helicase translocation and replisome progression remains controversial. Here, we show that CMG and replisome progressions are impaired when proteins crosslinked to the lagging-strand template enhance the stability of duplex DNA. In contrast, proteins that exclusively interact with the lagging-strand template influence neither the translocation of isolated CMG nor replisome progression in Xenopus egg extracts. Our data imply that CMG completely excludes the lagging-strand template from the helicase central channel while unwinding DNA at the replication fork, which clarifies how two CMG helicases could freely cross one another during replication initiation and termination.
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Affiliation(s)
- Hazal B Kose
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT London, UK
| | - Nicolai B Larsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT London, UK.
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32
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Mcm10 has potent strand-annealing activity and limits translocase-mediated fork regression. Proc Natl Acad Sci U S A 2018; 116:798-803. [PMID: 30598452 PMCID: PMC6338834 DOI: 10.1073/pnas.1819107116] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Fork regression is a way of circumventing or dealing with DNA lesions and is important to genome integrity. Fork regression is performed by double-strand DNA ATPases that initially cause newly synthesized strands to unpair from the parental strands, followed by pairing of the new strands and reversal of the fork. This study shows that Mcm10, an essential replication factor, efficiently anneals complementary strands and also inhibits fork regression by SMARCAL1. Moreover, the study localizes the Mcm10 DNA-binding domain to the N-terminal domains of the replicative CMG helicase at the forked nexus. Thus, forks that are unimpeded would contain Mcm10 at a strategic position where its DNA-binding and/or annealing function may block fork regression enzymes and thereby protect active forks from becoming reversed. The 11-subunit eukaryotic replicative helicase CMG (Cdc45, Mcm2-7, GINS) tightly binds Mcm10, an essential replication protein in all eukaryotes. Here we show that Mcm10 has a potent strand-annealing activity both alone and in complex with CMG. CMG-Mcm10 unwinds and then reanneals single strands soon after they have been unwound in vitro. Given the DNA damage and replisome instability associated with loss of Mcm10 function, we examined the effect of Mcm10 on fork regression. Fork regression requires the unwinding and pairing of newly synthesized strands, performed by a specialized class of ATP-dependent DNA translocases. We show here that Mcm10 inhibits fork regression by the well-known fork reversal enzyme SMARCAL1. We propose that Mcm10 inhibits the unwinding of nascent strands to prevent fork regression at normal unperturbed replication forks, either by binding the fork junction to form a block to SMARCAL1 or by reannealing unwound nascent strands to their parental template. Analysis of the CMG-Mcm10 complex by cross-linking mass spectrometry reveals Mcm10 interacts with six CMG subunits, with the DNA-binding region of Mcm10 on the N-face of CMG. This position on CMG places Mcm10 at the fork junction, consistent with a role in regulating fork regression.
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33
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Liu C, Wang R, Zhang Y. GINS complex subunit 2 (GINS2) plays a protective role in alcohol-induced brain injury. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2018; 47:1-9. [PMID: 30513217 DOI: 10.1080/21691401.2018.1540425] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Acute alcohol intoxication is a central nervous system disease that accounts for a large number of hospital admissions. In the present study, we have explored the role of GINS complex subunit 2 (GINS2) in acute alcohol intoxication and alcohol-induced brain injury. We began by determining that GINS2 mRNA expression was significantly increased in the serum of patients with alcohol abuse. We then found that GINS2 is increased in mouse brains after alcohol consumption. To explore the role of GINS2 in alcohol-induced microglia function, we knocked down GINS2 in mouse microglia and then treated the cells with alcohol. Knockdown of GINS2 significantly increased alcohol-induced ROS production and the oxidative stress marker malondialdehyde. To explore if GINS2 is involved in alcohol-induced microglia apoptosis, we examined cell viability in GINS2 knockdown cells by TUNEL staining and caspase activity assays. Consistently, results showed that alcohol-induced cell apoptosis was promoted by knockdown of GINS2. Finally, we assessed expression levels of inflammatory factors in GINS2 knockdown microglial cells as well as the effects of GINS2 knockdown on NF-κB signalling. Inflammatory factors were stimulated by alcohol and further promoted by GINS2 knockdown, and GINS2 knockdown promoted alcohol-induced NF-κB activity in microglia.
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Affiliation(s)
- Chunhua Liu
- a Department of Neurology , The Second Affiliated Hospital of Harbin Medical University , Harbin , China
| | - Renfu Wang
- b Department of Neurology , The Fourth Affiliated Hospital of Harbin Medical University , Harbin , China
| | - Yu Zhang
- b Department of Neurology , The Fourth Affiliated Hospital of Harbin Medical University , Harbin , China
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34
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Shen YL, Li HZ, Hu YW, Zheng L, Wang Q. Loss of GINS2 inhibits cell proliferation and tumorigenesis in human gliomas. CNS Neurosci Ther 2018; 25:273-287. [PMID: 30338650 DOI: 10.1111/cns.13064] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/26/2018] [Accepted: 08/27/2018] [Indexed: 12/12/2022] Open
Abstract
AIMS In this study, we examined the expression of GINS2 in glioma and determined its role in glioma development. METHODS The protein expression of GINS2 was assessed in 120 human glioma samples via immunohistochemistry. Then, we suppressed the expression of GINS2 in glioma cell strains U87 and U251 using a short hairpin RNA lentiviral vector. In addition, RNA sequencing and bioinformatics analysis were performed on glioma cells before and after GINS2 knockdown. Subsequent co-immunoprecipitation and western blot experiments indicated possible downstream regulatory molecules. RESULTS The present results showed that GINS2 can accelerate the growth of glioma cells, whereas the suppression of GINS2 expression decreased the proliferation and tumorigenicity of glioma cells. Mechanism research experiments proved that GINS2 can block the cell cycle by regulating certain downstream molecules, such as MCM2, ATM, and CHEK2. CONCLUSION GINS2 is closely related to the occurrence and development of glioma, and is likely to become a prognostic marker for glioma patients, as well as a potential therapeutic target in the treatment of glioma.
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Affiliation(s)
- Yun-Long Shen
- Department of Neurosurgery, The Fifth Affiliated Hospital, South Medical University, Guangzhou, China
| | - He-Zhen Li
- Department of Neurosurgery, The Fifth Affiliated Hospital, South Medical University, Guangzhou, China
| | - Yan-Wei Hu
- Clinical Laboratory Department, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Zheng
- Clinical Laboratory Department, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qian Wang
- Clinical Laboratory Department, Nanfang Hospital, Southern Medical University, Guangzhou, China
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35
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Abstract
Nucleosomes compact and organize genetic material on a structural level. However, they also alter local chromatin accessibility through changes in their position, through the incorporation of histone variants, and through a vast array of histone posttranslational modifications. The dynamic nature of chromatin requires histone chaperones to process, deposit, and evict histones in different tissues and at different times in the cell cycle. This review focuses on the molecular details of canonical and variant H3-H4 histone chaperone pathways that lead to histone deposition on DNA as they are currently understood. Emphasis is placed on the most established pathways beginning with the folding, posttranslational modification, and nuclear import of newly synthesized H3-H4 histones. Next, we review the deposition of replication-coupled H3.1-H4 in S-phase and replication-independent H3.3-H4 via alternative histone chaperone pathways. Highly specialized histone chaperones overseeing the deposition of histone variants are also briefly discussed.
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Affiliation(s)
- Prerna Grover
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada;
| | - Jonathon S Asa
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada; .,Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5G 0A4, Canada
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36
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GINS2 promotes cell proliferation and inhibits cell apoptosis in thyroid cancer by regulating CITED2 and LOXL2. Cancer Gene Ther 2018; 26:103-113. [PMID: 30177819 DOI: 10.1038/s41417-018-0045-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 12/27/2022]
Abstract
To explore the mechanisms of GINS2 on cell proliferation and apoptosis in thyroid cancer (TC) cells. Expressions of GINS2 were inhibited in K1 and SW579 cells using gene interference technology. The abilities of proliferation and apoptosis, and cell cycle were determined by MTT assay and flow cytometric assay. The downstream molecules of GINS2 were searched by microarray and bioinformatics and validated by qRT-PCR and western blotting. In the in vivo study, the tumor growth was compared and the whole-body fluorescent imaging was analyzed. After GINS2 was interfered, cell proliferation was significantly inhibited (P < 0.01) and apoptosis rate increased (P < 0.01) in both K1 and SW579 cells. Cell cycle changed significantly in K1 cells, but not in SW579 cells. With bioinformatics upstream analysis, TGF-β1 was found as the most significantly upstream regulator. Expressions of TGF-β1 and its downstream target molecules CITED2 and LOXL2 were validated and found downregulated significantly in mRNA and protein levels (P < 0.05). The results of the nude mouse xenograft assay suggested that the volume and weight of tumor in ones infected with shGINS2 were statistically smaller than controls (P < 0.05). GINS2 plays an important role in cell proliferation and apoptosis of thyroid cancer by regulating the expressions of CITED2 and LOXL2, which may be a potential biomarker for diagnosis or prognosis and a drug target for therapy.
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37
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Cdc45/Mcm2-7/GINS complex down-regulation mediates S phase arrest in okadaic acid-induced cell damage. Toxicon 2018; 152:16-22. [DOI: 10.1016/j.toxicon.2018.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/30/2018] [Accepted: 07/08/2018] [Indexed: 02/07/2023]
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38
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Evrin C, Maman JD, Diamante A, Pellegrini L, Labib K. Histone H2A-H2B binding by Pol α in the eukaryotic replisome contributes to the maintenance of repressive chromatin. EMBO J 2018; 37:embj.201899021. [PMID: 30104407 PMCID: PMC6166128 DOI: 10.15252/embj.201899021] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/18/2018] [Accepted: 07/24/2018] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic replisome disassembles parental chromatin at DNA replication forks, but then plays a poorly understood role in the re‐deposition of the displaced histone complexes onto nascent DNA. Here, we show that yeast DNA polymerase α contains a histone‐binding motif that is conserved in human Pol α and is specific for histones H2A and H2B. Mutation of this motif in budding yeast cells does not affect DNA synthesis, but instead abrogates gene silencing at telomeres and mating‐type loci. Similar phenotypes are produced not only by mutations that displace Pol α from the replisome, but also by mutation of the previously identified histone‐binding motif in the CMG helicase subunit Mcm2, the human orthologue of which was shown to bind to histones H3 and H4. We show that chromatin‐derived histone complexes can be bound simultaneously by Mcm2, Pol α and the histone chaperone FACT that is also a replisome component. These findings indicate that replisome assembly unites multiple histone‐binding activities, which jointly process parental histones to help preserve silent chromatin during the process of chromosome duplication.
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Affiliation(s)
- Cecile Evrin
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joseph D Maman
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Aurora Diamante
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
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39
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Yan T, Liang W, Jiang E, Ye A, Wu Q, Xi M. GINS2 regulates cell proliferation and apoptosis in human epithelial ovarian cancer. Oncol Lett 2018; 16:2591-2598. [PMID: 30013653 DOI: 10.3892/ol.2018.8944] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 05/24/2018] [Indexed: 12/22/2022] Open
Abstract
Go-Ichi-Ni-San 2 (GINS2), also known as partner of Sld five 2, is involved in the initiation of DNA replication and cell cycle progression. GINS2 is abundantly expressed in a number of malignant solid tumors, including breast cancer, melanoma and hepatic carcinoma. However, the functions of GINS2 in epithelial ovarian cancer (EOC) remain unclear. The aim of the present study was to investigate these functions. GINS2 expression was detected in EOC and normal ovarian tissues using immunohistochemistry. To investigate the functions of GINS2 in EOC, GINS2 expression was stably knocked down in SKOV-3 cells using lentiviral short hairpin RNA (shRNA). The expression of GINS2 mRNA and protein in SKOV-3 cells was examined using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and western blot analyses, respectively. Cell proliferation was determined using high-content screening and MTT assays. Cell cycle progression and apoptosis were detected using flow cytometry. Compared with normal ovarian tissues, EOC tissues expressed increased levels of GINS2 expression (16.7 vs. 58.3%). Increased expression of GINS2 mRNA was also observed in SKOV-3 and OVCAR3 cells. In the investigation of GINS2 functions in EOC, GINS2 expression at the mRNA and protein levels was significantly inhibited by specific GINS2 shRNA. GINS2 knockdown significantly inhibited the proliferation and viability of SKOV-3 cells and induced cell cycle arrest in S phase. Furthermore, GINS2 knockdown in SKOV-3 cells significantly increased cell apoptosis. GINS2 is markedly expressed in EOC tissues and cell lines. Stable GINS2 knockdown in SKOV-3 cells significantly inhibited cell proliferation and induced cell cycle arrest and cell apoptosis. Therefore, GINS2 may be involved in EOC progression.
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Affiliation(s)
- Ting Yan
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China.,Department of Gynecology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Wentong Liang
- Department of Gynecology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Enli Jiang
- Department of Gynecology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Aizhu Ye
- Department of Clinical Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Qian Wu
- Department of Pathology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Mingrong Xi
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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Seo YS, Kang YH. The Human Replicative Helicase, the CMG Complex, as a Target for Anti-cancer Therapy. Front Mol Biosci 2018; 5:26. [PMID: 29651420 PMCID: PMC5885281 DOI: 10.3389/fmolb.2018.00026] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/12/2018] [Indexed: 12/14/2022] Open
Abstract
DNA helicases unwind or rearrange duplex DNA during replication, recombination and repair. Helicases of many pathogenic organisms such as viruses, bacteria, and protozoa have been studied as potential therapeutic targets to treat infectious diseases, and human DNA helicases as potential targets for anti-cancer therapy. DNA replication machineries perform essential tasks duplicating genome in every cell cycle, and one of the important functions of these machineries are played by DNA helicases. Replicative helicases are usually multi-subunit protein complexes, and the minimal complex active as eukaryotic replicative helicase is composed of 11 subunits, requiring a functional assembly of two subcomplexes and one protein. The hetero-hexameric MCM2-7 helicase is activated by forming a complex with Cdc45 and the hetero-tetrameric GINS complex; the Cdc45-Mcm2-7-GINS (CMG) complex. The CMG complex can be a potential target for a treatment of cancer and the feasibility of this replicative helicase as a therapeutic target has been tested recently. Several different strategies have been implemented and are under active investigations to interfere with helicase activity of the CMG complex. This review focuses on the molecular function of the CMG helicase during DNA replication and its relevance to cancers based on data published in the literature. In addition, current efforts made to identify small molecules inhibiting the CMG helicase to develop anti-cancer therapeutic strategies were summarized, with new perspectives to advance the discovery of the CMG-targeting drugs.
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Affiliation(s)
- Yeon-Soo Seo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Young-Hoon Kang
- Core Protein Resources Center, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
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41
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Tsuda M, Terada K, Ooka M, Kobayashi K, Sasanuma H, Fujisawa R, Tsurimoto T, Yamamoto J, Iwai S, Kadoda K, Akagawa R, Huang SYN, Pommier Y, Sale JE, Takeda S, Hirota K. The dominant role of proofreading exonuclease activity of replicative polymerase ε in cellular tolerance to cytarabine (Ara-C). Oncotarget 2018; 8:33457-33474. [PMID: 28380422 PMCID: PMC5464882 DOI: 10.18632/oncotarget.16508] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/28/2017] [Indexed: 11/25/2022] Open
Abstract
Chemotherapeutic nucleoside analogs, such as Ara-C, 5-Fluorouracil (5-FU) and Trifluridine (FTD), are frequently incorporated into DNA by the replicative DNA polymerases. However, it remains unclear how this incorporation kills cycling cells. There are two possibilities: Nucleoside analog triphosphates inhibit the replicative DNA polymerases, and/or nucleotide analogs mis-incorporated into genomic DNA interfere with the next round of DNA synthesis as replicative DNA polymerases recognize them as template DNA lesions, arresting synthesis. To address the first possibility, we selectively disrupted the proofreading exonuclease activity of DNA polymerase ε (Polε), the leading-strand replicative polymerase in avian DT40 and human TK6 cell lines. To address the second, we disrupted RAD18, a gene involved in translesion DNA synthesis, a mechanism that relieves stalled replication. Strikingly, POLE1exo−/− cells, but not RAD18−/− cells, were hypersensitive to Ara-C, while RAD18−/− cells were hypersensitive to FTD. gH2AX focus formation following a pulse of Ara-C was immediate and did not progress into the next round of replication, while gH2AX focus formation following a pulse of 5-FU and FTD was delayed to the next round of replication. Biochemical studies indicate that human proofreading-deficient Polε-exo− holoenzyme incorporates Ara-CTP, but subsequently extend from this base several times less efficiently than from intact nucleotides. Together our results suggest that Ara-C acts by blocking extension of the nascent DNA strand and is counteracted by the proofreading activity of Polε, while 5-FU and FTD are efficiently incorporated but act as replication fork blocks in the subsequent S phase, which is counteracted by translesion synthesis.
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Affiliation(s)
- Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Kazuhiro Terada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Masato Ooka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-Shi, Tokyo 192-0397, Japan
| | - Koji Kobayashi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-Shi, Tokyo 192-0397, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Ryo Fujisawa
- Department of Biology, School of Sciences, Kyushu University, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kei Kadoda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan.,Division of Radiation Life Science, Research Reactor Institute, Kyoto University, Kumatori, Sennan, Osaka 590-0494, Japan
| | - Remi Akagawa
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Kouji Hirota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan.,Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-Shi, Tokyo 192-0397, Japan
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42
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Li H, O'Donnell ME. The Eukaryotic CMG Helicase at the Replication Fork: Emerging Architecture Reveals an Unexpected Mechanism. Bioessays 2018; 40. [PMID: 29405332 DOI: 10.1002/bies.201700208] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/27/2017] [Indexed: 01/12/2023]
Abstract
The eukaryotic helicase is an 11-subunit machine containing an Mcm2-7 motor ring that encircles DNA, Cdc45 and the GINS tetramer, referred to as CMG (Cdc45, Mcm2-7, GINS). CMG is "built" on DNA at origins in two steps. First, two Mcm2-7 rings are assembled around duplex DNA at origins in G1 phase, forming the Mcm2-7 "double hexamer." In a second step, in S phase Cdc45 and GINS are assembled onto each Mcm2-7 ring, hence producing two CMGs that ultimately form two replication forks that travel in opposite directions. Here, we review recent findings about CMG structure and function. The CMG unwinds the parental duplex and is also the organizing center of the replisome: it binds DNA polymerases and other factors. EM studies reveal a 20-subunit core replisome with the leading Pol ϵ and lagging Pol α-primase on opposite faces of CMG, forming a fundamentally asymmetric architecture. Structural studies of CMG at a replication fork reveal unexpected details of how CMG engages the DNA fork. The structures of CMG and the Mcm2-7 double hexamer on DNA suggest a completely unanticipated process for formation of bidirectional replication forks at origins.
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Affiliation(s)
- Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Michael E O'Donnell
- Department of DNA Replication, Rockefeller University and HHMI, New York, NY 10065, USA
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43
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You Z, Masai H. Potent DNA strand annealing activity associated with mouse Mcm2∼7 heterohexameric complex. Nucleic Acids Res 2017; 45:6494-6506. [PMID: 28449043 PMCID: PMC5499727 DOI: 10.1093/nar/gkx269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/05/2017] [Indexed: 01/08/2023] Open
Abstract
Mini-chromosome maintenance (Mcm) is a central component for DNA unwinding reaction during eukaryotic DNA replication. Mcm2∼7, each containing a conserved ATPase motif, form a six subunit-heterohexamer. Although the reconstituted Mcm2∼7–Cdc45–GINS (CMG) complex displays DNA unwinding activity, the Mcm2∼7 complex does not generally exhibit helicase activity under a normal assay condition. We detected a strong DNA strand annealing activity in the purified mouse Mcm2∼7 heterohexamer, which promotes rapid reassociation of displaced complementary single-stranded DNAs, suggesting a potential cause for its inability to exhibit DNA helicase activity. Indeed, DNA unwinding activity of Mcm2∼7 could be detected in the presence of a single-stranded DNA that is complementary to the displaced strand, which would prevent its reannealing to the template. ATPase-deficient mutations in Mcm2, 4, 5 and 6 subunits inactivated the annealing activity, while those in Mcm2 and 5 subunits alone did not. The annealing activity of Mcm2∼7 does not require Mg2+ and ATP, and is adversely inhibited by the presence of high concentration of Mg2+ and ATP while activated by similar concentrations of ADP. Our findings show that the DNA helicase activity of Mcm2∼7 may be masked by its unexpectedly strong annealing activity, and suggest potential physiological roles of strand annealing activity of Mcm during replication stress responses.
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Affiliation(s)
- Zhiying You
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
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44
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Checkpoint Kinase Rad53 Couples Leading- and Lagging-Strand DNA Synthesis under Replication Stress. Mol Cell 2017; 68:446-455.e3. [PMID: 29033319 DOI: 10.1016/j.molcel.2017.09.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/07/2017] [Accepted: 09/13/2017] [Indexed: 02/05/2023]
Abstract
The checkpoint kinase Rad53 is activated during replication stress to prevent fork collapse, an essential but poorly understood process. Here we show that Rad53 couples leading- and lagging-strand synthesis under replication stress. In rad53-1 cells stressed by dNTP depletion, the replicative DNA helicase, MCM, and the leading-strand DNA polymerase, Pol ε, move beyond the site of DNA synthesis, likely unwinding template DNA. Remarkably, DNA synthesis progresses further along the lagging strand than the leading strand, resulting in the exposure of long stretches of single-stranded leading-strand template. The asymmetric DNA synthesis in rad53-1 cells is suppressed by elevated levels of dNTPs in vivo, and the activity of Pol ε is compromised more than lagging-strand polymerase Pol δ at low dNTP concentrations in vitro. Therefore, we propose that Rad53 prevents the generation of excessive ssDNA under replication stress by coordinating DNA unwinding with synthesis of both strands.
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45
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Fujisawa R, Ohashi E, Hirota K, Tsurimoto T. Human CTF18-RFC clamp-loader complexed with non-synthesising DNA polymerase ε efficiently loads the PCNA sliding clamp. Nucleic Acids Res 2017; 45:4550-4563. [PMID: 28199690 PMCID: PMC5416766 DOI: 10.1093/nar/gkx096] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 02/08/2017] [Indexed: 12/26/2022] Open
Abstract
The alternative proliferating-cell nuclear antigen (PCNA)-loader CTF18-RFC forms a stable complex with DNA polymerase ε (Polε). We observed that, under near-physiological conditions, CTF18-RFC alone loaded PCNA inefficiently, but loaded it efficiently when complexed with Polε. During efficient PCNA loading, CTF18-RFC and Polε assembled at a 3΄ primer–template junction cooperatively, and directed PCNA to the loading site. Site-specific photo-crosslinking of directly interacting proteins at the primer–template junction showed similar cooperative binding, in which the catalytic N-terminal portion of Polε acted as the major docking protein. In the PCNA-loading intermediate with ATPγS, binding of CTF18 to the DNA structures increased, suggesting transient access of CTF18-RFC to the primer terminus. Polε placed in DNA synthesis mode using a substrate DNA with a deoxidised 3΄ primer end did not stimulate PCNA loading, suggesting that DNA synthesis and PCNA loading are mutually exclusive at the 3΄ primer–template junction. Furthermore, PCNA and CTF18-RFC–Polε complex engaged in stable trimeric assembly on the template DNA and synthesised DNA efficiently. Thus, CTF18-RFC appears to be involved in leading-strand DNA synthesis through its interaction with Polε, and can load PCNA onto DNA when Polε is not in DNA synthesis mode to restore DNA synthesis.
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Affiliation(s)
- Ryo Fujisawa
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Eiji Ohashi
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Toshiki Tsurimoto
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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46
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Langston LD, Mayle R, Schauer GD, Yurieva O, Zhang D, Yao NY, Georgescu RE, O'Donnell ME. Mcm10 promotes rapid isomerization of CMG-DNA for replisome bypass of lagging strand DNA blocks. eLife 2017; 6:e29118. [PMID: 28869037 PMCID: PMC5599239 DOI: 10.7554/elife.29118] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/03/2017] [Indexed: 12/18/2022] Open
Abstract
Replicative helicases in all cell types are hexameric rings that unwind DNA by steric exclusion in which the helicase encircles the tracking strand only and excludes the other strand from the ring. This mode of translocation allows helicases to bypass blocks on the strand that is excluded from the central channel. Unlike other replicative helicases, eukaryotic CMG helicase partially encircles duplex DNA at a forked junction and is stopped by a block on the non-tracking (lagging) strand. This report demonstrates that Mcm10, an essential replication protein unique to eukaryotes, binds CMG and greatly stimulates its helicase activity in vitro. Most significantly, Mcm10 enables CMG and the replisome to bypass blocks on the non-tracking DNA strand. We demonstrate that bypass occurs without displacement of the blocks and therefore Mcm10 must isomerize the CMG-DNA complex to achieve the bypass function.
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Affiliation(s)
- Lance D Langston
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Ryan Mayle
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | | | - Olga Yurieva
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | | | - Nina Y Yao
- The Rockefeller UniversityNew YorkUnited States
| | - Roxana E Georgescu
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Mike E O'Donnell
- The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
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47
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Szambowska A, Tessmer I, Prus P, Schlott B, Pospiech H, Grosse F. Cdc45-induced loading of human RPA onto single-stranded DNA. Nucleic Acids Res 2017; 45:3217-3230. [PMID: 28100698 PMCID: PMC5389570 DOI: 10.1093/nar/gkw1364] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 01/02/2017] [Indexed: 11/14/2022] Open
Abstract
Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8–10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA. This placement reaction required physical contacts of Cdc45 with the RPA70A subdomain. Our results imply that Cdc45 controlled stabilization of the 8-nt RPA binding mode, the subsequent RPA transition into 30-mer mode and facilitated an ordered binding to ssDNA. We propose that a Cdc45-mediated loading guarantees a seamless deposition of RPA on newly emerging ssDNA at the nascent replication fork.
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Affiliation(s)
- Anna Szambowska
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Strasse 2, D-97080 Würzburg, Germany
| | - Piotr Prus
- Biocenter Oulu, P.O. Box 5000, 90014 University of Oulu, Finland
| | - Bernhard Schlott
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Proteomics Core Facility, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Helmut Pospiech
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Faculty of Biochemistry and Molecular Medicine, P.O. Box 5000, 90014 University of Oulu, Finland
| | - Frank Grosse
- Research Group Biochemistry, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.,Center for Molecular Biomedicine, Friedrich-Schiller University, Biochemistry Department, Jena, Germany
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48
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Sun J, Shi R, Zhao S, Li X, Lu S, Bu H, Ma X. Cell division cycle 45 promotes papillary thyroid cancer progression via regulating cell cycle. Tumour Biol 2017; 39:1010428317705342. [PMID: 28474999 DOI: 10.1177/1010428317705342] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cell division cycle 45 was reported to be overexpressed in some cancer-derived cell lines and was predicted to be a candidate oncogene in cervical cancer. However, the clinical and biological significance of cell division cycle 45 in papillary thyroid cancer has never been investigated. We determined the expression level and clinical significance of cell division cycle 45 using The Cancer Genome Atlas, quantitative real-time polymerase chain reaction, and immunohistochemistry. A great upregulation of cell division cycle 45 was observed in papillary thyroid cancer tissues compared with adjacent normal tissues. Furthermore, overexpression of cell division cycle 45 positively correlates with more advanced clinical characteristics. Silence of cell division cycle 45 suppressed proliferation of papillary thyroid cancer cells via G1-phase arrest and inducing apoptosis. The oncogenic activity of cell division cycle 45 was also confirmed in vivo. In conclusion, cell division cycle 45 may serve as a novel biomarker and a potential therapeutic target for papillary thyroid cancer.
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Affiliation(s)
- Jing Sun
- 1 Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Run Shi
- 2 The Fourth Clinical College of Nanjing Medical University, Nanjing, China
| | - Sha Zhao
- 3 Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaona Li
- 4 Health Management Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shan Lu
- 5 Department of Nutriology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hemei Bu
- 1 Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xianghua Ma
- 1 Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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49
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Abstract
The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation.
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50
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Yurieva O, O'Donnell M. Reconstitution of a eukaryotic replisome reveals the mechanism of asymmetric distribution of DNA polymerases. Nucleus 2017; 7:360-8. [PMID: 27416113 PMCID: PMC5039002 DOI: 10.1080/19491034.2016.1205774] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eukaryotes require 3 DNA polymerases for normal replisome operations, DNA polymerases (Pol) α, delta and epsilon. Recent biochemical and structural studies support the asymmetric use of these polymerases on the leading and lagging strands. Pol epsilon interacts with the 11-subunit CMG helicase, forming a 15-protein leading strand complex that acts processively in leading strand synthesis in vitro, but Pol epsilon is inactive on the lagging strand. The opposite results are observed for Pol delta with CMG. Pol delta is highly active on the lagging strand in vitro, but has only feeble activity with CMG on the leading strand. Pol α also functions with CMG to prime both strands, and is even capable of extending both strands with CMG present. However, extensive DNA synthesis by Pol α is sharply curtailed by the presence of either Pol epsilon or Pol delta, which limits the role of the low fidelity Pol α to the initial priming of synthesis.
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Affiliation(s)
- Olga Yurieva
- a Howard Hughes Medical Institute and DNA Replication Laboratory, The Rockefeller University , New York , NY , USA
| | - Mike O'Donnell
- a Howard Hughes Medical Institute and DNA Replication Laboratory, The Rockefeller University , New York , NY , USA
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