1
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Ito M, Fujita Y, Shinohara A. Positive and negative regulators of RAD51/DMC1 in homologous recombination and DNA replication. DNA Repair (Amst) 2024; 134:103613. [PMID: 38142595 DOI: 10.1016/j.dnarep.2023.103613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/10/2023] [Accepted: 12/10/2023] [Indexed: 12/26/2023]
Abstract
RAD51 recombinase plays a central role in homologous recombination (HR) by forming a nucleoprotein filament on single-stranded DNA (ssDNA) to catalyze homology search and strand exchange between the ssDNA and a homologous double-stranded DNA (dsDNA). The catalytic activity of RAD51 assembled on ssDNA is critical for the DNA-homology-mediated repair of DNA double-strand breaks in somatic and meiotic cells and restarting stalled replication forks during DNA replication. The RAD51-ssDNA complex also plays a structural role in protecting the regressed/reversed replication fork. Two types of regulators control RAD51 filament formation, stability, and dynamics, namely positive regulators, including mediators, and negative regulators, so-called remodelers. The appropriate balance of action by the two regulators assures genome stability. This review describes the roles of positive and negative RAD51 regulators in HR and DNA replication and its meiosis-specific homolog DMC1 in meiotic recombination. We also provide future study directions for a comprehensive understanding of RAD51/DMC1-mediated regulation in maintaining and inheriting genome integrity.
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Affiliation(s)
- Masaru Ito
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
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2
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Keymakh M, Dau J, Hu J, Ferlez B, Lisby M, Crickard JB. Rdh54 stabilizes Rad51 at displacement loop intermediates to regulate genetic exchange between chromosomes. PLoS Genet 2022; 18:e1010412. [PMID: 36099310 PMCID: PMC9506641 DOI: 10.1371/journal.pgen.1010412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/23/2022] [Accepted: 09/04/2022] [Indexed: 11/20/2022] Open
Abstract
Homologous recombination (HR) is a double-strand break DNA repair pathway that preserves chromosome structure. To repair damaged DNA, HR uses an intact donor DNA sequence located elsewhere in the genome. After the double-strand break is repaired, DNA sequence information can be transferred between donor and recipient DNA molecules through different mechanisms, including DNA crossovers that form between homologous chromosomes. Regulation of DNA sequence transfer is an important step in effectively completing HR and maintaining genome integrity. For example, mitotic exchange of information between homologous chromosomes can result in loss-of-heterozygosity (LOH), and in higher eukaryotes, the development of cancer. The DNA motor protein Rdh54 is a highly conserved DNA translocase that functions during HR. Several existing phenotypes in rdh54Δ strains suggest that Rdh54 may regulate effective exchange of DNA during HR. In our current study, we used a combination of biochemical and genetic techniques to dissect the role of Rdh54 on the exchange of genetic information during DNA repair. Our data indicate that RDH54 regulates DNA strand exchange by stabilizing Rad51 at an early HR intermediate called the displacement loop (D-loop). Rdh54 acts in opposition to Rad51 removal by the DNA motor protein Rad54. Furthermore, we find that expression of a catalytically inactivate allele of Rdh54, rdh54K318R, favors non-crossover outcomes. From these results, we propose a model for how Rdh54 may kinetically regulate strand exchange during homologous recombination. Homologous recombination is an important pathway in repairing DNA double strand breaks. For the purposes of this study, HR can be divided into two stages. The first is a DNA repair stage in which the broken DNA molecule is fixed. In the second stage, information can move from one DNA molecule to another. Enzymes that use the power of ATP hydrolysis to move along dsDNA aid in regulating both stages of HR. In this work we focused on the understudied DNA motor protein Rdh54. We combined genetic and biochemical approaches to show that Rdh54 regulates HR by stabilizing the recombinase protein Rad51 at early HR intermediates.
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Affiliation(s)
- Margaret Keymakh
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
| | - Jennifer Dau
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
| | - Jingyi Hu
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
| | - Bryan Ferlez
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - J. Brooks Crickard
- Deparment of Molecular Biology and Genetics, Cornell University Ithaca, Ithaca, New York, United States of America
- * E-mail:
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3
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Pérez-Martínez L, Wagner T, Luke B. Telomere Interacting Proteins and TERRA Regulation. Front Genet 2022; 13:872636. [PMID: 35464834 PMCID: PMC9024143 DOI: 10.3389/fgene.2022.872636] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/17/2022] [Indexed: 01/10/2023] Open
Abstract
Telomere shortening rates inversely correlate with life expectancy and hence it is critical to understand how telomere shortening is regulated. Recently, the telomeric non-coding RNA, TERRA has been implicated in the regulation of replicative senescence. To better understand how TERRA is regulated we employed a proteomics approach to look for potential RNA regulators that associate with telomeric sequences. Based on the results, we have identified proteins that may regulate TERRA in both a positive and negative manner, depending on the state of the telomere. In this mini-review, we discuss and speculate about these data to expand our understanding of TERRA and telomere interactors with respect to telomere shortening dynamics.
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Affiliation(s)
- Lara Pérez-Martínez
- Institute of Molecular Biology (IMB), Mainz, Germany
- IMDEA Food Institute, Madrid, Spain
| | - Tina Wagner
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg Universität, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg Universität, Mainz, Germany
- *Correspondence: Brian Luke,
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4
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Mackenroth B, Alani E. Collaborations between chromatin and nuclear architecture to optimize DNA repair fidelity. DNA Repair (Amst) 2021; 97:103018. [PMID: 33285474 PMCID: PMC8486310 DOI: 10.1016/j.dnarep.2020.103018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 01/22/2023]
Abstract
Homologous recombination (HR), considered the highest fidelity DNA double-strand break (DSB) repair pathway that a cell possesses, is capable of repairing multiple DSBs without altering genetic information. However, in "last resort" scenarios, HR can be directed to low fidelity subpathways which often use non-allelic donor templates. Such repair mechanisms are often highly mutagenic and can also yield chromosomal rearrangements and/or deletions. While the choice between HR and its less precise counterpart, non-homologous end joining (NHEJ), has received much attention, less is known about how cells manage and prioritize HR subpathways. In this review, we describe work focused on how chromatin and nuclear architecture orchestrate subpathway choice and repair template usage to maintain genome integrity without sacrificing cell survival. Understanding the relationships between nuclear architecture and recombination mechanics will be critical to understand these cellular repair decisions.
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Affiliation(s)
- Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States.
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5
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Brannvoll A, Xue X, Kwon Y, Kompocholi S, Simonsen AKW, Viswalingam KS, Gonzalez L, Hickson ID, Oestergaard VH, Mankouri HW, Sung P, Lisby M. The ZGRF1 Helicase Promotes Recombinational Repair of Replication-Blocking DNA Damage in Human Cells. Cell Rep 2020; 32:107849. [PMID: 32640219 PMCID: PMC7473174 DOI: 10.1016/j.celrep.2020.107849] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/10/2020] [Accepted: 06/11/2020] [Indexed: 01/05/2023] Open
Abstract
Replication-blocking DNA lesions are particularly toxic to proliferating cells because they can lead to chromosome mis-segregation if not repaired prior to mitosis. In this study, we report that ZGRF1 null cells accumulate chromosome aberrations following replication perturbation and show sensitivity to two potent replication-blocking anticancer drugs: mitomycin C and camptothecin. Moreover, ZGRF1 null cells are defective in catalyzing DNA damage-induced sister chromatid exchange despite accumulating excessive FANCD2, RAD51, and γ-H2AX foci upon induction of interstrand DNA crosslinks. Consistent with a direct role in promoting recombinational DNA repair, we show that ZGRF1 is a 5'-to-3' helicase that catalyzes D-loop dissociation and Holliday junction branch migration. Moreover, ZGRF1 physically interacts with RAD51 and stimulates strand exchange catalyzed by RAD51-RAD54. On the basis of these data, we propose that ZGRF1 promotes repair of replication-blocking DNA lesions through stimulation of homologous recombination.
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Affiliation(s)
- André Brannvoll
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Xiaoyu Xue
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | | | | | | | - Leticia Gonzalez
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Vibe H Oestergaard
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hocine W Mankouri
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Michael Lisby
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark.
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6
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Rad9/53BP1 promotes DNA repair via crossover recombination by limiting the Sgs1 and Mph1 helicases. Nat Commun 2020; 11:3181. [PMID: 32576832 PMCID: PMC7311424 DOI: 10.1038/s41467-020-16997-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 06/05/2020] [Indexed: 12/16/2022] Open
Abstract
The DNA damage checkpoint (DDC) is often robustly activated during the homologous recombination (HR) repair of DNA double strand breaks (DSBs). DDC activation controls several HR repair factors by phosphorylation, preventing premature segregation of entangled chromosomes formed during HR repair. The DDC mediator 53BP1/Rad9 limits the nucleolytic processing (resection) of a DSB, controlling the formation of the 3′ single-stranded DNA (ssDNA) filament needed for recombination, from yeast to human. Here we show that Rad9 promotes stable annealing between the recombinogenic filament and the donor template in yeast, limiting strand rejection by the Sgs1 and Mph1 helicases. This regulation allows repair by long tract gene conversion, crossover recombination and break-induced replication (BIR), only after DDC activation. These findings shed light on how cells couple DDC with the choice and effectiveness of HR sub-pathways, with implications for genome instability and cancer. In budding yeast, the 53BP1 ortholog Rad9 limits the resection nucleolytic processing of DNA double strand breaks. Here the authors reveal that Rad9 promotes long tract gene conversions, BIR and CO, during the HR repair of a DSB via modulation of Sgs1 and Mph1 helicases.
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7
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Resolvases, Dissolvases, and Helicases in Homologous Recombination: Clearing the Road for Chromosome Segregation. Genes (Basel) 2020; 11:genes11010071. [PMID: 31936378 PMCID: PMC7017083 DOI: 10.3390/genes11010071] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/29/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
The execution of recombinational pathways during the repair of certain DNA lesions or in the meiotic program is associated to the formation of joint molecules that physically hold chromosomes together. These structures must be disengaged prior to the onset of chromosome segregation. Failure in the resolution of these linkages can lead to chromosome breakage and nondisjunction events that can alter the normal distribution of the genomic material to the progeny. To avoid this situation, cells have developed an arsenal of molecular complexes involving helicases, resolvases, and dissolvases that recognize and eliminate chromosome links. The correct orchestration of these enzymes promotes the timely removal of chromosomal connections ensuring the efficient segregation of the genome during cell division. In this review, we focus on the role of different DNA processing enzymes that collaborate in removing the linkages generated during the activation of the homologous recombination machinery as a consequence of the appearance of DNA breaks during the mitotic and meiotic programs. We will also discuss about the temporal regulation of these factors along the cell cycle, the consequences of their loss of function, and their specific role in the removal of chromosomal links to ensure the accurate segregation of the genomic material during cell division.
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8
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Wong IN, Neo JPS, Oehler J, Schafhauser S, Osman F, Carr SB, Whitby MC. The Fml1-MHF complex suppresses inter-fork strand annealing in fission yeast. eLife 2019; 8:e49784. [PMID: 31855181 PMCID: PMC6952179 DOI: 10.7554/elife.49784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022] Open
Abstract
Previously we reported that a process called inter-fork strand annealing (IFSA) causes genomic deletions during the termination of DNA replication when an active replication fork converges on a collapsed fork (Morrow et al., 2017). We also identified the FANCM-related DNA helicase Fml1 as a potential suppressor of IFSA. Here, we confirm that Fml1 does indeed suppress IFSA, and show that this function depends on its catalytic activity and ability to interact with Mhf1-Mhf2 via its C-terminal domain. Finally, a plausible mechanism of IFSA suppression is demonstrated by the finding that Fml1 can catalyse regressed fork restoration in vitro.
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Affiliation(s)
- Io Nam Wong
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | | | - Judith Oehler
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | | | - Fekret Osman
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Stephen B Carr
- Research Complex at Harwell, Rutherford Appleton LaboratoryHarwellUnited Kingdom
| | - Matthew C Whitby
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
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9
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Bernal M, Yang X, Lisby M, Mazón G. The FANCM family Mph1 helicase localizes to the mitochondria and contributes to mtDNA stability. DNA Repair (Amst) 2019; 82:102684. [DOI: 10.1016/j.dnarep.2019.102684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/24/2022]
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10
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Wild P, Susperregui A, Piazza I, Dörig C, Oke A, Arter M, Yamaguchi M, Hilditch AT, Vuina K, Chan KC, Gromova T, Haber JE, Fung JC, Picotti P, Matos J. Network Rewiring of Homologous Recombination Enzymes during Mitotic Proliferation and Meiosis. Mol Cell 2019; 75:859-874.e4. [PMID: 31351878 PMCID: PMC6715774 DOI: 10.1016/j.molcel.2019.06.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/24/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023]
Abstract
Homologous recombination (HR) is essential for high-fidelity DNA repair during mitotic proliferation and meiosis. Yet, context-specific modifications must tailor the recombination machinery to avoid (mitosis) or enforce (meiosis) the formation of reciprocal exchanges-crossovers-between recombining chromosomes. To obtain molecular insight into how crossover control is achieved, we affinity purified 7 DNA-processing enzymes that channel HR intermediates into crossovers or noncrossovers from vegetative cells or cells undergoing meiosis. Using mass spectrometry, we provide a global characterization of their composition and reveal mitosis- and meiosis-specific modules in the interaction networks. Functional analyses of meiosis-specific interactors of MutLγ-Exo1 identified Rtk1, Caf120, and Chd1 as regulators of crossing-over. Chd1, which transiently associates with Exo1 at the prophase-to-metaphase I transition, enables the formation of MutLγ-dependent crossovers through its conserved ability to bind and displace nucleosomes. Thus, rewiring of the HR network, coupled to chromatin remodeling, promotes context-specific control of the recombination outcome.
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Affiliation(s)
- Philipp Wild
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Aitor Susperregui
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ilaria Piazza
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Christian Dörig
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ashwini Oke
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Meret Arter
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Miyuki Yamaguchi
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - Alexander T Hilditch
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Karla Vuina
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ki Choi Chan
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Tatiana Gromova
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - Jennifer C Fung
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Paola Picotti
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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11
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Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira-da-Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. MICROBIAL CELL 2019; 6:65-101. [PMID: 30652106 PMCID: PMC6334232 DOI: 10.15698/mic2019.01.665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L Klein
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Kenny K H Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Yi-Hsuan Chang
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Michael J Morten
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Sucheta Mukherjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Elizabeth S Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - João P Vieira-da-Rocha
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Shuang Wang
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Julie S Biteen
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France.,Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Eli Rothenberg
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
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12
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Sutherland JH, Holloman WK. Loss of Cohesin Subunit Rec8 Switches Rad51 Mediator Dependence in Resistance to Formaldehyde Toxicity in Ustilago maydis. Genetics 2018; 210:559-572. [PMID: 30082279 PMCID: PMC6216591 DOI: 10.1534/genetics.118.301439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/03/2018] [Indexed: 01/08/2023] Open
Abstract
DNA-protein cross-links (DPCs) are frequently occurring lesions that provoke continual threats to the integrity of the genome by interference with replication and transcription. Reactive aldehydes generated from endogenous metabolic processes or produced in the environment are sources that trigger cross-linking of DNA with associated proteins. DNA repair pathways in place for removing DPCs, or for bypassing them to enable completion of replication, include homologous recombination (HR) and replication fork remodeling (FR) systems. Here, we surveyed a set of mutants defective in known HR and FR components to determine their contribution toward maintaining resistance to chronic formaldehyde (FA) exposure in Ustilago maydis, a fungus that relies on the BRCA2-family member Brh2 as the principal Rad51 mediator in repair of DNA strand breaks. We found that, in addition to Brh2, Rad52 was also vital for resistance to FA. Deleting the gene for Rec8, a kleisin subunit of cohesin, eliminated the requirement for Brh2, but not Rad52, in FA resistance. The Rad51K133R mutant variant that is able to bind DNA but unable to dissociate from it was able to support resistance to FA. These findings suggest a model for DPC repair and tolerance that features a specialized role for Rad52, enabling Rad51 to access DNA in its noncanonical capacity of replication fork protection rather than DNA strand transfer.
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Affiliation(s)
- Jeanette H Sutherland
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
| | - William K Holloman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
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13
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Zhang R, Jing Y, Zhang H, Niu Y, Liu C, Wang J, Zen K, Zhang CY, Li D. Comprehensive Evolutionary Analysis of the Major RNA-Induced Silencing Complex Members. Sci Rep 2018; 8:14189. [PMID: 30242207 PMCID: PMC6155107 DOI: 10.1038/s41598-018-32635-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 09/12/2018] [Indexed: 01/10/2023] Open
Abstract
RNA-induced silencing complex (RISC) plays a critical role in small interfering RNA (siRNA) and microRNAs (miRNA) pathways. Accumulating evidence has demonstrated that the major RISC members (AGO, DICER, TRBP, PACT and GW182) represent expression discrepancies or multiple orthologues/paralogues in different species. To elucidate their evolutionary characteristics, an integrated evolutionary analysis was performed. Here, animal and plant AGOs were divided into three classes (multifunctional AGOs, siRNA-associated AGOs and piRNA-associated AGOs for animal AGOs and multifunctional AGOs, siRNA-associated AGOs and complementary functioning AGOs for plant AGOs). Animal and plant DICERs were grouped into one class (multifunctional DICERs) and two classes (multifunctional DICERs and siRNA-associated DICERs), respectively. Protista/fungi AGOs or DICERs were specifically associated with the siRNA pathway. Additionally, TRBP/PACT/GW182 were identified only in animals, and all of them functioned in the miRNA pathway. Mammalian AGOs, animal DICERs and chordate TRBP/PACT were found to be monophyletic. A large number of gene duplications were identified in AGO and DICER groups. Taken together, we provide a comprehensive evolutionary analysis, describe a phylogenetic tree-based classification of the major RISC members and quantify their gene duplication events. These findings are potentially useful for classifying RISCs, optimizing species-specific RISCs and developing research model organisms.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China
| | - Ying Jing
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China
| | - Haiyang Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China
| | - Yahan Niu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China
| | - Chang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China
| | - Jin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China
| | - Ke Zen
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China
| | - Donghai Li
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P.R. China.
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14
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Lafuente-Barquero J, Luke-Glaser S, Graf M, Silva S, Gómez-González B, Lockhart A, Lisby M, Aguilera A, Luke B. The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage. PLoS Genet 2017; 13:e1007136. [PMID: 29281624 PMCID: PMC5760084 DOI: 10.1371/journal.pgen.1007136] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 01/09/2018] [Accepted: 11/28/2017] [Indexed: 01/08/2023] Open
Abstract
RNA-DNA hybrids are naturally occurring obstacles that must be overcome by the DNA replication machinery. In the absence of RNase H enzymes, RNA-DNA hybrids accumulate, resulting in replication stress, DNA damage and compromised genomic integrity. We demonstrate that Mph1, the yeast homolog of Fanconi anemia protein M (FANCM), is required for cell viability in the absence of RNase H enzymes. The integrity of the Mph1 helicase domain is crucial to prevent the accumulation of RNA-DNA hybrids and RNA-DNA hybrid-dependent DNA damage, as determined by Rad52 foci. Mph1 forms foci when RNA-DNA hybrids accumulate, e.g. in RNase H or THO-complex mutants and at short telomeres. Mph1, however is a double-edged sword, whose action at hybrids must be regulated by the Smc5/6 complex. This is underlined by the observation that simultaneous inactivation of RNase H2 and Smc5/6 results in Mph1-dependent synthetic lethality, which is likely due to an accumulation of toxic recombination intermediates. The data presented here support a model, where Mph1’s helicase activity plays a crucial role in responding to persistent RNA-DNA hybrids. DNA damage can either occur exogenously through DNA damaging agents such as UV light and exposure to chemotherapeutics, or endogenously via metabolic, cellular processes. The RNA product of transcription, for example, can engage in the formation of RNA-DNA hybrids. Such RNA-DNA hybrids can impede replication fork progression and cause genomic instability, a hallmark of cancer. The misregulation of RNA-DNA hybrids has also been implicated in several neurological disorders. Recently, it has become evident that RNA-DNA hybrids may also have beneficial roles and therefore, these structures have to be tightly controlled. We found that Mph1 (mutator phenotype 1), the budding yeast homolog of Fanconi Anemia protein M, counteracts the accumulation of RNA-DNA hybrids. The inactivation of MPH1 results in a severe growth defect when combined with mutations in the well-characterized RNase H enzymes, that degrade the RNA moiety of an RNA-DNA hybrid. Based on the data presented here, we propose a model, where Mph1 itself has to be kept in check by the SMC (structural maintenance of chromosome) 5/6 complex at replication forks stalled by RNA-DNA hybrids. Mph1 acts as a double-edged sword, as both its deletion and the inability to control its helicase activity cause DNA damage and growth arrest when RNA-DNA hybrids accumulate.
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Affiliation(s)
- Juan Lafuente-Barquero
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
| | - Sarah Luke-Glaser
- Institute of Molecular Biology (IMB), Mainz, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marco Graf
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sonia Silva
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
- Department of Biology, University of Copenhagen, Ole Maaloeesvej 5, Copenhagen N, Denmark
| | - Belén Gómez-González
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
| | | | - Michael Lisby
- Department of Biology, University of Copenhagen, Ole Maaloeesvej 5, Copenhagen N, Denmark
| | - Andrés Aguilera
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avda. Americo Vespucio 24, Seville, Spain
- * E-mail: (BL); (AA)
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Institute of Neurobiology and Developmental Biology, JGU Mainz, Mainz, Germany
- * E-mail: (BL); (AA)
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15
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Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae. Genetics 2017; 206:1187-1225. [PMID: 28684602 PMCID: PMC5500125 DOI: 10.1534/genetics.112.145805] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/26/2017] [Indexed: 12/13/2022] Open
Abstract
Genome rearrangements result in mutations that underlie many human diseases, and ongoing genome instability likely contributes to the development of many cancers. The tools for studying genome instability in mammalian cells are limited, whereas model organisms such as Saccharomyces cerevisiae are more amenable to these studies. Here, we discuss the many genetic assays developed to measure the rate of occurrence of Gross Chromosomal Rearrangements (called GCRs) in S. cerevisiae. These genetic assays have been used to identify many types of GCRs, including translocations, interstitial deletions, and broken chromosomes healed by de novo telomere addition, and have identified genes that act in the suppression and formation of GCRs. Insights from these studies have contributed to the understanding of pathways and mechanisms that suppress genome instability and how these pathways cooperate with each other. Integrated models for the formation and suppression of GCRs are discussed.
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16
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Hoopes JI, Hughes AL, Hobson LA, Cortez LM, Brown AJ, Roberts SA. Avoidance of APOBEC3B-induced mutation by error-free lesion bypass. Nucleic Acids Res 2017; 45:5243-5254. [PMID: 28334887 PMCID: PMC5605239 DOI: 10.1093/nar/gkx169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/06/2017] [Indexed: 12/17/2022] Open
Abstract
APOBEC cytidine deaminases mutate cancer genomes by converting cytidines into uridines within ssDNA during replication. Although uracil DNA glycosylases limit APOBEC-induced mutation, it is unknown if subsequent base excision repair (BER) steps function on replication-associated ssDNA. Hence, we measured APOBEC3B-induced CAN1 mutation frequencies in yeast deficient in BER endonucleases or DNA damage tolerance proteins. Strains lacking Apn1, Apn2, Ntg1, Ntg2 or Rev3 displayed wild-type frequencies of APOBEC3B-induced canavanine resistance (CanR). However, strains without error-free lesion bypass proteins Ubc13, Mms2 and Mph1 displayed respective 4.9-, 2.8- and 7.8-fold higher frequency of APOBEC3B-induced CanR. These results indicate that mutations resulting from APOBEC activity are avoided by deoxyuridine conversion to abasic sites ahead of nascent lagging strand DNA synthesis and subsequent bypass by error-free template switching. We found this mechanism also functions during telomere re-synthesis, but with a diminished requirement for Ubc13. Interestingly, reduction of G to C substitutions in Ubc13-deficient strains uncovered a previously unknown role of Ubc13 in controlling the activity of the translesion synthesis polymerase, Rev1. Our results highlight a novel mechanism for error-free bypass of deoxyuridines generated within ssDNA and suggest that the APOBEC mutation signature observed in cancer genomes may under-represent the genomic damage these enzymes induce.
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Affiliation(s)
- James I Hoopes
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Amber L Hughes
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Lauren A Hobson
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Luis M Cortez
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Alexander J Brown
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Steven A Roberts
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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17
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Abstract
One major challenge during genome duplication is the stalling of DNA replication forks by various forms of template blockages. As these barriers can lead to incomplete replication, multiple mechanisms have to act concertedly to correct and rescue stalled replication forks. Among these mechanisms, replication fork regression entails simultaneous annealing of nascent and template strands, which leads to regression of replication forks and formation of four-way DNA junctions. In principle, this process can lead to either positive outcomes, such as DNA repair and replication resumption, or less desirable outcomes, such as misalignment between nascent and template DNA and DNA cleavage. While our understanding of replication fork regression and its various possible outcomes is still at an early stage, recent studies using combinational approaches in multiple organisms have begun to identify the enzymes that catalyze this DNA transaction and how these enzymes are regulated, as well as the specific manners by which fork regression can influence replication. This review summarizes these recent progresses. In keeping with the theme of this series of reviews, we focus on studies in yeast and compare to findings in higher eukaryotes. It is anticipated that these findings will form the basis for future endeavors to further elucidate replication fork remodeling and its implications for genome maintenance.
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18
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FANCM, BRCA1, and BLM cooperatively resolve the replication stress at the ALT telomeres. Proc Natl Acad Sci U S A 2017; 114:E5940-E5949. [PMID: 28673972 DOI: 10.1073/pnas.1708065114] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In the mammalian genome, certain genomic loci/regions pose greater challenges to the DNA replication machinery (i.e., the replisome) than others. Such known genomic loci/regions include centromeres, common fragile sites, subtelomeres, and telomeres. However, the detailed mechanism of how mammalian cells cope with the replication stress at these loci/regions is largely unknown. Here we show that depletion of FANCM, or of one of its obligatory binding partners, FAAP24, MHF1, and MHF2, induces replication stress primarily at the telomeres of cells that use the alternative lengthening of telomeres (ALT) pathway as their telomere maintenance mechanism. Using the telomere-specific single-molecule analysis of replicated DNA technique, we found that depletion of FANCM dramatically reduces the replication efficiency at ALT telomeres. We further show that FANCM, BRCA1, and BLM are actively recruited to the ALT telomeres that are experiencing replication stress and that the recruitment of BRCA1 and BLM to these damaged telomeres is interdependent and is regulated by both ATR and Chk1. Mechanistically, we demonstrated that, in FANCM-depleted ALT cells, BRCA1 and BLM help to resolve the telomeric replication stress by stimulating DNA end resection and homologous recombination (HR). Consistent with their roles in resolving the replication stress induced by FANCM deficiency, simultaneous depletion of BLM and FANCM, or of BRCA1 and FANCM, leads to increased micronuclei formation and synthetic lethality in ALT cells. We propose that these synthetic lethal interactions can be explored for targeting the ALT cancers.
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19
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Rendeková J, Ward TA, Šimoničová L, Thomas PH, Nosek J, Tomáška Ľ, McHugh PJ, Chovanec M. Mgm101: A double-duty Rad52-like protein. Cell Cycle 2016; 15:3169-3176. [PMID: 27636878 PMCID: PMC5176325 DOI: 10.1080/15384101.2016.1231288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mgm101 has well-characterized activity for the repair and replication of the mitochondrial genome. Recent work has demonstrated a further role for Mgm101 in nuclear DNA metabolism, contributing to an S-phase specific DNA interstrand cross-link repair pathway that acts redundantly with a pathway controlled by Pso2 exonuclease. Due to involvement of FANCM, FANCJ and FANCP homologues (Mph1, Chl1 and Slx4), this pathway has been described as a Fanconi anemia-like pathway. In this pathway, Mgm101 physically interacts with the DNA helicase Mph1 and the MutSα (Msh2/Msh6) heterodimer, but its precise role is yet to be elucidated. Data presented here suggests that Mgm101 functionally overlaps with Rad52, supporting previous suggestions that, based on protein structure and biochemical properties, Mgm101 and Rad52 belong to a family of proteins with similar function. In addition, our data shows that this overlap extends to the function of both proteins at telomeres, where Mgm101 is required for telomere elongation during chromosome replication in rad52 defective cells. We hypothesize that Mgm101 could, in Rad52-like manner, preferentially bind single-stranded DNAs (such as at stalled replication forks, broken chromosomes and natural chromosome ends), stabilize them and mediate single-strand annealing-like homologous recombination event to prevent them from converting into toxic structures.
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Affiliation(s)
- Jana Rendeková
- a Department of Genetics , Cancer Research Institute, Biomedical Research Center, Slovak Academy of Science , Bratislava , Slovak Republic
| | - Thomas A Ward
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Lucia Šimoničová
- c Department of Genetics , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Peter H Thomas
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Jozef Nosek
- d Department of Biochemistry , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Ľubomír Tomáška
- c Department of Genetics , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Peter J McHugh
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Miroslav Chovanec
- a Department of Genetics , Cancer Research Institute, Biomedical Research Center, Slovak Academy of Science , Bratislava , Slovak Republic
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20
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Replication-Associated Recombinational Repair: Lessons from Budding Yeast. Genes (Basel) 2016; 7:genes7080048. [PMID: 27548223 PMCID: PMC4999836 DOI: 10.3390/genes7080048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 12/23/2022] Open
Abstract
Recombinational repair processes multiple types of DNA lesions. Though best understood in the repair of DNA breaks, recombinational repair is intimately linked to other situations encountered during replication. As DNA strands are decorated with many types of blocks that impede the replication machinery, a great number of genomic regions cannot be duplicated without the help of recombinational repair. This replication-associated recombinational repair employs both the core recombination proteins used for DNA break repair and the specialized factors that couple replication with repair. Studies from multiple organisms have provided insights into the roles of these specialized factors, with the findings in budding yeast being advanced through use of powerful genetics and methods for detecting DNA replication and repair intermediates. In this review, we summarize recent progress made in this organism, ranging from our understanding of the classical template switch mechanisms to gap filling and replication fork regression pathways. As many of the protein factors and biological principles uncovered in budding yeast are conserved in higher eukaryotes, these findings are crucial for stimulating studies in more complex organisms.
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Dbl2 Regulates Rad51 and DNA Joint Molecule Metabolism to Ensure Proper Meiotic Chromosome Segregation. PLoS Genet 2016; 12:e1006102. [PMID: 27304859 PMCID: PMC4909299 DOI: 10.1371/journal.pgen.1006102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 05/12/2016] [Indexed: 11/19/2022] Open
Abstract
To identify new proteins required for faithful meiotic chromosome segregation, we screened a Schizosaccharomyces pombe deletion mutant library and found that deletion of the dbl2 gene led to missegregation of chromosomes during meiosis. Analyses of both live and fixed cells showed that dbl2Δ mutant cells frequently failed to segregate homologous chromosomes to opposite poles during meiosis I. Removing Rec12 (Spo11 homolog) to eliminate meiotic DNA double-strand breaks (DSBs) suppressed the segregation defect in dbl2Δ cells, indicating that Dbl2 acts after the initiation of meiotic recombination. Analyses of DSBs and Holliday junctions revealed no significant defect in their formation or processing in dbl2Δ mutant cells, although some Rec12-dependent DNA joint molecules persisted late in meiosis. Failure to segregate chromosomes in the absence of Dbl2 correlated with persistent Rad51 foci, and deletion of rad51 or genes encoding Rad51 mediators also suppressed the segregation defect of dbl2Δ. Formation of foci of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments, was impaired in dbl2Δ cells. Our results suggest that Dbl2 is a novel regulator of Fbh1 and thereby Rad51-dependent DSB repair required for proper meiotic chromosome segregation and viable sex cell formation. The wide conservation of these proteins suggests that our results apply to many species. Meiosis produces haploid gametes from diploid precursor cells. This reduction of chromosome number is achieved by two successive divisions after only a single round of DNA replication. To identify novel regulators of meiosis, we screened a library of fission yeast deletion mutants and found that deletion of the dbl2 gene led to missegregation of chromosomes during meiosis. Analysis of live dbl2Δ cells by fluorescence microscopy showed that chromosomes frequently failed to segregate during the first meiotic division. Further cytological and biochemical analyses revealed that this segregation defect is due to persistent intermediates of DNA double-strand break repair, also called DNA joint molecules. Our results indicate that Dbl2 is required for formation of Fbh1 DNA helicase foci at the sites of DNA double-strand break repair in order to process DNA joint molecules and allow segregation of chromosomes during meiotic divisions. Our bioinformatics searches revealed that Dbl2 is highly conserved in fungi, animals and plants, suggesting that Dbl2 plays a similar role in other organisms–the formation of viable sex cells and healthy progeny.
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Xue X, Papusha A, Choi K, Bonner JN, Kumar S, Niu H, Kaur H, Zheng XF, Donnianni RA, Lu L, Lichten M, Zhao X, Ira G, Sung P. Differential regulation of the anti-crossover and replication fork regression activities of Mph1 by Mte1. Genes Dev 2016; 30:687-99. [PMID: 26966246 PMCID: PMC4803054 DOI: 10.1101/gad.276139.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/17/2016] [Indexed: 02/03/2023]
Abstract
Xue et al. identified Mte1 as a multifunctional regulator of S. cerevisiae Mph1. Mte1 stimulates Mph1-mediated DNA replication fork regression and branch migration in a model substrate. Surprisingly, Mte1 antagonizes the D-loop-dissociative activity of Mph1–MHF and exerts a procrossover role in mitotic recombination. We identified Mte1 (Mph1-associated telomere maintenance protein 1) as a multifunctional regulator of Saccharomyces cerevisiae Mph1, a member of the FANCM family of DNA motor proteins important for DNA replication fork repair and crossover suppression during homologous recombination. We show that Mte1 interacts with Mph1 and DNA species that resemble a DNA replication fork and the D loop formed during recombination. Biochemically, Mte1 stimulates Mph1-mediated DNA replication fork regression and branch migration in a model substrate. Consistent with this activity, genetic analysis reveals that Mte1 functions with Mph1 and the associated MHF complex in replication fork repair. Surprisingly, Mte1 antagonizes the D-loop-dissociative activity of Mph1–MHF and exerts a procrossover role in mitotic recombination. We further show that the influence of Mte1 on Mph1 activities requires its binding to Mph1 and DNA. Thus, Mte1 differentially regulates Mph1 activities to achieve distinct outcomes in recombination and replication fork repair.
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Affiliation(s)
- Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Alma Papusha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Koyi Choi
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jacob N Bonner
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hengyao Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Hardeep Kaur
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Xiao-Feng Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Roberto A Donnianni
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, USA
| | - Lucy Lu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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