1
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Tan Q, Xu X. PTIP UFMylation promotes replication fork degradation in BRCA1-deficient cells. J Biol Chem 2024:107312. [PMID: 38657865 DOI: 10.1016/j.jbc.2024.107312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
"BRCAness" defines cancers that are homologous recombination (HR)-deficient due to BRCA1 or BRCA2 mutations. These mutations confer synthetic lethality with PARP1/2 inhibitors. The chromatin regulator PTIP promotes stalled replication fork degradation in "BRCAness" cells, but the underlying mechanism by which PTIP regulates stalled replication fork stability is unclear. Here, we performed a series of in vitro analyses to dissect the function of UFMylation in regulating fork stabilization in BRCA1-deficient cells. By denaturing co-immunoprecipitation, we first found that replication stress can induce PTIP UFMylation. Interestingly, this post-translational modification promotes end resection and degradation of nascent DNA at stalled replication forks in BRCA1-deficient cells. By cell viability assay, we found that PTIP-depleted and UFL1-depleted BRCA1 knockdown cells are less sensitive to PARP inhibitors than the siRNA targeting negative control BRCA1-deficient cells. These results identify a new mechanism by which PTIP UFMylation confers chemoresistance in BRCA1-deficient cells.
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Affiliation(s)
- Qunsong Tan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China.
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2
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Yates LA, Zhang X. Phosphoregulation of the checkpoint kinase Mec1 ATR. DNA Repair (Amst) 2023; 129:103543. [PMID: 37480741 DOI: 10.1016/j.dnarep.2023.103543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Yeast Mec1, and its mammalian ortholog, Ataxia-Telangiectasia and Rad3-related, are giant protein kinases central to replication stress and double strand DNA break repair. Mec1ATR, in complex with Ddc2ATRIP, is a 'sensor' of single stranded DNA, and phosphorylates numerous cell cycle and DNA repair factors to enforce cell cycle arrest and facilitate repair. Over the last several years, new techniques - particularly in structural biology - have provided molecular mechanisms for Mec1ATR function. It is becoming increasingly clear how post-translational modification of Mec1ATR and its interaction partners modulates the DNA damage checkpoint. In this review, we summarise the most recent work unravelling Mec1ATR function in the DNA damage checkpoint and provide a molecular context for its regulation by phosphorylation.
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Affiliation(s)
- Luke A Yates
- Section of Structural, Department of Infectious Disease, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK; DNA processing machines laboratory, Francis Crick Institute, London NW1 1AT, UK.
| | - Xiaodong Zhang
- Section of Structural, Department of Infectious Disease, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK; DNA processing machines laboratory, Francis Crick Institute, London NW1 1AT, UK.
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3
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Panessa GM, Tassoni-Tsuchida E, Pires MR, Felix RR, Jekabson R, de Souza-Pinto NC, da Cunha FM, Brandman O, Cussiol JRR. Opi1-mediated transcriptional modulation orchestrates genotoxic stress response in budding yeast. Genetics 2023; 225:iyad130. [PMID: 37440469 PMCID: PMC10691878 DOI: 10.1093/genetics/iyad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
In budding yeast, the transcriptional repressor Opi1 regulates phospholipid biosynthesis by repressing expression of genes containing inositol-sensitive upstream activation sequences. Upon genotoxic stress, cells activate the DNA damage response to coordinate a complex network of signaling pathways aimed at preserving genomic integrity. Here, we reveal that Opi1 is important to modulate transcription in response to genotoxic stress. We find that cells lacking Opi1 exhibit hypersensitivity to genotoxins, along with a delayed G1-to-S-phase transition and decreased gamma-H2A levels. Transcriptome analysis using RNA sequencing reveals that Opi1 plays a central role in modulating essential biological processes during methyl methanesulfonate (MMS)-associated stress, including repression of phospholipid biosynthesis and transduction of mating signaling. Moreover, Opi1 induces sulfate assimilation and amino acid metabolic processes, such as arginine and histidine biosynthesis and glycine catabolism. Furthermore, we observe increased mitochondrial DNA instability in opi1Δ cells upon MMS treatment. Notably, we show that constitutive activation of the transcription factor Ino2-Ino4 is responsible for genotoxin sensitivity in Opi1-deficient cells, and the production of inositol pyrophosphates by Kcs1 counteracts Opi1 function specifically during MMS-induced stress. Overall, our findings highlight Opi1 as a critical sensor of genotoxic stress in budding yeast, orchestrating gene expression to facilitate appropriate stress responses.
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Affiliation(s)
- Giovanna Marques Panessa
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Eduardo Tassoni-Tsuchida
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Marina Rodrigues Pires
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Rodrigo Rodrigues Felix
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Rafaella Jekabson
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | | | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - José Renato Rosa Cussiol
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
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4
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Wong RP, Petriukov K, Ulrich HD. Daughter-strand gaps in DNA replication - substrates of lesion processing and initiators of distress signalling. DNA Repair (Amst) 2021; 105:103163. [PMID: 34186497 DOI: 10.1016/j.dnarep.2021.103163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
Dealing with DNA lesions during genome replication is particularly challenging because damaged replication templates interfere with the progression of the replicative DNA polymerases and thereby endanger the stability of the replisome. A variety of mechanisms for the recovery of replication forks exist, but both bacteria and eukaryotic cells also have the option of continuing replication downstream of the lesion, leaving behind a daughter-strand gap in the newly synthesized DNA. In this review, we address the significance of these single-stranded DNA structures as sites of DNA damage sensing and processing at a distance from ongoing genome replication. We describe the factors controlling the emergence of daughter-strand gaps from stalled replication intermediates, the benefits and risks of their expansion and repair via translesion synthesis or recombination-mediated template switching, and the mechanisms by which they activate local as well as global replication stress signals. Our growing understanding of daughter-strand gaps not only identifies them as targets of fundamental genome maintenance mechanisms, but also suggests that proper control over their activities has important practical implications for treatment strategies and resistance mechanisms in cancer therapy.
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Affiliation(s)
- Ronald P Wong
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany
| | - Kirill Petriukov
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, D - 55128 Mainz, Germany.
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5
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Panichnantakul P, Patel A, Tse EYW, Wyatt HDM. An open-source platform to quantify subnuclear foci and protein colocalization in response to replication stress. DNA Repair (Amst) 2021; 105:103156. [PMID: 34139663 DOI: 10.1016/j.dnarep.2021.103156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/28/2022]
Abstract
Nuclear reorganization, including the localization of proteins into discrete subnuclear foci, is a hallmark of the cellular response to DNA damage and replication stress. These foci are thought to represent transient environments or repair factories, in which the lesion is sequestered with molecules and co-factors that catalyze repair. For example, nuclear foci contain signaling proteins that recruit transducer proteins. One important class of transducers is the structure-selective endonucleases, such as SLX1-SLX4, MUS81-EME1, and XPF-ERCC1, which remove branched DNA structures that form during repair. The relocalization of structure-selective endonucleases into subnuclear foci provides a visual read-out for the presence of direct DNA damage, replication barriers, or DNA entanglements and can be monitored using fluorescence microscopy. By simultaneously probing for two or more fluorescent signals, fluorescence microscopy can also provide insights into the proximal association of proteins within a local environment. Here, we report an open-source and semi-automated method to detect and quantify subnuclear foci, as well as foci colocalization and the accompanying pixel-based colocalization metrics. We use this pipeline to show that pre-mitotic nuclei contain a basal threshold of foci marked by SLX1-SLX4, MUS81, or XPF. Some of these foci colocalize with FANCD2 and have a high degree of correlation and co-occurrence. We also show that pre-mitotic cells experiencing replication stress contain elevated levels of foci containing SLX1-SLX4 or XPF, but not MUS81. These results point towards a role for SLX1-SLX4 and XPF-ERCC1 in the early cellular response to replication stress. Nevertheless, most of the foci that form in response to replication stress contain either FANCD2 or one of the three endonucleases. Altogether, our work highlights the compositional heterogeneity of subnuclear foci that form in response to replication stress. We also describe a user-friendly pipeline that can be used to characterize these dynamic structures.
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Affiliation(s)
- Pudchalaluck Panichnantakul
- Department of Biochemistry, University of Toronto, MaRS Centre, 661 University Ave., Toronto, ON, M5G 1M1, Canada
| | - Ayushi Patel
- Department of Biochemistry, University of Toronto, MaRS Centre, 661 University Ave., Toronto, ON, M5G 1M1, Canada
| | - Elizabeth Y W Tse
- Department of Biochemistry, University of Toronto, MaRS Centre, 661 University Ave., Toronto, ON, M5G 1M1, Canada
| | - Haley D M Wyatt
- Department of Biochemistry, University of Toronto, MaRS Centre, 661 University Ave., Toronto, ON, M5G 1M1, Canada; Canada Research Chairs Program, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
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6
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Litwin I, Mucha S, Pilarczyk E, Wysocki R, Maciaszczyk-Dziubinska E. Complex Mechanisms of Antimony Genotoxicity in Budding Yeast Involves Replication and Topoisomerase I-Associated DNA Lesions, Telomere Dysfunction and Inhibition of DNA Repair. Int J Mol Sci 2021; 22:4510. [PMID: 33925940 DOI: 10.3390/ijms22094510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 11/26/2022] Open
Abstract
Antimony is a toxic metalloid with poorly understood mechanisms of toxicity and uncertain carcinogenic properties. By using a combination of genetic, biochemical and DNA damage assays, we investigated the genotoxic potential of trivalent antimony in the model organism Saccharomyces cerevisiae. We found that low doses of Sb(III) generate various forms of DNA damage including replication and topoisomerase I-dependent DNA lesions as well as oxidative stress and replication-independent DNA breaks accompanied by activation of DNA damage checkpoints and formation of recombination repair centers. At higher concentrations of Sb(III), moderately increased oxidative DNA damage is also observed. Consistently, base excision, DNA damage tolerance and homologous recombination repair pathways contribute to Sb(III) tolerance. In addition, we provided evidence suggesting that Sb(III) causes telomere dysfunction. Finally, we showed that Sb(III) negatively effects repair of double-strand DNA breaks and distorts actin and microtubule cytoskeleton. In sum, our results indicate that Sb(III) exhibits a significant genotoxic activity in budding yeast.
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7
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Sadoughi F, Hallajzadeh J, Asemi Z, Mansournia MA, Alemi F, Yousefi B. Signaling pathways involved in cell cycle arrest during the DNA breaks. DNA Repair (Amst) 2021; 98:103047. [PMID: 33454524 DOI: 10.1016/j.dnarep.2021.103047] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
Our genome bears tens of thousands of harms and devastations per day; In this regard, numerous sophisticated and complicated mechanisms are embedded by our cells in furtherance of remitting an unchanged and stable genome to their next generation. These mechanisms, that are collectively called DDR, have the duty of detecting the lesions and repairing them. it's necessary for the viability of any living cell that sustain the integrity and stability of its genetic content and this highlights the role of mediators that transduce the signals of DNA damage to the cell cycle in order to prevent the replication of a defective DNA. In this paper, we review the signaling pathways that lie between these processes and define how different ingredients of DDR are also able to affect the checkpoint signaling.
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8
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Kaushal S, Wollmuth CE, Das K, Hile SE, Regan SB, Barnes RP, Haouzi A, Lee SM, House NCM, Guyumdzhyan M, Eckert KA, Freudenreich CH. Sequence and Nuclease Requirements for Breakage and Healing of a Structure-Forming (AT)n Sequence within Fragile Site FRA16D. Cell Rep 2020; 27:1151-1164.e5. [PMID: 31018130 DOI: 10.1016/j.celrep.2019.03.103] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/07/2019] [Accepted: 03/27/2019] [Indexed: 01/20/2023] Open
Abstract
Common fragile sites (CFSs) are genomic regions that display gaps and breaks in human metaphase chromosomes under replication stress and are often deleted in cancer cells. We studied an ∼300-bp subregion (Flex1) of human CFS FRA16D in yeast and found that it recapitulates characteristics of CFS fragility in human cells. Flex1 fragility is dependent on the ability of a variable-length AT repeat to form a cruciform structure that stalls replication. Fragility at Flex1 is initiated by structure-specific endonuclease Mus81-Mms4 acting together with the Slx1-4/Rad1-10 complex, whereas Yen1 protects Flex1 against breakage. Sae2 is required for healing of Flex1 after breakage. Our study shows that breakage within a CFS can be initiated by nuclease cleavage at forks stalled at DNA structures. Furthermore, our results suggest that CFSs are not just prone to breakage but also are impaired in their ability to heal, and this deleterious combination accounts for their fragility.
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Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Charles E Wollmuth
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Kohal Das
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Suzanne E Hile
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Samantha B Regan
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Ryan P Barnes
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Alice Haouzi
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Soo Mi Lee
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Nealia C M House
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Michael Guyumdzhyan
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA.
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9
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Delamarre A, Barthe A, de la Roche Saint-André C, Luciano P, Forey R, Padioleau I, Skrzypczak M, Ginalski K, Géli V, Pasero P, Lengronne A. MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading. Mol Cell 2020; 77:395-410.e3. [PMID: 31759824 DOI: 10.1016/j.molcel.2019.10.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/09/2019] [Accepted: 10/17/2019] [Indexed: 01/04/2023]
Abstract
The recovery of stalled replication forks depends on the controlled resection of nascent DNA and on the loading of cohesin. These processes operate in the context of nascent chromatin, but the impact of nucleosome structure on a fork restart remains poorly understood. Here, we show that the Mre11-Rad50-Xrs2 (MRX) complex acts together with the chromatin modifiers Gcn5 and Set1 and the histone remodelers RSC, Chd1, and Isw1 to promote chromatin remodeling at stalled forks. Increased chromatin accessibility facilitates the resection of nascent DNA by the Exo1 nuclease and the Sgs1 and Chl1 DNA helicases. Importantly, increased ssDNA promotes the recruitment of cohesin to arrested forks in a Scc2-Scc4-dependent manner. Altogether, these results indicate that MRX cooperates with chromatin modifiers to orchestrate the action of remodelers, nucleases, and DNA helicases, promoting the resection of nascent DNA and the loading of cohesin, two key processes involved in the recovery of arrested forks.
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Affiliation(s)
- Axel Delamarre
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Christophe de la Roche Saint-André
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Pierre Luciano
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Ismaël Padioleau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
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10
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Becker JR, Gallo D, Leung W, Croissant T, Thu YM, Nguyen HD, Starr TK, Brown GW, Bielinsky AK. Flap endonuclease overexpression drives genome instability and DNA damage hypersensitivity in a PCNA-dependent manner. Nucleic Acids Res 2019; 46:5634-5650. [PMID: 29741650 PMCID: PMC6009675 DOI: 10.1093/nar/gky313] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/16/2018] [Indexed: 12/31/2022] Open
Abstract
Overexpression of the flap endonuclease FEN1 has been observed in a variety of cancer types and is a marker for poor prognosis. To better understand the cellular consequences of FEN1 overexpression we utilized a model of its Saccharomyces cerevisiae homolog, RAD27. In this system, we discovered that flap endonuclease overexpression impedes replication fork progression and leads to an accumulation of cells in mid-S phase. This was accompanied by increased phosphorylation of the checkpoint kinase Rad53 and histone H2A-S129. RAD27 overexpressing cells were hypersensitive to treatment with DNA damaging agents, and defective in ubiquitinating the replication clamp proliferating cell nuclear antigen (PCNA) at lysine 164. These effects were reversed when the interaction between overexpressed Rad27 and PCNA was ablated, suggesting that the observed phenotypes were linked to problems in DNA replication. RAD27 overexpressing cells also exhibited an unexpected dependence on the SUMO ligases SIZ1 and MMS21 for viability. Importantly, we found that overexpression of FEN1 in human cells also led to phosphorylation of CHK1, CHK2, RPA32 and histone H2AX, all markers of genome instability. Our data indicate that flap endonuclease overexpression is a driver of genome instability in yeast and human cells that impairs DNA replication in a manner dependent on its interaction with PCNA.
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Affiliation(s)
- Jordan R Becker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Gallo
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, ON M5S 3E2, Canada
| | - Wendy Leung
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Taylor Croissant
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yee Mon Thu
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hai Dang Nguyen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, ON M5S 3E2, Canada
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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11
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Wan B, Wu J, Meng X, Lei M, Zhao X. Molecular Basis for Control of Diverse Genome Stability Factors by the Multi-BRCT Scaffold Rtt107. Mol Cell 2019; 75:238-251.e5. [PMID: 31348879 DOI: 10.1016/j.molcel.2019.05.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/11/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023]
Abstract
BRCT domains support myriad protein-protein interactions involved in genome maintenance. Although di-BRCT recognition of phospho-proteins is well known to support the genotoxic response, whether multi-BRCT domains can acquire distinct structures and functions is unclear. Here we present the tetra-BRCT structures from the conserved yeast protein Rtt107 in free and ligand-bound forms. The four BRCT repeats fold into a tetrahedral structure that recognizes unmodified ligands using a bi-partite mechanism, suggesting repeat origami enabling function acquisition. Functional studies show that Rtt107 binding of partner proteins of diverse activities promotes genome replication and stability in both distinct and concerted manners. A unified theme is that tetra- and di-BRCT domains of Rtt107 collaborate to recruit partner proteins to chromatin. Our work thus illustrates how a master regulator uses two types of BRCT domains to recognize distinct genome factors and direct them to chromatin for constitutive genome protection.
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Affiliation(s)
- Bingbing Wan
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jian Wu
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Xiangzhou Meng
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ming Lei
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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12
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Gallo D, Kim T, Szakal B, Saayman X, Narula A, Park Y, Branzei D, Zhang Z, Brown GW. Rad5 Recruits Error-Prone DNA Polymerases for Mutagenic Repair of ssDNA Gaps on Undamaged Templates. Mol Cell 2019; 73:900-914.e9. [PMID: 30733119 DOI: 10.1016/j.molcel.2019.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 09/13/2018] [Accepted: 12/27/2018] [Indexed: 12/30/2022]
Abstract
Post-replication repair (PRR) allows tolerance of chemical- and UV-induced DNA base lesions in both an error-free and an error-prone manner. In classical PRR, PCNA monoubiquitination recruits translesion synthesis (TLS) DNA polymerases that can replicate through lesions. We find that PRR responds to DNA replication stress that does not cause base lesions. Rad5 forms nuclear foci during normal S phase and after exposure to types of replication stress where DNA base lesions are likely absent. Rad5 binds to the sites of stressed DNA replication forks, where it recruits TLS polymerases to repair single-stranded DNA (ssDNA) gaps, preventing mitotic defects and chromosome breaks. In contrast to the prevailing view of PRR, our data indicate that Rad5 promotes both mutagenic and error-free repair of undamaged ssDNA that arises during physiological and exogenous replication stress.
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Affiliation(s)
- David Gallo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - TaeHyung Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada
| | - Barnabas Szakal
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
| | - Xanita Saayman
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Ashrut Narula
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Yoona Park
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada
| | - Dana Branzei
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
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13
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Kim SM, Forsburg SL. Regulation of Structure-Specific Endonucleases in Replication Stress. Genes (Basel) 2018; 9:genes9120634. [PMID: 30558228 PMCID: PMC6316474 DOI: 10.3390/genes9120634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/16/2022] Open
Abstract
Replication stress results in various forms of aberrant replication intermediates that need to be resolved for faithful chromosome segregation. Structure-specific endonucleases (SSEs) recognize DNA secondary structures rather than primary sequences and play key roles during DNA repair and replication stress. Holliday junction resolvase MUS81 (methyl methane sulfonate (MMS), and UV-sensitive protein 81) and XPF (xeroderma pigmentosum group F-complementing protein) are a subset of SSEs that resolve aberrant replication structures. To ensure genome stability and prevent unnecessary DNA breakage, these SSEs are tightly regulated by the cell cycle and replication checkpoints. We discuss the regulatory network that control activities of MUS81 and XPF and briefly mention other SSEs involved in the resolution of replication intermediates.
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Affiliation(s)
- Seong Min Kim
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
| | - Susan L Forsburg
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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14
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Moriel-carretero M, Pasero P, Pardo B. DDR Inc., one business, two associates. Curr Genet 2019; 65:445-51. [DOI: 10.1007/s00294-018-0908-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 01/03/2023]
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15
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Millan-Zambrano G, Santos-Rosa H, Puddu F, Robson SC, Jackson SP, Kouzarides T. Phosphorylation of Histone H4T80 Triggers DNA Damage Checkpoint Recovery. Mol Cell 2018; 72:625-635.e4. [PMID: 30454561 PMCID: PMC6242705 DOI: 10.1016/j.molcel.2018.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/08/2018] [Accepted: 09/18/2018] [Indexed: 11/24/2022]
Abstract
In response to genotoxic stress, cells activate a signaling cascade known as the DNA damage checkpoint (DDC) that leads to a temporary cell cycle arrest and activation of DNA repair mechanisms. Because persistent DDC activation compromises cell viability, this process must be tightly regulated. However, despite its importance, the mechanisms regulating DDC recovery are not completely understood. Here, we identify a DNA-damage-regulated histone modification in Saccharomyces cerevisiae, phosphorylation of H4 threonine 80 (H4T80ph), and show that it triggers checkpoint inactivation. H4T80ph is critical for cell survival to DNA damage, and its absence causes impaired DDC recovery and persistent cell cycle arrest. We show that, in response to genotoxic stress, p21-activated kinase Cla4 phosphorylates H4T80 to recruit Rtt107 to sites of DNA damage. Rtt107 displaces the checkpoint adaptor Rad9, thereby interrupting the checkpoint-signaling cascade. Collectively, our results indicate that H4T80ph regulates DDC recovery.
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Affiliation(s)
- Gonzalo Millan-Zambrano
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Helena Santos-Rosa
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Fabio Puddu
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Samuel C Robson
- School of Pharmacy and Biomedical Science, University of Portsmouth, White Swan Road, Portsmouth PO1 2DT, UK
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Tony Kouzarides
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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16
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Abstract
The SLX4/FANCP tumor suppressor has emerged as a key player in the maintenance of genome stability, making pivotal contributions to the repair of interstrand cross-links, homologous recombination, and in response to replication stress genome-wide as well as at specific loci such as common fragile sites and telomeres. SLX4 does so in part by acting as a scaffold that controls and coordinates the XPF-ERCC1, MUS81-EME1, and SLX1 structure-specific endonucleases in different DNA repair and recombination mechanisms. It also interacts with other important DNA repair and cell cycle control factors including MSH2, PLK1, TRF2, and TOPBP1 as well as with ubiquitin and SUMO. This review aims at providing an up-to-date and comprehensive view on the key functions that SLX4 fulfills to maintain genome stability as well as to highlight and discuss areas of uncertainty and emerging concepts.
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Affiliation(s)
- Jean-Hugues Guervilly
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
| | - Pierre Henri Gaillard
- a CRCM, CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes , Marseille , France
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17
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Abstract
DNA double-strand breaks (DSBs) are particularly hazardous lesions as their inappropriate repair can result in chromosome rearrangements, an important driving force of tumorigenesis. DSBs can be repaired by end joining mechanisms or by homologous recombination (HR). HR requires the action of several nucleases that preferentially remove the 5′-terminated strands at both DSB ends in a process called DNA end resection. The same nucleases are also involved in the processing of replication fork structures. Much of our understanding of these pathways has come from studies in the model organism Saccharomyces cerevisiae. Here, we review the current knowledge of the mechanism of resection at DNA DSBs and replication forks.
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Affiliation(s)
- Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | | | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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18
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Lanz MC, Oberly S, Sanford EJ, Sharma S, Chabes A, Smolka MB. Separable roles for Mec1/ATR in genome maintenance, DNA replication, and checkpoint signaling. Genes Dev 2018; 32:822-835. [PMID: 29899143 PMCID: PMC6049512 DOI: 10.1101/gad.308148.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/27/2018] [Indexed: 02/02/2023]
Abstract
In this study, Lanz et al. investigated how the Mec1/ATR kinase functions in genome maintenance and replication and, using a novel genetic system to spatially manipulate Mec1 activation and action, show that the ability of Mec1 to suppress genomic instabilities is separate from a novel role in promoting DNA replication. These findings establish that the Mec1/ATR kinase initiates checkpoint signaling, promotes DNA replication, and maintains genetic stability through distinct modes of action. The Mec1/ATR kinase coordinates multiple cellular responses to replication stress. In addition to its canonical role in activating the checkpoint kinase Rad53, Mec1 also plays checkpoint-independent roles in genome maintenance that are not well understood. Here we used a combined genetic–phosphoproteomic approach to manipulate Mec1 activation and globally monitor Mec1 signaling, allowing us to delineate distinct checkpoint-independent modes of Mec1 action. Using cells in which endogenous Mec1 activators were genetically ablated, we found that expression of “free” Mec1 activation domains (MADs) can robustly activate Mec1 and rescue the severe DNA replication and growth defects of these cells back to wild-type levels. However, unlike the activation mediated by endogenous activator proteins, “free” MADs are unable to stimulate Mec1-mediated suppression of gross chromosomal rearrangements (GCRs), revealing that Mec1's role in genome maintenance is separable from a previously unappreciated proreplicative function. Both Mec1's functions in promoting replication and suppressing GCRs are independent of the downstream checkpoint kinases. Additionally, Mec1-dependent GCR suppression seems to require localized Mec1 action at DNA lesions, which correlates with the phosphorylation of activator-proximal substrates involved in homologous recombination-mediated DNA repair. These findings establish that Mec1 initiates checkpoint signaling, promotes DNA replication, and maintains genetic stability through distinct modes of action.
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Affiliation(s)
- Michael Charles Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Susannah Oberly
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics.,Laboratory for Molecular Infection Medicine (MIMS), Umeå University, Umeå SE 90187, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics.,Laboratory for Molecular Infection Medicine (MIMS), Umeå University, Umeå SE 90187, Sweden
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
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19
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Díaz-Mejía JJ, Celaj A, Mellor JC, Coté A, Balint A, Ho B, Bansal P, Shaeri F, Gebbia M, Weile J, Verby M, Karkhanina A, Zhang Y, Wong C, Rich J, Prendergast D, Gupta G, Öztürk S, Durocher D, Brown GW, Roth FP. Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics. Mol Syst Biol 2018; 14:e7985. [PMID: 29807908 PMCID: PMC5974512 DOI: 10.15252/msb.20177985] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Condition‐dependent genetic interactions can reveal functional relationships between genes that are not evident under standard culture conditions. State‐of‐the‐art yeast genetic interaction mapping, which relies on robotic manipulation of arrays of double‐mutant strains, does not scale readily to multi‐condition studies. Here, we describe barcode fusion genetics to map genetic interactions (BFG‐GI), by which double‐mutant strains generated via en masse “party” mating can also be monitored en masse for growth to detect genetic interactions. By using site‐specific recombination to fuse two DNA barcodes, each representing a specific gene deletion, BFG‐GI enables multiplexed quantitative tracking of double mutants via next‐generation sequencing. We applied BFG‐GI to a matrix of DNA repair genes under nine different conditions, including methyl methanesulfonate (MMS), 4‐nitroquinoline 1‐oxide (4NQO), bleomycin, zeocin, and three other DNA‐damaging environments. BFG‐GI recapitulated known genetic interactions and yielded new condition‐dependent genetic interactions. We validated and further explored a subnetwork of condition‐dependent genetic interactions involving MAG1,SLX4, and genes encoding the Shu complex, and inferred that loss of the Shu complex leads to an increase in the activation of the checkpoint protein kinase Rad53.
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Affiliation(s)
- J Javier Díaz-Mejía
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Albi Celaj
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Joseph C Mellor
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Atina Coté
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Attila Balint
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Brandon Ho
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Pritpal Bansal
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Fatemeh Shaeri
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Marinella Gebbia
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jochen Weile
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Marta Verby
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Anna Karkhanina
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - YiFan Zhang
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Justin Rich
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - D'Arcy Prendergast
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Gaurav Gupta
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Sedide Öztürk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Daniel Durocher
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada
| | - Grant W Brown
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Canadian Institute for Advanced Research, Toronto, ON, Canada
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20
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García-Rodríguez N, Morawska M, Wong RP, Daigaku Y, Ulrich HD. Spatial separation between replisome- and template-induced replication stress signaling. EMBO J 2018; 37:embj.201798369. [PMID: 29581097 PMCID: PMC5920239 DOI: 10.15252/embj.201798369] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/29/2018] [Accepted: 02/26/2018] [Indexed: 11/09/2022] Open
Abstract
Polymerase‐blocking DNA lesions are thought to elicit a checkpoint response via accumulation of single‐stranded DNA at stalled replication forks. However, as an alternative to persistent fork stalling, re‐priming downstream of lesions can give rise to daughter‐strand gaps behind replication forks. We show here that the processing of such structures by an exonuclease, Exo1, is required for timely checkpoint activation, which in turn prevents further gap erosion in S phase. This Rad9‐dependent mechanism of damage signaling is distinct from the Mrc1‐dependent, fork‐associated response to replication stress induced by conditions such as nucleotide depletion or replisome‐inherent problems, but reminiscent of replication‐independent checkpoint activation by single‐stranded DNA. Our results indicate that while replisome stalling triggers a checkpoint response directly at the stalled replication fork, the response to replication stress elicited by polymerase‐blocking lesions mainly emanates from Exo1‐processed, postreplicative daughter‐strand gaps, thus offering a mechanistic explanation for the dichotomy between replisome‐ versus template‐induced checkpoint signaling.
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Affiliation(s)
| | - Magdalena Morawska
- Institute of Molecular Biology (IMB), Mainz, Germany.,Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane South Mimms, UK
| | - Ronald P Wong
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Yasukazu Daigaku
- Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane South Mimms, UK
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21
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Villa M, Bonetti D, Carraro M, Longhese MP. Rad9/53BP1 protects stalled replication forks from degradation in Mec1/ATR-defective cells. EMBO Rep 2018; 19:351-367. [PMID: 29301856 PMCID: PMC5797966 DOI: 10.15252/embr.201744910] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/16/2022] Open
Abstract
Nucleolytic processing by nucleases can be a relevant mechanism to allow repair/restart of stalled replication forks. However, nuclease action needs to be controlled to prevent overprocessing of damaged replication forks that can be detrimental to genome stability. The checkpoint protein Rad9/53BP1 is known to limit nucleolytic degradation (resection) of DNA double-strand breaks (DSBs) in both yeast and mammals. Here, we show that loss of the inhibition that Rad9 exerts on resection exacerbates the sensitivity to replication stress of Mec1/ATR-defective yeast cells by exposing stalled replication forks to Dna2-dependent degradation. This Rad9 protective function is independent of checkpoint activation and relies mainly on Rad9-Dpb11 interaction. We propose that Rad9/53BP1 supports cell viability by protecting stalled replication forks from extensive resection when the intra-S checkpoint is not fully functional.
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Affiliation(s)
- Matteo Villa
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Massimo Carraro
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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22
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Reubens MC, Rozenzhak S, Russell P. Multi-BRCT Domain Protein Brc1 Links Rhp18/Rad18 and γH2A To Maintain Genome Stability during S Phase. Mol Cell Biol 2017; 37:e00260-17. [PMID: 28784724 DOI: 10.1128/MCB.00260-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/04/2017] [Indexed: 12/17/2022] Open
Abstract
DNA replication involves the inherent risk of genome instability, since replisomes invariably encounter DNA lesions or other structures that stall or collapse replication forks during the S phase. In the fission yeast Schizosaccharomyces pombe, the multi-BRCT domain protein Brc1, which is related to budding yeast Rtt107 and mammalian PTIP, plays an important role in maintaining genome integrity and cell viability when cells experience replication stress. The C-terminal pair of BRCT domains in Brc1 were previously shown to bind phosphohistone H2A (γH2A) formed by Rad3/ATR checkpoint kinase at DNA lesions; however, the putative scaffold interactions involving the N-terminal BRCT domains 1 to 4 of Brc1 have remained obscure. Here, we show that these domains bind Rhp18/Rad18, which is an E3 ubiquitin protein ligase that has crucial functions in postreplication repair. A missense allele in BRCT domain 4 of Brc1 disrupts binding to Rhp18 and causes sensitivity to replication stress. Brc1 binding to Rhp18 and γH2A are required for the Brc1 overexpression suppression of smc6-74, a mutation that impairs the Smc5/6 structural maintenance of chromosomes complex required for chromosome integrity and repair of collapsed replication forks. From these findings, we propose that Brc1 provides scaffolding functions linking γH2A, Rhp18, and Smc5/6 complex at damaged replication forks.
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23
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Loll-Krippleber R, Brown GW. P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance. Nat Commun 2017; 8:558. [PMID: 28916784 PMCID: PMC5601920 DOI: 10.1038/s41467-017-00632-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 07/12/2017] [Indexed: 12/12/2022] Open
Abstract
mRNA-processing (P-) bodies are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant downregulation of a network of genes critical for DNA replication stress resistance and leads to toxic acetaldehyde accumulation. Our data reveal the scope and the targets of regulation by P-body proteins during the DNA replication stress response. P-bodies form in response to stress and act as sites of mRNA storage and degradation. Here the authors identify the mRNA targets of P-bodies during DNA replication stress, and show that P-body proteins act to prevent toxic accumulation of these target transcripts.
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Affiliation(s)
- Raphael Loll-Krippleber
- Department of Biochemistry and Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON, Canada, M5S 3E1
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON, Canada, M5S 3E1.
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24
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Abstract
Structure-specific endonucleases (SSEs) have key roles in DNA replication, recombination and repair, and emerging roles in transcription. These enzymes have specificity for DNA secondary structure rather than for sequence, and therefore their activity must be precisely controlled to ensure genome stability. In this Review, we discuss how SSEs are controlled as part of genome maintenance pathways in eukaryotes, with an emphasis on the elaborate mechanisms that regulate the members of the major SSE families - including the xeroderma pigmentosum group F-complementing protein (XPF) and MMS and UV-sensitive protein 81 (MUS81)-dependent nucleases, and the flap endonuclease 1 (FEN1), XPG and XPG-like endonuclease 1 (GEN1) enzymes - during processes such as DNA adduct repair, Holliday junction processing and replication stress. We also discuss newly characterized connections between SSEs and other classes of DNA-remodelling enzymes and cell cycle control machineries, which reveal the importance of SSE scaffolds such as the synthetic lethal of unknown function 4 (SLX4) tumour suppressor for the maintenance of genome stability.
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Affiliation(s)
- Pierre-Marie Dehé
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| | - Pierre-Henri L Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
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25
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Abstract
Checkpoint recovery is integral to a successful checkpoint response. Checkpoint pathways monitor progress during cell division so that in the event of an error, the checkpoint is activated to block the cell cycle and activate repair pathways. Intrinsic to this process is that once repair has been achieved, the checkpoint signaling pathway is inactivated and cell cycle progression resumes. We use the term “checkpoint recovery” to describe the pathways responsible for the inactivation of checkpoint signaling and cell cycle re-entry after the initial stress has been alleviated. The DNA replication or S-phase checkpoint monitors the integrity of DNA synthesis. When replication stress is encountered, replication forks are stalled, and the checkpoint signaling pathway is activated. Central to recovery from the S-phase checkpoint is the restart of stalled replication forks. If checkpoint recovery fails, stalled forks may become unstable and lead to DNA breaks or unusual DNA structures that are difficult to resolve, causing genomic instability. Alternatively, if cell cycle resumption mechanisms become uncoupled from checkpoint inactivation, cells with under-replicated DNA might proceed through the cell cycle, also diminishing genomic stability. In this review, we discuss the molecular mechanisms that contribute to inactivation of the S-phase checkpoint signaling pathway and the restart of replication forks during recovery from replication stress.
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26
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Abstract
Genome maintenance requires coordinated actions of diverse DNA metabolism processes. Scaffolding proteins, such as those containing multiple BRCT domains, can influence these processes by collaborating with numerous partners. The best-studied examples of multi-BRCT scaffolds are the budding yeast Dpb11 and its homologues in other organisms, which regulate DNA replication, repair, and damage checkpoints. Recent studies have shed light on another group of multi-BRCT scaffolds, including Rtt107 in budding yeast and related proteins in other organisms. These proteins also influence several DNA metabolism pathways, though they use strategies unlike those employed by the Dpb11 family of proteins. Yet, at the same time, these 2 classes of multi-BRCT proteins can collaborate under specific situations. This review summarizes recent advances in our understanding of how these multi-BRCT proteins function in distinct manners and how they collaborate, with a focus on Dpb11 and Rtt107.
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Affiliation(s)
- Bingbing Wan
- a Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York , NY , USA
| | - Lisa E Hang
- a Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York , NY , USA
| | - Xiaolan Zhao
- a Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York , NY , USA
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27
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Abstract
Faithful duplication of the entire genome during each cell cycle is key for genome maintenance. Each stage of DNA replication, including initiation, progression, and termination, is tightly regulated. Some of these regulations enable replisomes to overcome tens of thousands of template obstacles that block DNA synthesis. Previous studies have identified a large number of proteins that are dedicated to this mission, including protein modification enzymes and scaffold proteins. Protein modification enzymes can bestow fast and reversible changes on many substrates, and thus are ideal for coordinating multiple events needed to promptly overcome replication impediments. Scaffold proteins can support specific protein-protein interactions that enable protein complex formation, protein recruitment, and partner enzyme functions. Taken together with previous studies, our recent work elucidates that a group of modification and scaffold proteins form several complexes to aid replication progression and are particularly important for synthesizing large replicons. Additionally, our work reveals that the intrinsic plasticity of the replication initiation program can be used to compensate for deficient replication progression. (1).
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Affiliation(s)
- Lisa Hang
- a Molecular Biology Program, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
| | - Xiaolan Zhao
- a Molecular Biology Program, Memorial Sloan-Kettering Cancer Center , New York , NY , USA
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28
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Cussiol JR, Dibitetto D, Pellicioli A, Smolka MB. Slx4 scaffolding in homologous recombination and checkpoint control: lessons from yeast. Chromosoma 2016; 126:45-58. [PMID: 27165041 DOI: 10.1007/s00412-016-0600-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 01/07/2023]
Abstract
Homologous recombination-mediated DNA repair is essential for maintaining genome integrity. It is a multi-step process that involves resection of DNA ends, strand invasion, DNA synthesis and/or DNA end ligation, and finally, the processing of recombination intermediates such as Holliday junctions or other joint molecules. Over the last 15 years, it has been established that the Slx4 protein plays key roles in the processing of recombination intermediates, functioning as a scaffold to coordinate the action of structure-specific endonucleases. Recent work in budding yeast has uncovered unexpected roles for Slx4 in the initial step of DNA-end resection and in the modulation of DNA damage checkpoint signaling. Here we review these latest findings and discuss the emerging role of yeast Slx4 as an important coordinator of DNA damage signaling responses and a regulator of multiple steps in homologous recombination-mediated repair.
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Affiliation(s)
- José R Cussiol
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Diego Dibitetto
- Department of Biosciences, University of Milan, 20133, Milan, Italy
| | | | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
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29
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Yimit A, Kim T, Anand RP, Meister S, Ou J, Haber JE, Zhang Z, Brown GW. MTE1 Functions with MPH1 in Double-Strand Break Repair. Genetics 2016; 203:147-57. [PMID: 26920759 DOI: 10.1534/genetics.115.185454] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/22/2016] [Indexed: 11/18/2022] Open
Abstract
Double-strand DNA breaks occur upon exposure of cells to ionizing radiation and certain chemical agents or indirectly through replication fork collapse at DNA damage sites. If left unrepaired, double-strand breaks can cause genome instability and cell death, and their repair can result in loss of heterozygosity. In response to DNA damage, proteins involved in double-strand break repair by homologous recombination relocalize into discrete nuclear foci. We identified 29 proteins that colocalize with recombination repair protein Rad52 in response to DNA damage. Of particular interest, Ygr042w/Mte1, a protein of unknown function, showed robust colocalization with Rad52. Mte1 foci fail to form when the DNA helicase gene MPH1 is absent. Mte1 and Mph1 form a complex and are recruited to double-strand breaks in vivo in a mutually dependent manner. MTE1 is important for resolution of Rad52 foci during double-strand break repair and for suppressing break-induced replication. Together our data indicate that Mte1 functions with Mph1 in double-strand break repair.
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30
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Simoneau A, Ricard É, Weber S, Hammond-Martel I, Wong LH, Sellam A, Giaever G, Nislow C, Raymond M, Wurtele H. Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress. Nucleic Acids Res 2016; 44:2706-26. [PMID: 26748095 PMCID: PMC4824096 DOI: 10.1093/nar/gkv1537] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/24/2015] [Indexed: 12/13/2022] Open
Abstract
The Saccharomyces cerevisiae genome encodes five sirtuins (Sir2 and Hst1-4), which constitute a conserved family of NAD-dependent histone deacetylases. Cells lacking any individual sirtuin display mild growth and gene silencing defects. However, hst3Δ hst4Δ double mutants are exquisitely sensitive to genotoxins, and hst3Δ hst4Δ sir2Δmutants are inviable. Our published data also indicate that pharmacological inhibition of sirtuins prevents growth of several fungal pathogens, although the biological basis is unclear. Here, we present genome-wide fitness assays conducted with nicotinamide (NAM), a pan-sirtuin inhibitor. Our data indicate that NAM treatment causes yeast to solicit specific DNA damage response pathways for survival, and that NAM-induced growth defects are mainly attributable to inhibition of Hst3 and Hst4 and consequent elevation of histone H3 lysine 56 acetylation (H3K56ac). Our results further reveal that in the presence of constitutive H3K56ac, the Slx4 scaffolding protein and PP4 phosphatase complex play essential roles in preventing hyperactivation of the DNA damage-response kinase Rad53 in response to spontaneous DNA damage caused by reactive oxygen species. Overall, our data support the concept that chromosome-wide histone deacetylation by sirtuins is critical to mitigate growth defects caused by endogenous genotoxins.
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Affiliation(s)
- Antoine Simoneau
- Maisonneuve-Rosemont Hospital Research Center, 5415 Assomption boulevard, Montreal, H1T 2M4, Canada Molecular biology program, Université de Montréal, P.O. Box 6128, Succursale Centre-ville, Montreal, H3C 3J7, Canada
| | - Étienne Ricard
- Maisonneuve-Rosemont Hospital Research Center, 5415 Assomption boulevard, Montreal, H1T 2M4, Canada Molecular biology program, Université de Montréal, P.O. Box 6128, Succursale Centre-ville, Montreal, H3C 3J7, Canada
| | - Sandra Weber
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada
| | - Ian Hammond-Martel
- Maisonneuve-Rosemont Hospital Research Center, 5415 Assomption boulevard, Montreal, H1T 2M4, Canada Molecular biology program, Université de Montréal, P.O. Box 6128, Succursale Centre-ville, Montreal, H3C 3J7, Canada
| | - Lai Hong Wong
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Adnane Sellam
- Infectious Diseases Research Centre-CRI, CHU de Québec Research Center (CHUQ), Université Laval, Québec, G1V 4G2, Canada Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Québec, G1V 0A6, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Martine Raymond
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, H3C 3J7, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, 5415 Assomption boulevard, Montreal, H1T 2M4, Canada Department of Medicine, Université de Montréal, Montreal, H3T 1J4, Canada
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31
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Dibitetto D, Ferrari M, Rawal CC, Balint A, Kim T, Zhang Z, Smolka MB, Brown GW, Marini F, Pellicioli A. Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaks. Nucleic Acids Res 2015; 44:669-82. [PMID: 26490958 PMCID: PMC4737138 DOI: 10.1093/nar/gkv1080] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/06/2015] [Indexed: 11/13/2022] Open
Abstract
The DNA damage checkpoint pathway is activated in response to DNA lesions and replication stress to preserve genome integrity. However, hyper-activation of this surveillance system is detrimental to the cell, because it might prevent cell cycle re-start after repair, which may also lead to senescence. Here we show that the scaffold proteins Slx4 and Rtt107 limit checkpoint signalling at a persistent double-strand DNA break (DSB) and at uncapped telomeres. We found that Slx4 is recruited within a few kilobases of an irreparable DSB, through the interaction with Rtt107 and the multi-BRCT domain scaffold Dpb11. In the absence of Slx4 or Rtt107, Rad9 binding near the irreparable DSB is increased, leading to robust checkpoint signalling and slower nucleolytic degradation of the 5′ strand. Importantly, in slx4Δ sae2Δ double mutant cells these phenotypes are exacerbated, causing a severe Rad9-dependent defect in DSB repair. Our study sheds new light on the molecular mechanism that coordinates the processing and repair of DSBs with DNA damage checkpoint signalling, preserving genome integrity.
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Affiliation(s)
- Diego Dibitetto
- Department of Biosciences, University of Milan, 20133, Milano, Italy
| | - Matteo Ferrari
- Department of Biosciences, University of Milan, 20133, Milano, Italy
| | - Chetan C Rawal
- Department of Biosciences, University of Milan, 20133, Milano, Italy
| | - Attila Balint
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S3E1, Canada Donnelly Centre, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - TaeHyung Kim
- Donnelly Centre, University of Toronto, Toronto, Ontario, M5S3E1, Canada Department of Computer Science, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, Ontario, M5S3E1, Canada Department of Computer Science, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S3E1, Canada Donnelly Centre, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Federica Marini
- Department of Biosciences, University of Milan, 20133, Milano, Italy
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32
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Abstract
Phosphorylation of histone H2AX by ATM and ATR establishes a chromatin recruitment platform for DNA damage response proteins. Phospho-H2AX (γH2AX) has been most intensively studied in the context of DNA double-strand breaks caused by exogenous clastogens, but recent studies suggest that DNA replication stress also triggers formation of γH2A (ortholog of γH2AX) in Schizosaccharomyces pombe. Here, a focused genetic screen in fission yeast reveals that γH2A is critical when there are defects in Replication Factor C (RFC), which loads proliferating cell nuclear antigen (PCNA) clamp onto duplex DNA. Surprisingly Chk1, Cds1/Chk2 and the Rad9-Hus1-Rad1 checkpoint clamp, which are crucial for surviving many genotoxins, are fully dispensable in RFC-defective cells. Immunoblot analysis confirms that Rad9-Hus1-Rad1 is not required for formation of γH2A by Rad3/ATR in S-phase. Defects in DNA polymerase epsilon, which binds PCNA in the replisome, also create an acute need for γH2A. These requirements for γH2A were traced to its role in docking with Brc1, which is a 6-BRCT-domain protein that is structurally related to budding yeast Rtt107 and mammalian PTIP. Brc1, which localizes at stalled replication forks by binding γH2A, prevents aberrant formation of Replication Protein A (RPA) foci in RFC-impaired cells, suggesting that Brc1-coated chromatin stabilizes replisomes when PCNA or DNA polymerase availability limits DNA synthesis. ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3 related) are evolutionary conserved protein kinases that phosphorylate the carboxyl-tail of histone H2AX in chromatin flanking DNA lesions. Phosphorylated histone H2AX (aka γH2AX) tethers important DNA damage response (DDR) proteins to DNA double-strand breaks but its function during DNA replication is unclear. A novel genetic screen reveals that a partial defect in Replication Factor C (RFC) creates a critical requirement for γH2AX in fission yeast. These studies indicate that γH2AX stabilizes replication forks by recruiting Brc1 when RFC is unable to load the DNA clamp known as proliferating cell nuclear antigen (PCNA) onto duplex DNA. Surprisingly, this activity of γH2AX is more critical than ATM/ATR-mediated activation of the checkpoint kinase Chk1 and Chk2.
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Affiliation(s)
- Eva Mejia-Ramirez
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Oliver Limbo
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Petra Langerak
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Paul Russell
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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33
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Jablonowski CM, Cussiol JR, Oberly S, Yimit A, Balint A, Kim T, Zhang Z, Brown GW, Smolka MB. Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase. Genetics 2015; 201:937-49. [PMID: 26362319 DOI: 10.1534/genetics.115.181479] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/09/2015] [Indexed: 12/22/2022] Open
Abstract
In response to replication stress, signaling mediated by DNA damage checkpoint kinases protects genome integrity. However, following repair or bypass of DNA lesions, checkpoint signaling needs to be terminated for continued cell cycle progression and proliferation. In budding yeast, the PP4 phosphatase has been shown to play a key role in preventing hyperactivation of the checkpoint kinase Rad53. In addition, we recently uncovered a phosphatase-independent mechanism for downregulating Rad53 in which the DNA repair scaffold Slx4 decreases engagement of the checkpoint adaptor Rad9 at DNA lesions. Here we reveal that proper termination of checkpoint signaling following the bypass of replication blocks imposed by alkylated DNA adducts requires the concerted action of these two fundamentally distinct mechanisms of checkpoint downregulation. Cells lacking both SLX4 and the PP4-subunit PPH3 display a synergistic increase in Rad53 signaling and are exquisitely sensitive to the DNA alkylating agent methyl methanesulfonate, which induces replication blocks and extensive formation of chromosomal linkages due to template switching mechanisms required for fork bypass. Rad53 hypersignaling in these cells seems to converge to a strong repression of Mus81-Mms4, the endonuclease complex responsible for resolving chromosomal linkages, thus explaining the selective sensitivity of slx4Δ pph3Δ cells to alkylation damage. Our results support a model in which Slx4 acts locally to downregulate Rad53 activation following fork bypass, while PP4 acts on pools of active Rad53 that have diffused from the site of lesions. We propose that the proper spatial coordination of the Slx4 scaffold and PP4 action is crucial to allow timely activation of Mus81-Mms4 and, therefore, proper chromosome segregation.
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