1
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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] [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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2
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Evstyukhina TA, Alekseeva EA, Peshekhonov VT, Skobeleva II, Fedorov DV, Korolev VG. The Role of Chromatin Assembly Factors in Induced Mutagenesis at Low Levels of DNA Damage. Genes (Basel) 2023; 14:1242. [PMID: 37372422 DOI: 10.3390/genes14061242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The problem of low-dose irradiation has been discussed in the scientific literature for several decades, but it is impossible to come to a generally accepted conclusion about the presence of any specific features of low-dose irradiation in contrast to acute irradiation. We were interested in the effect of low doses of UV radiation on the physiological processes, including repair processes in cells of the yeast Saccharomyces cerevisiae, in contrast to high doses of radiation. Cells utilize excision repair and DNA damage tolerance pathways without significant delay of the cell cycle to address low levels of DNA damage (such as spontaneous base lesions). For genotoxic agents, there is a dose threshold below which checkpoint activation is minimal despite the measurable activity of the DNA repair pathways. Here we report that at ultra-low levels of DNA damage, the role of the error-free branch of post-replicative repair in protection against induced mutagenesis is key. However, with an increase in the levels of DNA damage, the role of the error-free repair branch is rapidly decreasing. We demonstrate that with an increase in the amount of DNA damage from ultra-small to high, asf1Δ-specific mutagenesis decreases catastrophically. A similar dependence is observed for mutants of gene-encoding subunits of the NuB4 complex. Elevated levels of dNTPs caused by the inactivation of the SML1 gene are responsible for high spontaneous reparative mutagenesis. The Rad53 kinase plays a key role in reparative UV mutagenesis at high doses, as well as in spontaneous repair mutagenesis at ultra-low DNA damage levels.
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Affiliation(s)
- Tatiyana A Evstyukhina
- Chromatin and Repair Genetic Research Group of the Laboratory of Experimental Genetics, Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", 188300 Gatchina, Russia
- Laboratory of Molecular Genetic and Recombination Technologies, Kurchatov Genome Center-Petersburg Nuclear Physics Institute, 188300 Gatchina, Russia
| | - Elena A Alekseeva
- Chromatin and Repair Genetic Research Group of the Laboratory of Experimental Genetics, Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", 188300 Gatchina, Russia
- Laboratory of Molecular Genetic and Recombination Technologies, Kurchatov Genome Center-Petersburg Nuclear Physics Institute, 188300 Gatchina, Russia
| | - Vyacheslav T Peshekhonov
- Chromatin and Repair Genetic Research Group of the Laboratory of Experimental Genetics, Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", 188300 Gatchina, Russia
- Laboratory of Molecular Genetic and Recombination Technologies, Kurchatov Genome Center-Petersburg Nuclear Physics Institute, 188300 Gatchina, Russia
| | - Irina I Skobeleva
- Chromatin and Repair Genetic Research Group of the Laboratory of Experimental Genetics, Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", 188300 Gatchina, Russia
| | - Dmitriy V Fedorov
- Chromatin and Repair Genetic Research Group of the Laboratory of Experimental Genetics, Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", 188300 Gatchina, Russia
| | - Vladimir G Korolev
- Chromatin and Repair Genetic Research Group of the Laboratory of Experimental Genetics, Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", 188300 Gatchina, Russia
- Laboratory of Molecular Genetic and Recombination Technologies, Kurchatov Genome Center-Petersburg Nuclear Physics Institute, 188300 Gatchina, Russia
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3
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Yao S, Feng Y, Zhang Y, Feng J. DNA damage checkpoint and repair: From the budding yeast Saccharomyces cerevisiae to the pathogenic fungus Candida albicans. Comput Struct Biotechnol J 2021; 19:6343-6354. [PMID: 34938410 PMCID: PMC8645783 DOI: 10.1016/j.csbj.2021.11.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 01/09/2023] Open
Abstract
Cells are constantly challenged by internal or external genotoxic assaults, which may induce a high frequency of DNA lesions, leading to genome instability. Accumulation of damaged DNA is severe or even lethal to cells and can result in abnormal proliferation that can cause cancer in multicellular organisms, aging or cell death. Eukaryotic cells have evolved a comprehensive defence system termed the DNA damage response (DDR) to monitor and remove lesions in their DNA. The DDR has been extensively studied in the budding yeast Saccharomyces cerevisiae. Emerging evidence indicates that DDR genes in the pathogenic fungus Candida albicans show functional consistency with their orthologs in S. cerevisiae, but may act through distinct mechanisms. In particular, the DDR in C. albicans appears critical for resisting DNA damage stress induced by reactive oxygen species (ROS) produced from immune cells, and this plays a vital role in pathogenicity. Therefore, DDR genes could be considered as potential targets for clinical therapies. This review summarizes the identified DNA damage checkpoint and repair genes in C. albicans based on their orthologs in S. cerevisiae, and discusses their contribution to pathogenicity in C. albicans.
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Affiliation(s)
- Shuangyan Yao
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, Jiangsu, China
- Nantong Health College of Jiangsu Province, Nantong 226016, Jiangsu, China
| | - Yuting Feng
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Yan Zhang
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Jinrong Feng
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, Jiangsu, China
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4
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Park J, Lee DH. Functional roles of protein phosphatase 4 in multiple aspects of cellular physiology: a friend and a foe. BMB Rep 2021. [PMID: 32192570 PMCID: PMC7196183 DOI: 10.5483/bmbrep.2020.53.4.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protein phosphatase 4 (PP4), one of serine/threonine phosphatases, is involved in many critical cellular pathways, including DNA damage response (DNA repair, cell cycle regulation, and apoptosis), tumorigenesis, cell migration, immune response, stem cell development, glucose metabolism, and diabetes. PP4 has been steadily studied over the past decade about wide spectrum of physiological activities in cells. Given the many vital functions in cells, PP4 has great potential to develop into the finding of key working mechanisms and effective treatments for related diseases such as cancer and diabetes. In this review, we provide an overview of the cellular and molecular mechanisms by which PP4 impacts and also discuss the functional significance of it in cell health.
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Affiliation(s)
- Jaehong Park
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju 61186, Korea
| | - Dong-Hyun Lee
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju 61186; Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Korea
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5
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Ariño J, Velázquez D, Casamayor A. Ser/Thr protein phosphatases in fungi: structure, regulation and function. MICROBIAL CELL 2019; 6:217-256. [PMID: 31114794 PMCID: PMC6506691 DOI: 10.15698/mic2019.05.677] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reversible phospho-dephosphorylation of proteins is a major mechanism for the control of cellular functions. By large, Ser and Thr are the most frequently residues phosphorylated in eukar-yotes. Removal of phosphate from these amino acids is catalyzed by a large family of well-conserved enzymes, collectively called Ser/Thr protein phosphatases. The activity of these enzymes has an enormous impact on cellular functioning. In this work we pre-sent the members of this family in S. cerevisiae and other fungal species, and review the most recent findings concerning their regu-lation and the roles they play in the most diverse aspects of cell biology.
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Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Diego Velázquez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Antonio Casamayor
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
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6
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Budding yeast Rtt107 prevents checkpoint hyperactivation after replicative stress by limiting DNA damage. DNA Repair (Amst) 2019; 74:1-16. [DOI: 10.1016/j.dnarep.2019.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 12/20/2018] [Accepted: 01/04/2019] [Indexed: 01/08/2023]
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7
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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] [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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8
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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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9
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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] [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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10
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Simoneau A, Ricard É, Wurtele H. An interplay between multiple sirtuins promotes completion of DNA replication in cells with short telomeres. PLoS Genet 2018; 14:e1007356. [PMID: 29659581 PMCID: PMC5919697 DOI: 10.1371/journal.pgen.1007356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 04/26/2018] [Accepted: 04/09/2018] [Indexed: 01/08/2023] Open
Abstract
The evolutionarily-conserved sirtuin family of histone deacetylases regulates a multitude of DNA-associated processes. A recent genome-wide screen conducted in the yeast Saccharomyces cerevisiae identified Yku70/80, which regulate nonhomologous end-joining (NHEJ) and telomere structure, as being essential for cell proliferation in the presence of the pan-sirtuin inhibitor nicotinamide (NAM). Here, we show that sirtuin-dependent deacetylation of both histone H3 lysine 56 and H4 lysine 16 promotes growth of yku70Δ and yku80Δ cells, and that the NAM sensitivity of these mutants is not caused by defects in DNA double-strand break repair by NHEJ, but rather by their inability to maintain normal telomere length. Indeed, our results indicate that in the absence of sirtuin activity, cells with abnormally short telomeres, e.g., yku70/80Δ or est1/2Δ mutants, present striking defects in S phase progression. Our data further suggest that early firing of replication origins at short telomeres compromises the cellular response to NAM- and genotoxin-induced replicative stress. Finally, we show that reducing H4K16ac in yku70Δ cells limits activation of the DNA damage checkpoint kinase Rad53 in response to replicative stress, which promotes usage of translesion synthesis and S phase progression. Our results reveal a novel interplay between sirtuin-mediated regulation of chromatin structure and telomere-regulating factors in promoting timely completion of S phase upon replicative stress.
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Affiliation(s)
- Antoine Simoneau
- Centre de recherche de l’Hôpital Maisonneuve-Rosemont, boulevard de l’Assomption, Montréal, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Canada
| | - Étienne Ricard
- Centre de recherche de l’Hôpital Maisonneuve-Rosemont, boulevard de l’Assomption, Montréal, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Canada
| | - Hugo Wurtele
- Centre de recherche de l’Hôpital Maisonneuve-Rosemont, boulevard de l’Assomption, Montréal, Canada
- Département de Médecine, Université de Montréal, Montréal, Canada
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11
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Yadav RK, Jablonowski CM, Fernandez AG, Lowe BR, Henry RA, Finkelstein D, Barnum KJ, Pidoux AL, Kuo YM, Huang J, O’Connell MJ, Andrews AJ, Onar-Thomas A, Allshire RC, Partridge JF. Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe. eLife 2017; 6:e27406. [PMID: 28718400 PMCID: PMC5515577 DOI: 10.7554/elife.27406] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 06/20/2017] [Indexed: 12/12/2022] Open
Abstract
Recurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R/V mutant histone H3.3. H3.3-G34R/V mutants are common in tumors with mutations in p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of H3-G34R, we generated fission yeast that express only the mutant histone H3. H3-G34R specifically reduces H3K36 tri-methylation and H3K36 acetylation, and mutants show partial transcriptional overlap with set2 deletions. H3-G34R mutants exhibit genomic instability and increased replication stress, including slowed replication fork restart, although DNA replication checkpoints are functional. H3-G34R mutants are defective for DNA damage repair by homologous recombination (HR), and have altered HR protein dynamics in both damaged and untreated cells. These data suggest H3-G34R slows resolution of HR-mediated repair and that unresolved replication intermediates impair chromosome segregation. This analysis of H3-G34R mutant fission yeast provides mechanistic insight into how G34R mutation may promote genomic instability in glioma.
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Affiliation(s)
- Rajesh K Yadav
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
| | - Carolyn M Jablonowski
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
| | - Alfonso G Fernandez
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
| | - Brandon R Lowe
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States
| | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States
| | - David Finkelstein
- Department of Bioinformatics, St. Jude Children’s Research Hospital, Memphis, United States
| | - Kevin J Barnum
- Department of Oncological Sciences and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Alison L Pidoux
- Wellcome Trust School for Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Yin-Ming Kuo
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States
| | - Jie Huang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, United States
| | - Matthew J O’Connell
- Department of Oncological Sciences and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, United States
| | - Arzu Onar-Thomas
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, United States
| | - Robin C Allshire
- Wellcome Trust School for Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Janet F Partridge
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, United States,
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12
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Recovery from the DNA Replication Checkpoint. Genes (Basel) 2016; 7:genes7110094. [PMID: 27801838 PMCID: PMC5126780 DOI: 10.3390/genes7110094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/20/2016] [Accepted: 10/23/2016] [Indexed: 11/17/2022] Open
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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13
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Hang L, Zhao X. The Rtt107 BRCT scaffold and its partner modification enzymes collaborate to promote replication. Nucleus 2016; 7:346-51. [PMID: 27385431 DOI: 10.1080/19491034.2016.1201624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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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14
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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] [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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15
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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] [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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