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Polo Rivera C, Deegan TD, Labib KPM. CMG helicase disassembly is essential and driven by two pathways in budding yeast. EMBO J 2024; 43:3818-3845. [PMID: 39039287 PMCID: PMC11405719 DOI: 10.1038/s44318-024-00161-x] [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: 03/24/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 07/24/2024] Open
Abstract
The CMG helicase is the stable core of the eukaryotic replisome and is ubiquitylated and disassembled during DNA replication termination. Fungi and animals use different enzymes to ubiquitylate the Mcm7 subunit of CMG, suggesting that CMG ubiquitylation arose repeatedly during eukaryotic evolution. Until now, it was unclear whether cells also have ubiquitin-independent pathways for helicase disassembly and whether CMG disassembly is essential for cell viability. Using reconstituted assays with budding yeast CMG, we generated the mcm7-10R allele that compromises ubiquitylation by SCFDia2. mcm7-10R delays helicase disassembly in vivo, driving genome instability in the next cell cycle. These data indicate that defective CMG ubiquitylation explains the major phenotypes of cells lacking Dia2. Notably, the viability of mcm7-10R and dia2∆ is dependent upon the related Rrm3 and Pif1 DNA helicases that have orthologues in all eukaryotes. We show that Rrm3 acts during S-phase to disassemble old CMG complexes from the previous cell cycle. These findings indicate that CMG disassembly is essential in yeast cells and suggest that Pif1-family helicases might have mediated CMG disassembly in ancestral eukaryotes.
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Affiliation(s)
- Cristian Polo Rivera
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom D Deegan
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Karim P M Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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2
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Ramu VS, Pal G, Oh S, Mysore KS. Proteasomal Degradation of JAZ9 by Salt- and Drought-Induced Ring Finger 1 During Pathogen Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1358-1364. [PMID: 34615361 DOI: 10.1094/mpmi-07-21-0192-sc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
E3 ubiquitin ligase salt- and drought-induced ring finger 1 (SDIR1) plays a novel role in modulating plant immunity against pathogens. The molecular interactors of SDIR1 during pathogen infection are not known. SDIR1-interacting jasmonate zinc-finger inflorescence meristem domain (JAZ) proteins were identified through a yeast two-hybrid (Y2H) screen. Full-length JAZ9 interacts with SDIR1 only in the presence of coronatine (a bacteria-secreted toxin) or jasmonic acid (JA) in a Y2H assay. The bimolecular fluorescence complementation and pull-down assays confirm the in planta interaction of these proteins. JAZ9 proteins, negative regulators of JA-mediated plant defense, were degraded during the pathogen infection by SDIR1 through a proteasomal pathway causing disease susceptibility against hemibiotrophic pathogens.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2021.
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Affiliation(s)
- Vemanna S Ramu
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, Faridabad, Haryana 121001, India
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Garima Pal
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, Faridabad, Haryana 121001, India
| | - Sunhee Oh
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Kirankumar S Mysore
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, U.S.A
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, U.S.A
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3
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Corda Y, Maestroni L, Luciano P, Najem MY, Géli V. Genome stability is guarded by yeast Rtt105 through multiple mechanisms. Genetics 2021; 217:6126811. [PMID: 33724421 DOI: 10.1093/genetics/iyaa035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/03/2021] [Indexed: 12/15/2022] Open
Abstract
Ty1 mobile DNA element is the most abundant and mutagenic retrotransposon present in the genome of the budding yeast Saccharomyces cerevisiae. Protein regulator of Ty1 transposition 105 (Rtt105) associates with large subunit of RPA and facilitates its loading onto a single-stranded DNA at replication forks. Here, we dissect the role of RTT105 in the maintenance of genome stability under normal conditions and upon various replication stresses through multiple genetic analyses. RTT105 is essential for viability in cells experiencing replication problems and in cells lacking functional S-phase checkpoints and DNA repair pathways involving homologous recombination. Our genetic analyses also indicate that RTT105 is crucial when cohesion is affected and is required for the establishment of normal heterochromatic structures. Moreover, RTT105 plays a role in telomere maintenance as its function is important for the telomere elongation phenotype resulting from the Est1 tethering to telomeres. Genetic analyses indicate that rtt105Δ affects the growth of several rfa1 mutants but does not aggravate their telomere length defects. Analysis of the phenotypes of rtt105Δ cells expressing NLS-Rfa1 fusion protein reveals that RTT105 safeguards genome stability through its role in RPA nuclear import but also by directly affecting RPA function in genome stability maintenance during replication.
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Affiliation(s)
- Yves Corda
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Pierre Luciano
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Maria Y Najem
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Vincent Géli
- CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
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4
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Ramu VS, Oh S, Lee HK, Nandety RS, Oh Y, Lee S, Nakashima J, Tang Y, Senthil-Kumar M, Mysore KS. A Novel Role of Salt- and Drought-Induced RING 1 Protein in Modulating Plant Defense Against Hemibiotrophic and Necrotrophic Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:297-308. [PMID: 33231502 DOI: 10.1094/mpmi-09-20-0257-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Many plant-encoded E3 ligases are known to be involved in plant defense. Here, we report a novel role of E3 ligase SALT- AND DROUGHT-INDUCED RING FINGER1 (SDIR1) in plant immunity. Even though SDIR1 is reasonably well-characterized, its role in biotic stress response is not known. The silencing of SDIR1 in Nicotiana benthamiana reduced the multiplication of the virulent bacterial pathogen Pseudomonas syringae pv. tabaci. The Arabidopsis sdir1 mutant is resistant to virulent pathogens, whereas SDIR1 overexpression lines are susceptible to both host and nonhost hemibiotrophic bacterial pathogens. However, sdir1 mutant and SDIR1 overexpression lines showed hypersusceptibility and resistance, respectively, against the necrotrophic pathogen Erwinia carotovora. The mutant of SDIR1 target protein, i.e., SDIR-interacting protein 1 (SDIR1P1), also showed resistance to host and nonhost pathogens. In SDIR1 overexpression plants, transcripts of NAC transcription factors were less accumulated and the levels of jasmonic acid (JA) and abscisic acid were increased. In the sdir1 mutant, JA signaling genes JAZ7 and JAZ8 were downregulated. These data suggest that SDIR1 is a susceptibility factor and its activation or overexpression enhances disease caused by P. syringae pv. tomato DC3000 in Arabidopsis. Our results show a novel role of SDIR1 in modulating plant defense gene expression and plant immunity.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Vemanna S Ramu
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, Faridabad, India
| | - Sunhee Oh
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Hee-Kyung Lee
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Youngjae Oh
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL 33598, U.S.A
| | - Seonghee Lee
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL 33598, U.S.A
| | - Jin Nakashima
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Yuhong Tang
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
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Deshpande I, Keusch JJ, Challa K, Iesmantavicius V, Gasser SM, Gut H. The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin. EMBO J 2019; 38:e101744. [PMID: 31515872 PMCID: PMC6792019 DOI: 10.15252/embj.2019101744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/24/2019] [Accepted: 08/11/2019] [Indexed: 12/22/2022] Open
Abstract
In Saccharomyces cerevisiae, the silent information regulator (SIR) proteins Sir2/3/4 form a complex that suppresses transcription in subtelomeric regions and at the homothallic mating-type (HM) loci. Here, we identify a non-canonical BRCA1 C-terminal domain (H-BRCT) in Sir4, which is responsible for tethering telomeres to the nuclear periphery. We show that Sir4 H-BRCT and the closely related Dbf4 H-BRCT serve as selective phospho-epitope recognition domains that bind to a variety of phosphorylated target peptides. We present detailed structural information about the binding mode of established Sir4 interactors (Esc1, Ty5, Ubp10) and identify several novel interactors of Sir4 H-BRCT, including the E3 ubiquitin ligase Tom1. Based on these findings, we propose a phospho-peptide consensus motif for interaction with Sir4 H-BRCT and Dbf4 H-BRCT. Ablation of the Sir4 H-BRCT phospho-peptide interaction disrupts SIR-mediated repression and perinuclear localization. In conclusion, the Sir4 H-BRCT domain serves as a hub for recruitment of phosphorylated target proteins to heterochromatin to properly regulate silencing and nuclear order.
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Affiliation(s)
- Ishan Deshpande
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of Natural SciencesUniversity of BaselBaselSwitzerland
- Present address:
Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCAUSA
| | - Jeremy J Keusch
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | | | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of Natural SciencesUniversity of BaselBaselSwitzerland
| | - Heinz Gut
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
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6
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Fang O, Hu X, Wang L, Jiang N, Yang J, Li B, Luo Z. Amn1 governs post-mitotic cell separation in Saccharomyces cerevisiae. PLoS Genet 2018; 14:e1007691. [PMID: 30273335 PMCID: PMC6181423 DOI: 10.1371/journal.pgen.1007691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 10/11/2018] [Accepted: 09/12/2018] [Indexed: 11/18/2022] Open
Abstract
Post-mitotic cell separation is one of the most prominent events in the life cycle of eukaryotic cells, but the molecular underpinning of this fundamental biological process is far from being concluded and fully characterized. We use budding yeast Saccharomyces cerevisiae as a model and demonstrate AMN1 as a major gene underlying post-mitotic cell separation in a natural yeast strain, YL1C. Specifically, we define a novel 11-residue domain by which Amn1 binds to Ace2. Moreover, we demonstrate that Amn1 induces proteolysis of Ace2 through the ubiquitin proteasome system and in turn, down-regulates Ace2’s downstream target genes involved in hydrolysis of the primary septum, thus leading to inhibition of cell separation and clumping of haploid yeast cells. Using ChIP assays and site-specific mutation experiments, we show that Ste12 and the a1-α12 heterodimer are two direct regulators of AMN1. Specifically, a1-α2, a diploid-specific heterodimer, prevents Ste12 from inactivating AMN1 through binding to its promoter. This demonstrates how the Amn1-governed cell separation is highly cell type dependent. Finally, we show that AMN1368D from YL1C is a dominant allele in most strains of S. cerevisiae and evolutionarily conserved in both genic structure and phenotypic effect in two closely related yeast species, K. lactis and C. glabrata. Separation of mother and daughter cells after mitosis in eukaryotes enacts various functional and/or developmental needs and has significant medical and industrial implications. How this cellular behaviour is regulated is far from being concluded. We report here a novel Amn1 mediated post-mitotic cell separation in a budding yeast strain, YL1C and demonstrate that the post-mitotic cell separation can be regulated through a ubiquitin-conjugated protein degradation of Ace2 by Amn1. The Amn1-governed switch of cell separation is evolutionarily conserved and highly cell type dependent. These findings provide insights into the molecular mechanism of how post-mitotic cell separation is regulated in budding yeast, and data for translating into medical and industrial applications.
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Affiliation(s)
- Ou Fang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
- School of Biosciences, the University of Birmingham, Birmingham, United Kingdom
- Department of Evolution and Ecology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaohua Hu
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Lin Wang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Jiang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jixuan Yang
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Bo Li
- Department of Evolution and Ecology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zewei Luo
- Laboratory of Population and Quantitative Genetics, Institute of Biostatistics and Genetics, School of Life Sciences, Fudan University, Shanghai, China
- School of Biosciences, the University of Birmingham, Birmingham, United Kingdom
- * E-mail: ,
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7
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The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae. Genetics 2017; 203:1563-99. [PMID: 27516616 DOI: 10.1534/genetics.112.145243] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/30/2016] [Indexed: 12/31/2022] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae occurs at several genomic sites including the silent mating-type loci, telomeres, and the ribosomal DNA (rDNA) tandem array. Epigenetic silencing at each of these domains is characterized by the absence of nearly all histone modifications, including most prominently the lack of histone H4 lysine 16 acetylation. In all cases, silencing requires Sir2, a highly-conserved NAD(+)-dependent histone deacetylase. At locations other than the rDNA, silencing also requires additional Sir proteins, Sir1, Sir3, and Sir4 that together form a repressive heterochromatin-like structure termed silent chromatin. The mechanisms of silent chromatin establishment, maintenance, and inheritance have been investigated extensively over the last 25 years, and these studies have revealed numerous paradigms for transcriptional repression, chromatin organization, and epigenetic gene regulation. Studies of Sir2-dependent silencing at the rDNA have also contributed to understanding the mechanisms for maintaining the stability of repetitive DNA and regulating replicative cell aging. The goal of this comprehensive review is to distill a wide array of biochemical, molecular genetic, cell biological, and genomics studies down to the "nuts and bolts" of silent chromatin and the processes that yield transcriptional silencing.
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8
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Nakatsukasa K, Okumura F, Kamura T. Proteolytic regulation of metabolic enzymes by E3 ubiquitin ligase complexes: lessons from yeast. Crit Rev Biochem Mol Biol 2015; 50:489-502. [PMID: 26362128 DOI: 10.3109/10409238.2015.1081869] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eukaryotic organisms use diverse mechanisms to control metabolic rates in response to changes in the internal and/or external environment. Fine metabolic control is a highly responsive, energy-saving process that is mediated by allosteric inhibition/activation and/or reversible modification of preexisting metabolic enzymes. In contrast, coarse metabolic control is a relatively long-term and expensive process that involves modulating the level of metabolic enzymes. Coarse metabolic control can be achieved through the degradation of metabolic enzymes by the ubiquitin-proteasome system (UPS), in which substrates are specifically ubiquitinated by an E3 ubiquitin ligase and targeted for proteasomal degradation. Here, we review select multi-protein E3 ligase complexes that directly regulate metabolic enzymes in Saccharomyces cerevisiae. The first part of the review focuses on the endoplasmic reticulum (ER) membrane-associated Hrd1 and Doa10 E3 ligase complexes. In addition to their primary roles in the ER-associated degradation pathway that eliminates misfolded proteins, recent quantitative proteomic analyses identified native substrates of Hrd1 and Doa10 in the sterol synthesis pathway. The second part focuses on the SCF (Skp1-Cul1-F-box protein) complex, an abundant prototypical multi-protein E3 ligase complex. While the best-known roles of the SCF complex are in the regulation of the cell cycle and transcription, accumulating evidence indicates that the SCF complex also modulates carbon metabolism pathways. The increasing number of metabolic enzymes whose stability is directly regulated by the UPS underscores the importance of the proteolytic regulation of metabolic processes for the acclimation of cells to environmental changes.
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Affiliation(s)
- Kunio Nakatsukasa
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
| | - Fumihiko Okumura
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
| | - Takumi Kamura
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
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Burgess RJ, Han J, Zhang Z. The Ddc1-Mec3-Rad17 sliding clamp regulates histone-histone chaperone interactions and DNA replication-coupled nucleosome assembly in budding yeast. J Biol Chem 2014; 289:10518-10529. [PMID: 24573675 DOI: 10.1074/jbc.m114.552463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The maintenance of genome integrity is regulated in part by chromatin structure and factors involved in the DNA damage response pathway. Nucleosome assembly is a highly regulated process that restores chromatin structure after DNA replication, DNA repair, and gene transcription. During S phase the histone chaperones Asf1, CAF-1, and Rtt106 coordinate to deposit newly synthesized histones H3-H4 onto replicated DNA in budding yeast. Here we describe synthetic genetic interactions between RTT106 and the DDC1-MEC3-RAD17 (9-1-1) complex, a sliding clamp functioning in the S phase DNA damage and replication checkpoint response, upon treatment with DNA damaging agents. The DNA damage sensitivity of rad17Δ rtt106Δ cells depends on the function of Rtt106 in nucleosome assembly. Epistasis analysis reveals that 9-1-1 complex components interact with multiple DNA replication-coupled nucleosome assembly factors, including Rtt106, CAF-1, and lysine residues of H3-H4. Furthermore, rad17Δ cells exhibit defects in the deposition of newly synthesized H3-H4 onto replicated DNA. Finally, deletion of RAD17 results in increased association of Asf1 with checkpoint kinase Rad53, which may lead to the observed reduction in Asf1-H3 interaction in rad17Δ mutant cells. In addition, we observed that the interaction between histone H3-H4 with histone chaperone CAF-1 or Rtt106 increases in cells lacking Rad17. These results support the idea that the 9-1-1 checkpoint protein regulates DNA replication-coupled nucleosome assembly in part through regulating histone-histone chaperone interactions.
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Affiliation(s)
- Rebecca J Burgess
- Department of Biochemistry and Molecular Biology, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55905
| | - Junhong Han
- Department of Biochemistry and Molecular Biology, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55905
| | - Zhiguo Zhang
- Department of Biochemistry and Molecular Biology, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55905.
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