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Krystosek JT, Bishop DK. Chk2 homolog Mek1 limits exonuclease 1-dependent DNA end resection during meiotic recombination in Saccharomyces cerevisiae. Genetics 2024; 228:iyae112. [PMID: 39005070 PMCID: PMC11373520 DOI: 10.1093/genetics/iyae112] [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: 04/11/2024] [Revised: 04/11/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
The conserved Rad2/XPG family 5'-3' exonuclease, exonuclease 1 (Exo1), plays many roles in DNA metabolism including during resolution of DNA double-strand breaks via homologous recombination. Prior studies provided evidence that the end resection activity of Exo1 is downregulated in yeast and mammals by Cdk1/2 family cyclin-dependent and checkpoint kinases, including budding yeast kinase Rad53 which functions in mitotic cells. Here, we provide evidence that the master meiotic kinase Mek1, a paralog of Rad53, limits 5'-3' single-strand resection at the sites of programmed meiotic DNA breaks. Mutational analysis suggests that the mechanism of Exo1 suppression by Mek1 differs from that of Rad53.
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Affiliation(s)
- Jennifer T Krystosek
- Department of Radiation and Cellular Oncology/Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E 58th Street, CLSC 817, Chicago, IL 60637, USA
| | - Douglas K Bishop
- Department of Radiation and Cellular Oncology/Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E 58th Street, CLSC 817, Chicago, IL 60637, USA
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2
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Grubb J, Bishop DK. Chk2 homologue Mek1 limits Exo1-dependent DNA end resection during meiotic recombination in S. cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589255. [PMID: 38645032 PMCID: PMC11030327 DOI: 10.1101/2024.04.12.589255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The conserved Rad2/XPG family 5'-3' exonuclease, Exonuclease 1 (Exo1), plays many roles in DNA metabolism including during resolution of DNA double strand breaks (DSBs) via homologous recombination. Prior studies provided evidence that the end-resection activity of Exo1 is downregulated in yeast and mammals by Cdk1/2 family cyclin-dependent and checkpoint kinases, including budding yeast kinase Rad53 which functions in mitotic cells. Here we provide evidence that the master meiotic kinase Mek1, a paralogue of Rad53, limits 5'-3' single strand resection at the sites of programmed meiotic DNA breaks. Mutational analysis suggests that the mechanism of Exo1 suppression by Mek1 differs from that of Rad53. Article Summary Meiotic recombination involves formation of programmed DNA double strand breaks followed by 5' to 3' single strand specific resection by nucleases including Exo1. We find that the activity of budding yeast Exo1 is downregulated during meiotic recombination by the master meiotic kinase Mek1. The mechanism of downregulation of Exo1 by Mek1 in meiosis does not depend on the same phospho-sites as those used by the mitotic kinase Rad53, a relative of Mek1 that downregulates Exo1 in mitosis.
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3
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Yan S, Gao S, Zhou P. Multi-functions of exonuclease 1 in DNA damage response and cancer susceptibility. RADIATION MEDICINE AND PROTECTION 2021. [DOI: 10.1016/j.radmp.2021.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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4
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Li Y, Shen J, Niu H. DNA duplex recognition activates Exo1 nuclease activity. J Biol Chem 2019; 294:11559-11567. [PMID: 31182486 DOI: 10.1074/jbc.ra119.008549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/09/2019] [Indexed: 11/06/2022] Open
Abstract
Exonuclease 1 (Exo1) is an evolutionarily conserved eukaryotic nuclease that plays a multifaceted role in maintaining genome stability. The biochemical attributes of Exo1 have been extensively characterized via conventional assays. However, the key step governing its activation remains elusive. Extending the previous finding that Exo1 can digest a randomly selected single-stranded DNA (ssDNA) but not a poly(dT) oligonucleotide and using purified recombinant Exo1 and nuclease and electrophoretic mobility shift assays, here we determined that DNA hairpins with a stem size of 4 bp or longer are able to activate Exo1-mediated digestion of ssDNA. We further provide evidence suggesting that Exo1 uses an evolutionarily conserved residue, Lys185 This residue interacted with the phosphate group bridging the third and fourth nucleotide on the digestion strand of the substrate DNA for duplex recognition, critical for Exo1 activation on not only ssDNA but also dsDNA. Additionally, the defect of an exo1-K185A mutant in duplex digestion was partially rescued by longer overhanging DNA. However, we noted that the enhanced Exo1 nuclease activity by longer overhanging DNA is largely eliminated by replication protein A (RPA), likely because of the previously reported RPA activity that strips Exo1 off the ssDNA. We conclude that duplex DNA contact by Exo1 is a general mechanism that controls its activation and that this mechanism is particularly important for digestion of duplex DNA whose nascent ssDNA is bound by RPA.
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Affiliation(s)
- Yuxi Li
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405.,Interdisciplinary Biochemistry Program, Indiana University, Bloomington, Indiana 47405
| | - Jiangchuan Shen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
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5
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The human Exonuclease-1 interactome and phosphorylation sites. Biochem Biophys Res Commun 2019; 514:567-573. [DOI: 10.1016/j.bbrc.2019.04.171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/25/2019] [Indexed: 01/16/2023]
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6
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Chappidi N, De Gregorio G, Ferrari S. Replication stress-induced Exo1 phosphorylation is mediated by Rad53/Pph3 and Exo1 nuclear localization is controlled by 14-3-3 proteins. Cell Div 2019; 14:1. [PMID: 30622624 PMCID: PMC6318887 DOI: 10.1186/s13008-018-0044-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/24/2018] [Indexed: 12/22/2022] Open
Abstract
Background Mechanisms controlling DNA resection at sites of damage and affecting genome stability have been the subject of deep investigation, though their complexity is not yet fully understood. Specifically, the regulatory role of post-translational modifications in the localization, stability and function of DNA repair proteins is an important aspect of such complexity. Results Here, we took advantage of the superior resolution of phosphorylated proteins provided by Phos-Tag technology to study pathways controlling the reversible phosphorylation of yeast Exo1, an exonuclease involved in a number of DNA repair pathways. We report that Rad53, a checkpoint kinase downstream of Mec1, is responsible for Exo1 phosphorylation in response to DNA replication stress and we demonstrate a role for the type-2A protein phosphatase Pph3 in the dephosphorylation of both Rad53 and Exo1 during checkpoint recovery. Fluorescence microscopy studies showed that Rad53-dependent phosphorylation is not required for the recruitment or the release of Exo1 from the nucleus, whereas 14-3-3 proteins are necessary for Exo1 nuclear translocation. Conclusions By shedding light on the mechanism of Exo1 control, these data underscore the importance of post-translational modifications and protein interactions in the regulation of DNA end resection.
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Affiliation(s)
- Nagaraja Chappidi
- Institute of Molecular Cancer Research, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Giuseppe De Gregorio
- Institute of Molecular Cancer Research, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Stefano Ferrari
- Institute of Molecular Cancer Research, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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7
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Abstract
DNA double-strand breaks (DSBs) are a potentially lethal DNA lesions that disrupt both the physical and genetic continuity of the DNA duplex. Homologous recombination (HR) is a universally conserved genome maintenance pathway that initiates via nucleolytic processing of the broken DNA ends (resection). Eukaryotic DNA resection is catalyzed by the resectosome-a multicomponent molecular machine consisting of the nucleases DNA2 or Exonuclease 1 (EXO1), Bloom's helicase (BLM), the MRE11-RAD50-NBS1 (MRN) complex, and additional regulatory factors. Here, we describe methods for purification and single-molecule imaging and analysis of EXO1, DNA2, and BLM. We also describe how to adapt resection assays to the high-throughput single-molecule DNA curtain assay. By organizing hundreds of individual molecules on the surface of a microfluidic flowcell, DNA curtains visualize protein complexes with the required spatial and temporal resolution to resolve the molecular choreography during critical DNA-processing reactions.
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8
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Chen CC, Avdievich E, Zhang Y, Zhang Y, Wei K, Lee K, Edelmann W, Jasin M, LaRocque JR. EXO1 suppresses double-strand break induced homologous recombination between diverged sequences in mammalian cells. DNA Repair (Amst) 2017; 57:98-106. [PMID: 28711786 DOI: 10.1016/j.dnarep.2017.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 07/05/2017] [Accepted: 07/07/2017] [Indexed: 11/17/2022]
Abstract
DNA double-strand breaks (DSBs) can be repaired through several mechanisms, including homologous recombination (HR). While HR between identical sequences is robust in mammalian cells, HR between diverged sequences is suppressed by DNA mismatch-repair (MMR) components such as MSH2. Exonuclease I (EXO1) interacts with the MMR machinery and has been proposed to act downstream of the mismatch recognition proteins in mismatch correction. EXO1 has also been shown to participate in extensive DSB end resection, an initial step in the HR pathway. To assess the contribution of EXO1 to HR in mammalian cells, DSB-inducible reporters were introduced into Exo1-/- mouse embryonic stem cells, including a novel GFP reporter containing several silent polymorphisms to monitor HR between diverged sequences. Compared to HR between identical sequences which was not clearly affected, HR between diverged sequences was substantially increased in Exo1-/- cells although to a lesser extent than seen in Msh2-/- cells. Thus, like canonical MMR proteins, EXO1 can restrain aberrant HR events between diverged sequence elements in the genome.
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Affiliation(s)
- Chun-Chin Chen
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Elena Avdievich
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA
| | - Yongwei Zhang
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA
| | - Yu Zhang
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA
| | - Kaichun Wei
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA
| | - Kyeryoung Lee
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, USA.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA.
| | - Jeannine R LaRocque
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., New York, NY, 10065, USA; Department of Human Science, Georgetown University Medical Center, 3700 Reservoir Rd. NW, Washington, D.C., 20057, USA.
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9
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DNA mismatch repair and its many roles in eukaryotic cells. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:174-187. [PMID: 28927527 DOI: 10.1016/j.mrrev.2017.07.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/01/2017] [Accepted: 07/06/2017] [Indexed: 02/06/2023]
Abstract
DNA mismatch repair (MMR) is an important DNA repair pathway that plays critical roles in DNA replication fidelity, mutation avoidance and genome stability, all of which contribute significantly to the viability of cells and organisms. MMR is widely-used as a diagnostic biomarker for human cancers in the clinic, and as a biomarker of cancer susceptibility in animal model systems. Prokaryotic MMR is well-characterized at the molecular and mechanistic level; however, MMR is considerably more complex in eukaryotic cells than in prokaryotic cells, and in recent years, it has become evident that MMR plays novel roles in eukaryotic cells, several of which are not yet well-defined or understood. Many MMR-deficient human cancer cells lack mutations in known human MMR genes, which strongly suggests that essential eukaryotic MMR components/cofactors remain unidentified and uncharacterized. Furthermore, the mechanism by which the eukaryotic MMR machinery discriminates between the parental (template) and the daughter (nascent) DNA strand is incompletely understood and how cells choose between the EXO1-dependent and the EXO1-independent subpathways of MMR is not known. This review summarizes recent literature on eukaryotic MMR, with emphasis on the diverse cellular roles of eukaryotic MMR proteins, the mechanism of strand discrimination and cross-talk/interactions between and co-regulation of MMR and other DNA repair pathways in eukaryotic cells. The main conclusion of the review is that MMR proteins contribute to genome stability through their ability to recognize and promote an appropriate cellular response to aberrant DNA structures, especially when they arise during DNA replication. Although the molecular mechanism of MMR in the eukaryotic cell is still not completely understood, increased used of single-molecule analyses in the future may yield new insight into these unsolved questions.
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10
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Dizman YA, Muratoglu H, Sandalli C, Nalcacioglu R, Demirbag Z. Chilo iridescent virus (CIV) ORF 012L encodes a protein with both exonuclease and endonuclease functions. Arch Virol 2016; 161:3029-37. [PMID: 27496102 DOI: 10.1007/s00705-016-3007-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
Abstract
Chilo iridescent virus (CIV) is the type member of the genus Iridovirus within the family Iridoviridae. The virions of CIV contain a single linear dsDNA molecule that is circularly permuted and terminally redundant. The genome of CIV contains an open reading frame (ORF 012L) encoding a protein homologous to exonuclease II of Schizosaccharomyces pombe. In this study, we focused on the characterization of CIV ORF 012L. The target ORF was cloned into the pET28a vector, expressed in E. coli strain BL21 (DE3) pLysS with an N-terminal His tag and purified to homogeneity by using Ni-NTA affinity chromatography. Biochemical characterization of the purified CIV 012L confirmed that this viral protein is a functional 5'-3' exonuclease that digests 3'-biotin-labelled oligonucleotides and linear double-stranded DNA (dsDNA) molecules from their 5' termini in a highly processive manner. CIV 012L also has a potent endonuclease activity on dsDNA in vitro. In addition, CIV 012L converted supercoiled plasmid DNA (replicative form I, RFI) into the open circular form (RFII) and then open circular form into linear form (RFIII). Endonuclease activity of CIV 012L was optimal in the presence of 10 mM Mg(2+) or 30 mM Mn(2+) ions and at 150 mM NaCl or KCl salt concentrations. The highest endonuclease activity was obtained at pH 8, and it reached a maximum at 55 °C. The CIV 012L protein showed deficiencies for both double- and single-stranded RNAs.
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Affiliation(s)
- Yesim Akturk Dizman
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey.,Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkey
| | - Hacer Muratoglu
- Department of Molecular Biology and Genetic, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Cemal Sandalli
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkey
| | - Remziye Nalcacioglu
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey.
| | - Zihni Demirbag
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey
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11
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Liu T, Huang J. DNA End Resection: Facts and Mechanisms. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:126-130. [PMID: 27240470 PMCID: PMC4936662 DOI: 10.1016/j.gpb.2016.05.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 01/05/2023]
Abstract
DNA double-strand breaks (DSBs), which arise following exposure to a number of endogenous and exogenous agents, can be repaired by either the homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways in eukaryotic cells. A vital step in HR repair is DNA end resection, which generates a long 3′ single-stranded DNA (ssDNA) tail that can invade the homologous DNA strand. The generation of 3′ ssDNA is not only essential for HR repair, but also promotes activation of the ataxia telangiectasia and Rad3-related protein (ATR). Multiple factors, including the MRN/X complex, C-terminal-binding protein interacting protein (CtIP)/Sae2, exonuclease 1 (EXO1), Bloom syndrome protein (BLM)/Sgs1, DNA2 nuclease/helicase, and several chromatin remodelers, cooperate to complete the process of end resection. Here we review the basic machinery involved in DNA end resection in eukaryotic cells.
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Affiliation(s)
- Ting Liu
- Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Jun Huang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou 310058, China.
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12
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End-processing nucleases and phosphodiesterases: An elite supporting cast for the non-homologous end joining pathway of DNA double-strand break repair. DNA Repair (Amst) 2016; 43:57-68. [PMID: 27262532 DOI: 10.1016/j.dnarep.2016.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 11/20/2022]
Abstract
Nonhomologous end joining (NHEJ) is an error-prone DNA double-strand break repair pathway that is active throughout the cell cycle. A substantial fraction of NHEJ repair events show deletions and, less often, insertions in the repair joints, suggesting an end-processing step comprising the removal of mismatched or damaged nucleotides by nucleases and other phosphodiesterases, as well as subsequent strand extension by polymerases. A wide range of nucleases, including Artemis, Metnase, APLF, Mre11, CtIP, APE1, APE2 and WRN, are biochemically competent to carry out such double-strand break end processing, and have been implicated in NHEJ by at least circumstantial evidence. Several additional DNA end-specific phosphodiesterases, including TDP1, TDP2 and aprataxin are available to resolve various non-nucleotide moieties at DSB ends. This review summarizes the biochemical specificities of these enzymes and the evidence for their participation in the NHEJ pathway.
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13
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Abstract
The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is initiated by nucleolytic degradation of the 5'-terminated strands in a process termed end resection. End resection generates 3'-single-stranded DNA tails, substrates for Rad51 to catalyze homologous pairing and DNA strand exchange, and for activation of the DNA damage checkpoint. The commonly accepted view is that end resection occurs by a two-step mechanism. In the first step, Sae2/CtIP activates the Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex to endonucleolytically cleave the 5'-terminated DNA strands close to break ends, and in the second step Exo1 and/or Dna2 nucleases extend the resected tracts to produce long 3'-ssDNA-tailed intermediates. Initiation of resection commits a cell to repair a DSB by HR because long ssDNA overhangs are poor substrates for non-homologous end joining (NHEJ). Thus, the initiation of end resection has emerged as a critical control point for repair pathway choice. Here, I review recent studies on the mechanism of end resection and how this process is regulated to ensure the most appropriate repair outcome.
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Affiliation(s)
- Lorraine S Symington
- a Department of Microbiology & Immunology , Columbia University Medical Center , New York , USA
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14
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The RecQ DNA helicase Rqh1 constrains Exonuclease 1-dependent recombination at stalled replication forks. Sci Rep 2016; 6:22837. [PMID: 26957021 PMCID: PMC4783781 DOI: 10.1038/srep22837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 01/28/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) involves resection of the break to expose a 3' single-stranded DNA tail. In budding yeast, resection occurs in two steps: initial short-range resection, performed by Mre11-Rad50-Xrs2 and Sae2; and long-range resection catalysed by either Exo1 or Sgs1-Dna2. Here we use genetic assays to investigate the importance of Exo1 and the Sgs1 homologue Rqh1 for DNA repair and promotion of direct repeat recombination in the fission yeast Schizosaccharomyces pombe. We find that Exo1 and Rqh1 function in alternative redundant pathways for promoting survival following replication fork breakage. Exo1 promotes replication fork barrier-induced direct repeat recombination but intriguingly limits recombination induced by fork breakage. Direct repeat recombination induced by ultraviolet light depends on either Exo1 or Rqh1. Finally, we show that Rqh1 plays a major role in limiting Exo1-dependent direct repeat recombination induced by replication fork stalling but only a minor role in constraining recombination induced by fork breakage. The implications of our findings are discussed in the context of the benefits that long-range resection may bring to processing perturbed replication forks.
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15
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Rodriges Blanko E, Kadyrova LY, Kadyrov FA. DNA Mismatch Repair Interacts with CAF-1- and ASF1A-H3-H4-dependent Histone (H3-H4)2 Tetramer Deposition. J Biol Chem 2016; 291:9203-17. [PMID: 26945061 DOI: 10.1074/jbc.m115.713271] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Indexed: 01/07/2023] Open
Abstract
DNA mismatch repair (MMR) is required for the maintenance of genome stability and protection of humans from several types of cancer. Human MMR occurs in the chromatin environment, but little is known about the interactions between MMR and the chromatin environment. Previous research has suggested that MMR coincides with replication-coupled assembly of the newly synthesized DNA into nucleosomes. The first step in replication-coupled nucleosome assembly is CAF-1-dependent histone (H3-H4)2 tetramer deposition, a process that involves ASF1A-H3-H4 complex. In this work we used reconstituted human systems to investigate interactions between MMR and CAF-1- and ASF1A-H3-H4-dependent histone (H3-H4)2 tetramer deposition. We have found that MutSα inhibits CAF-1- and ASF1A-H3-H4-dependent packaging of a DNA mismatch into a tetrasome. This finding supports the idea that MMR occurs before the DNA mismatch is packaged into the tetrasome. Our experiments have also revealed that CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers does not interfere with MMR reactions. In addition, we have established that unnecessary degradation of the discontinuous strand that takes place in both DNA polymerase δ (Pol δ)- and DNA polymerase ϵ (Pol ϵ)-dependent MMR reactions is suppressed by CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers. These data suggest that CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers is compatible with MMR and protects the discontinuous daughter strand from unnecessary degradation by MMR machinery.
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Affiliation(s)
- Elena Rodriges Blanko
- From the Department of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
| | - Lyudmila Y Kadyrova
- From the Department of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
| | - Farid A Kadyrov
- From the Department of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
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16
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Kolodner RD. A personal historical view of DNA mismatch repair with an emphasis on eukaryotic DNA mismatch repair. DNA Repair (Amst) 2016; 38:3-13. [PMID: 26698650 PMCID: PMC4740188 DOI: 10.1016/j.dnarep.2015.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 10/30/2015] [Accepted: 11/30/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Richard D Kolodner
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute for Molecular Medicine, University of CA, San Diego School of Medicine, La Jolla, CA 92093-0669, United States.
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17
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Ma L, Milman N, Nambiar M, Smith GR. Two separable functions of Ctp1 in the early steps of meiotic DNA double-strand break repair. Nucleic Acids Res 2015; 43:7349-59. [PMID: 26130711 PMCID: PMC4551917 DOI: 10.1093/nar/gkv644] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/09/2015] [Indexed: 12/02/2022] Open
Abstract
Meiotic programmed DNA double-strand break (DSB) repair is essential for crossing-over and viable gamete formation and requires removal of Spo11-oligonucleotide complexes from 5′ ends (clipping) and their resection to generate invasive 3′-end single-stranded DNA (resection). Ctp1 (Com1, Sae2, CtIP homolog) acting with the Mre11-Rad50-Nbs1 (MRN) complex is required in both steps. We isolated multiple S. pombe ctp1 mutants deficient in clipping but proficient in resection during meiosis. Remarkably, all of the mutations clustered in or near the conserved CxxC or RHR motif in the C-terminal portion. The mutants tested, like ctp1Δ, were clipping-deficient by both genetic and physical assays. But, unlike ctp1Δ, these mutants were recombination-proficient for Rec12 (Spo11 homolog)-independent break-repair and resection-proficient by physical assay. We conclude that the intracellular Ctp1 C-terminal portion is essential for clipping, while the N-terminal portion is sufficient for DSB end-resection. This conclusion agrees with purified human CtIP resection and endonuclease activities being independent. Our mutants provide intracellular evidence for separable functions of Ctp1. Some mutations truncate Ctp1 in the same region as one of the CtIP mutations linked to the Seckel and Jawad severe developmental syndromes, suggesting that these syndromes are caused by a lack of clipping at DSB ends that require repair.
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Affiliation(s)
- Lijuan Ma
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Neta Milman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mridula Nambiar
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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18
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Bologna S, Altmannova V, Valtorta E, Koenig C, Liberali P, Gentili C, Anrather D, Ammerer G, Pelkmans L, Krejci L, Ferrari S. Sumoylation regulates EXO1 stability and processing of DNA damage. Cell Cycle 2015; 14:2439-50. [PMID: 26083678 DOI: 10.1080/15384101.2015.1060381] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
DNA double-strand break repair by the error-free pathway of homologous recombination (HR) requires the concerted action of several factors. Among these, EXO1 and DNA2/BLM are responsible for the extensive resection of DNA ends to produce 3'-overhangs, which are essential intermediates for downstream steps of HR. Here we show that EXO1 is a SUMO target and that sumoylation affects EXO1 ubiquitylation and protein stability. We identify an UBC9-PIAS1/PIAS4-dependent mechanism controlling human EXO1 sumoylation in vivo and demonstrate conservation of this mechanism in yeast by the Ubc9-Siz1/Siz2 using an in vitro reconstituted system. Furthermore, we show physical interaction between EXO1 and the de-sumoylating enzyme SENP6 both in vitro and in vivo, promoting EXO1 stability. Finally, we identify the major sites of sumoylation in EXO1 and show that ectopic expression of a sumoylation-deficient form of EXO1 rescues the DNA damage-induced chromosomal aberrations observed upon wt-EXO1 expression. Thus, our study identifies a novel layer of regulation of EXO1, making the pathways that regulate its function an ideal target for therapeutic intervention.
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Affiliation(s)
- Serena Bologna
- a Institute of Molecular Cancer Research; University of Zurich ; Zurich , Switzerland
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19
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Abstract
DNA double-strand breaks (DSBs) in cells can undergo nucleolytic degradation to generate long 3' single-stranded DNA tails. This process is termed DNA end resection, and its occurrence effectively commits to break repair via homologous recombination, which entails the acquisition of genetic information from an intact, homologous donor DNA sequence. Recent advances, prompted by the identification of the nucleases that catalyze resection, have revealed intricate layers of functional redundancy, interconnectedness, and regulation. Here, we review the current state of the field with an emphasis on the major questions that remain to be answered. Topics addressed will include how resection initiates via the introduction of an endonucleolytic incision close to the break end, the molecular mechanism of the conserved MRE11 complex in conjunction with Sae2/CtIP within such a model, the role of BRCA1 and 53BP1 in regulating resection initiation in mammalian cells, the influence of chromatin in the resection process, and potential roles of novel factors.
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Affiliation(s)
- James M Daley
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Hengyao Niu
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Adam S Miller
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
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20
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Abstract
DNA mismatch repair (MMR) acts to repair mispaired bases resulting from misincorporation errors during DNA replication and also recognizes mispaired bases in recombination (HR) intermediates. Exonuclease 1 (Exo1) is a 5' → 3' exonuclease that participates in a number of DNA repair pathways. Exo1 was identified as an exonuclease that participates in Saccharomyces cerevisiae and human MMR where it functions to excise the daughter strand after mispair recognition, and additionally Exo1 functions in end resection during HR. However, Exo1 is not absolutely required for end resection during HR in vivo. Similarly, while Exo1 is required in MMR reactions that have been reconstituted in vitro, genetics studies have shown that it is not absolutely required for MMR in vivo suggesting the existence of Exo1-independent and Exo1-dependent MMR subpathways. Here, we review what is known about the Exo1-independent and Exo1-dependent subpathways, including studies of mutations in MMR genes that specifically disrupt either subpathway.
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Affiliation(s)
- Eva M Goellner
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
| | - Christopher D Putnam
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA; Departments of Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA; Departments of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA; Moores - UCSD Cancer Center, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA; Institute of Genomic Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA.
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21
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RecQ helicase and RecJ nuclease provide complementary functions to resect DNA for homologous recombination. Proc Natl Acad Sci U S A 2014; 111:E5133-42. [PMID: 25411316 DOI: 10.1073/pnas.1420009111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombinational DNA repair by the RecF pathway of Escherichia coli requires the coordinated activities of RecA, RecFOR, RecQ, RecJ, and single-strand DNA binding (SSB) proteins. These proteins facilitate formation of homologously paired joint molecules between linear double-stranded (dsDNA) and supercoiled DNA. Repair starts with resection of the broken dsDNA by RecQ, a 3'→5' helicase, RecJ, a 5'→3' exonuclease, and SSB protein. The ends of a dsDNA break can be blunt-ended, or they may possess either 5'- or 3'-single-stranded DNA (ssDNA) overhangs of undefined length. Here we show that RecJ nuclease alone can initiate nucleolytic resection of DNA with 5'-ssDNA overhangs, and that RecQ helicase can initiate resection of DNA with blunt-ends or 3'-ssDNA overhangs by DNA unwinding. We establish that in addition to its well-known ssDNA exonuclease activity, RecJ can display dsDNA exonuclease activity, degrading 100-200 nucleotides of the strand terminating with a 5'-ssDNA overhang. The dsDNA product, with a 3'-ssDNA overhang, is an optimal substrate for RecQ, which unwinds this intermediate to reveal the complementary DNA strand with a 5'-end that is degraded iteratively by RecJ. On the other hand, RecJ cannot resect duplex DNA that is either blunt-ended or terminated with 3'-ssDNA; however, such DNA is unwound by RecQ to create ssDNA for RecJ exonuclease. RecJ requires interaction with SSB for exonucleolytic degradation of ssDNA but not dsDNA. Thus, complementary action by RecJ and RecQ permits initiation of recombinational repair from all dsDNA ends: 5'-overhangs, blunt, or 3'-overhangs. Such helicase-nuclease coordination is a common mechanism underlying resection in all organisms.
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22
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The role of Exo1p exonuclease in DNA end resection to generate gene conversion tracts in Saccharomyces cerevisiae. Genetics 2014; 197:1097-109. [PMID: 24835424 PMCID: PMC4125386 DOI: 10.1534/genetics.114.164517] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The yeast Exo1p nuclease functions in multiple cellular roles: resection of DNA ends generated during recombination, telomere stability, DNA mismatch repair, and expansion of gaps formed during the repair of UV-induced DNA damage. In this study, we performed high-resolution mapping of spontaneous and UV-induced recombination events between homologs in exo1 strains, comparing the results with spontaneous and UV-induced recombination events in wild-type strains. One important comparison was the lengths of gene conversion tracts. Gene conversion events are usually interpreted as reflecting heteroduplex formation between interacting DNA molecules, followed by repair of mismatches within the heteroduplex. In most models of recombination, the length of the gene conversion tract is a function of the length of single-stranded DNA generated by end resection. Since the Exo1p has an important role in end resection, a reduction in the lengths of gene conversion tracts in exo1 strains was expected. In accordance with this expectation, gene conversion tract lengths associated with spontaneous crossovers in exo1 strains were reduced about twofold relative to wild type. For UV-induced events, conversion tract lengths associated with crossovers were also shorter for the exo1 strain than for the wild-type strain (3.2 and 7.6 kb, respectively). Unexpectedly, however, the lengths of conversion tracts that were unassociated with crossovers were longer in the exo1 strain than in the wild-type strain (6.2 and 4.8 kb, respectively). Alternative models of recombination in which the lengths of conversion tracts are determined by break-induced replication or oversynthesis during strand invasion are proposed to account for these observations.
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23
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Shao H, Baitinger C, Soderblom EJ, Burdett V, Modrich P. Hydrolytic function of Exo1 in mammalian mismatch repair. Nucleic Acids Res 2014; 42:7104-12. [PMID: 24829455 PMCID: PMC4066806 DOI: 10.1093/nar/gku420] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic and biochemical studies have previously implicated exonuclease 1 (Exo1) in yeast and mammalian mismatch repair, with results suggesting that function of the protein in the reaction depends on both its hydrolytic activity and its ability to interact with other components of the repair system. However, recent analysis of an Exo1-E109K knockin mouse has concluded that Exo1 function in mammalian mismatch repair is restricted to a structural role, a conclusion based on a prior report that N-terminal His-tagged Exo1-E109K is hydrolytically defective. Because Glu-109 is distant from the nuclease hydrolytic center, we have compared the activity of untagged full-length Exo1-E109K with that of wild type Exo1 and the hydrolytically defective active site mutant Exo1-D173A. We show that the activity of Exo1-E109K is comparable to that of wild type enzyme in a conventional exonuclease assay and that in contrast to a D173A active site mutant, Exo1-E109K is fully functional in mismatch-provoked excision and repair. We conclude that the catalytic function of Exo1 is required for its participation in mismatch repair. We also consider the other phenotypes of the Exo1-E109K mouse in the context of Exo1 hydrolytic function.
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Affiliation(s)
- Hongbing Shao
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Celia Baitinger
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Erik J Soderblom
- Proteomics Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Vickers Burdett
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Paul Modrich
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
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24
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Bregenhorn S, Jiricny J. Biochemical characterization of a cancer-associated E109K missense variant of human exonuclease 1. Nucleic Acids Res 2014; 42:7096-103. [PMID: 24829445 PMCID: PMC4066805 DOI: 10.1093/nar/gku419] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mutations in the mismatch repair (MMR) genes MSH2, MSH6, MLH1 and PMS2 are associated with Lynch Syndrome (LS), a familial predisposition to early-onset cancer of the colon and other organs. Because not all LS families carry mutations in these four genes, the search for cancer-associated mutations was extended to genes encoding other members of the mismatch repairosome. This effort identified mutations in EXO1, which encodes the sole exonuclease implicated in MMR. One of these mutations, E109K, was reported to abrogate the catalytic activity of the enzyme, yet, in the crystal structure of the EXO1/DNA complex, this glutamate is far away from both DNA and the catalytic site of the enzyme. In an attempt to elucidate the reason underlying the putative loss of function of this variant, we expressed it in Escherichia coli, and tested its activity in a series of biochemical assays. We now report that, contrary to earlier reports, and unlike the catalytic site mutant D173A, the EXO1 E109K variant resembled the wild-type (wt) enzyme on all tested substrates. In the light of our findings, we attempt here to reinterpret the results of the phenotypic characterization of a knock-in mouse carrying the E109K mutation and cells derived from it.
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Affiliation(s)
- Stephanie Bregenhorn
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Josef Jiricny
- Institute of Molecular Cancer Research of the University of Zurich and the ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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25
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Chen X, Paudyal SC, Chin RI, You Z. PCNA promotes processive DNA end resection by Exo1. Nucleic Acids Res 2013; 41:9325-38. [PMID: 23939618 PMCID: PMC3814391 DOI: 10.1093/nar/gkt672] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Exo1-mediated resection of DNA double-strand break ends generates 3′ single-stranded DNA overhangs required for homology-based DNA repair and activation of the ATR-dependent checkpoint. Despite its critical importance in inducing the overall DNA damage response, the mechanisms and regulation of the Exo1 resection pathway remain incompletely understood. Here, we identify the ring-shaped DNA clamp PCNA as a new factor in the Exo1 resection pathway. Using mammalian cells, Xenopus nuclear extracts and purified proteins, we show that after DNA damage, PCNA loads onto double-strand breaks and promotes Exo1 damage association through direct interaction with Exo1. By tethering Exo1 to the DNA substrate, PCNA confers processivity to Exo1 in resection. This role of PCNA in DNA resection is analogous to its function in DNA replication where PCNA serves as a processivity co-factor for DNA polymerases.
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Affiliation(s)
- Xiaoqing Chen
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
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26
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Mammalian Exo1 encodes both structural and catalytic functions that play distinct roles in essential biological processes. Proc Natl Acad Sci U S A 2013; 110:E2470-9. [PMID: 23754438 DOI: 10.1073/pnas.1308512110] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mammalian Exonuclease 1 (EXO1) is an evolutionarily conserved, multifunctional exonuclease involved in DNA damage repair, replication, immunoglobulin diversity, meiosis, and telomere maintenance. It has been assumed that EXO1 participates in these processes primarily through its exonuclease activity, but recent studies also suggest that EXO1 has a structural function in the assembly of higher-order protein complexes. To dissect the enzymatic and nonenzymatic roles of EXO1 in the different biological processes in vivo, we generated an EXO1-E109K knockin (Exo1(EK)) mouse expressing a stable exonuclease-deficient protein and, for comparison, a fully EXO1-deficient (Exo1(null)) mouse. In contrast to Exo1(null/null) mice, Exo1(EK/EK) mice retained mismatch repair activity and displayed normal class switch recombination and meiosis. However, both Exo1-mutant lines showed defects in DNA damage response including DNA double-strand break repair (DSBR) through DNA end resection, chromosomal stability, and tumor suppression, indicating that the enzymatic function is required for those processes. On a transformation-related protein 53 (Trp53)-null background, the DSBR defect caused by the E109K mutation altered the tumor spectrum but did not affect the overall survival as compared with p53-Exo1(null) mice, whose defects in both DSBR and mismatch repair also compromised survival. The separation of these functions demonstrates the differential requirement for the structural function and nuclease activity of mammalian EXO1 in distinct DNA repair processes and tumorigenesis in vivo.
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27
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Adkins NL, Niu H, Sung P, Peterson CL. Nucleosome dynamics regulates DNA processing. Nat Struct Mol Biol 2013; 20:836-42. [PMID: 23728291 PMCID: PMC3711194 DOI: 10.1038/nsmb.2585] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 04/12/2013] [Indexed: 11/18/2022]
Abstract
The repair of DNA double strand breaks (DSBs) is critical for the maintenance of genome integrity. The first step in DSB repair by homologous recombination is processing of the ends by one of two resection pathways, exemplified by Saccharomyces cerevisiae Exo1 and Sgs1–Dna2. Here we report in vitro and in vivo studies that characterize the impact of chromatin on each resection pathway. We find that efficient resection by the Sgs1-Dna2 -dependent machinery requires a nucleosome-free gap adjacent to the DSB. Resection by Exo1 is blocked by nucleosomes, and processing activity can be partially restored by removal of the H2A-H2B dimers. Our study also supports a role for the dynamic incorporation of the H2A.Z histone variant in Exo1 processing, and it further suggests that the two resection pathways require distinct chromatin remodeling events in order to navigate chromatin structure.
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Affiliation(s)
- Nicholas L Adkins
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
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28
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Kwon YI, Abe K, Osakabe K, Endo M, Nishizawa-Yokoi A, Saika H, Shimada H, Toki S. Overexpression of OsRecQl4 and/or OsExo1 enhances DSB-induced homologous recombination in rice. PLANT & CELL PHYSIOLOGY 2012; 53:2142-52. [PMID: 23161853 DOI: 10.1093/pcp/pcs155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
During homologous recombination (HR)-mediated DNA double-strand break (DSB) repair in eukaryotes, an initial step is the creation of a 3'-single-stranded DNA (ssDNA) overhang via resection of a 5' end. Rad51 polymerizes on this ssDNA to search for a homologous sequence, and the gapped sequence is then repaired using an undamaged homologous DNA strand as template. Recent studies in eukaryotes indicate that resection of the DSB site is promoted by the cooperative action of RecQ helicase family proteins: Bloom helicase (BLM) in mammals or Sgs1 in yeast, and exonuclease 1 (Exo1). However, the role of RecQ helicase and exonuclease during the 5'-resection process of HR in plant cells has not yet been defined. Here, we demonstrate that overexpression of rice proteins OsRecQl4 (BLM counterpart) and/or OsExo1 (Exo1 homolog) can enhance DSB processing, as evaluated by recombination substrate reporter lines in rice. These results could be applied to construct an efficient gene targeting system in rice.
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Affiliation(s)
- Yong-Ik Kwon
- Plant Genome Engineering Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
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29
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Garcia V, Phelps SEL, Gray S, Neale MJ. Bidirectional resection of DNA double-strand breaks by Mre11 and Exo1. Nature 2011; 479:241-4. [PMID: 22002605 PMCID: PMC3214165 DOI: 10.1038/nature10515] [Citation(s) in RCA: 339] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 08/30/2011] [Indexed: 01/22/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) by homologous recombination requires resection of 5'-termini to generate 3'-single-strand DNA tails. Key components of this reaction are exonuclease 1 and the bifunctional endo/exonuclease, Mre11 (refs 2-4). Mre11 endonuclease activity is critical when DSB termini are blocked by bound protein--such as by the DNA end-joining complex, topoisomerases or the meiotic transesterase Spo11 (refs 7-13)--but a specific function for the Mre11 3'-5' exonuclease activity has remained elusive. Here we use Saccharomyces cerevisiae to reveal a role for the Mre11 exonuclease during the resection of Spo11-linked 5'-DNA termini in vivo. We show that the residual resection observed in Exo1-mutant cells is dependent on Mre11, and that both exonuclease activities are required for efficient DSB repair. Previous work has indicated that resection traverses unidirectionally. Using a combination of physical assays for 5'-end processing, our results indicate an alternative mechanism involving bidirectional resection. First, Mre11 nicks the strand to be resected up to 300 nucleotides from the 5'-terminus of the DSB--much further away than previously assumed. Second, this nick enables resection in a bidirectional manner, using Exo1 in the 5'-3' direction away from the DSB, and Mre11 in the 3'-5' direction towards the DSB end. Mre11 exonuclease activity also confers resistance to DNA damage in cycling cells, suggesting that Mre11-catalysed resection may be a general feature of various DNA repair pathways.
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Affiliation(s)
- Valerie Garcia
- Genome Damage and Stability Centre, The University of Sussex, Brighton, BN1 9RQ, UK
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30
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Abstract
DNA double-strand breaks (DSBs) are cytotoxic lesions that can result in mutagenic events or cell death if left unrepaired or repaired inappropriately. Cells use two major pathways for DSB repair: nonhomologous end joining (NHEJ) and homologous recombination (HR). The choice between these pathways depends on the phase of the cell cycle and the nature of the DSB ends. A critical determinant of repair pathway choice is the initiation of 5'-3' resection of DNA ends, which commits cells to homology-dependent repair, and prevents repair by classical NHEJ. Here, we review the components of the end resection machinery, the role of end structure, and the cell-cycle phase on resection and the interplay of end processing with NHEJ.
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Affiliation(s)
- Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York 10032, USA.
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31
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14-3-3 Proteins regulate exonuclease 1-dependent processing of stalled replication forks. PLoS Genet 2011; 7:e1001367. [PMID: 21533173 PMCID: PMC3077382 DOI: 10.1371/journal.pgen.1001367] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 03/08/2011] [Indexed: 01/25/2023] Open
Abstract
Replication fork integrity, which is essential for the maintenance of genome stability, is monitored by checkpoint-mediated phosphorylation events. 14-3-3 proteins are able to bind phosphorylated proteins and were shown to play an undefined role under DNA replication stress. Exonuclease 1 (Exo1) processes stalled replication forks in checkpoint-defective yeast cells. We now identify 14-3-3 proteins as in vivo interaction partners of Exo1, both in yeast and mammalian cells. Yeast 14-3-3–deficient cells fail to induce Mec1–dependent Exo1 hyperphosphorylation and accumulate Exo1–dependent ssDNA gaps at stalled forks, as revealed by electron microscopy. This leads to persistent checkpoint activation and exacerbated recovery defects. Moreover, using DNA bi-dimensional electrophoresis, we show that 14-3-3 proteins promote fork progression under limiting nucleotide concentrations. We propose that 14-3-3 proteins assist in controlling the phosphorylation status of Exo1 and additional unknown targets, promoting fork progression, stability, and restart in response to DNA replication stress. Stalling and collapse of DNA replication forks is an important source of genome instability and has been implicated in early steps of carcinogenesis. The maintenance of stable intermediates upon stalled replication requires the coordinated action of a number of proteins and proper inhibitory control of dangerous enzymatic activities. In this study, we uncover an evolutionarily conserved mechanism through which 14-3-3 proteins modulate the checkpoint-mediated phosphorylation of, and in turn limit the activity of, an exonuclease (Exo1) previously implicated in pathological processing of stalled replication forks and other sensitive DNA intermediates. This represents an unprecedented link in the field of DNA repair and genome stability, providing a molecular rationale to the yet undefined role of 14-3-3 proteins in the maintenance of genome integrity after replication stress. In analogy to Exo1, our data suggest that additional factors at replication forks may be subjected to similar regulation, pointing to the 14-3-3 proteins as central components of the checkpoint triggered in response to replication stress.
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32
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Nimonkar AV, Genschel J, Kinoshita E, Polaczek P, Campbell JL, Wyman C, Modrich P, Kowalczykowski SC. BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair. Genes Dev 2011; 25:350-62. [PMID: 21325134 PMCID: PMC3042158 DOI: 10.1101/gad.2003811] [Citation(s) in RCA: 544] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Accepted: 01/04/2011] [Indexed: 01/23/2023]
Abstract
Repair of dsDNA breaks requires processing to produce 3'-terminated ssDNA. We biochemically reconstituted DNA end resection using purified human proteins: Bloom helicase (BLM); DNA2 helicase/nuclease; Exonuclease 1 (EXO1); the complex comprising MRE11, RAD50, and NBS1 (MRN); and Replication protein A (RPA). Resection occurs via two routes. In one, BLM and DNA2 physically and specifically interact to resect DNA in a process that is ATP-dependent and requires BLM helicase and DNA2 nuclease functions. RPA is essential for both DNA unwinding by BLM and enforcing 5' → 3' resection polarity by DNA2. MRN accelerates processing by recruiting BLM to the end. In the other, EXO1 resects the DNA and is stimulated by BLM, MRN, and RPA. BLM increases the affinity of EXO1 for ends, and MRN recruits and enhances the processivity of EXO1. Our results establish two of the core machineries that initiate recombinational DNA repair in human cells.
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Affiliation(s)
- Amitabh V. Nimonkar
- Department of Microbiology, University of California at Davis, Davis, California 95616, USA
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, California 95616, USA
| | - Jochen Genschel
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Eri Kinoshita
- Department of Cell Biology and Genetics, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Piotr Polaczek
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Judith L. Campbell
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Claire Wyman
- Department of Cell Biology and Genetics, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Paul Modrich
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Stephen C. Kowalczykowski
- Department of Microbiology, University of California at Davis, Davis, California 95616, USA
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, California 95616, USA
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33
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Bolderson E, Tomimatsu N, Richard DJ, Boucher D, Kumar R, Pandita TK, Burma S, Khanna KK. Phosphorylation of Exo1 modulates homologous recombination repair of DNA double-strand breaks. Nucleic Acids Res 2009; 38:1821-31. [PMID: 20019063 PMCID: PMC2847229 DOI: 10.1093/nar/gkp1164] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
DNA double-strand break (DSB) repair via the homologous recombination pathway is a multi-stage process, which results in repair of the DSB without loss of genetic information or fidelity. One essential step in this process is the generation of extended single-stranded DNA (ssDNA) regions at the break site. This ssDNA serves to induce cell cycle checkpoints and is required for Rad51 mediated strand invasion of the sister chromatid. Here, we show that human Exonuclease 1 (Exo1) is required for the normal repair of DSBs by HR. Cells depleted of Exo1 show chromosomal instability and hypersensitivity to ionising radiation (IR) exposure. We find that Exo1 accumulates rapidly at DSBs and is required for the recruitment of RPA and Rad51 to sites of DSBs, suggesting a role for Exo1 in ssDNA generation. Interestingly, the phosphorylation of Exo1 by ATM appears to regulate the activity of Exo1 following resection, allowing optimal Rad51 loading and the completion of HR repair. These data establish a role for Exo1 in resection of DSBs in human cells, highlighting the critical requirement of Exo1 for DSB repair via HR and thus the maintenance of genomic stability.
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Affiliation(s)
- Emma Bolderson
- Signal Transduction Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
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Meiotic DNA double-strand break repair requires two nucleases, MRN and Ctp1, to produce a single size class of Rec12 (Spo11)-oligonucleotide complexes. Mol Cell Biol 2009; 29:5998-6005. [PMID: 19752195 DOI: 10.1128/mcb.01127-09] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) in meiosis are formed by Spo11 (Rec12 in fission yeast), a topoisomerase II-like protein, which becomes covalently attached to DNA 5' ends. For DSB repair through homologous recombination, the protein must be removed from these DNA ends. We show here that Rec12 is endonucleolytically removed from DSB ends attached to a short oligonucleotide (Rec12-oligonucleotide complex), as is Spo11 in budding yeast. Fission yeast, however, has only one size class of Rec12-oligonucleotide complexes, whereas budding yeast has two size classes, suggesting different endonucleolytic regulatory mechanisms. Rec12-oligonucleotide generation strictly requires Ctp1 (Sae2 nuclease homolog), the Rad32 (Mre11) nuclease domain, and Rad50 of the MRN complex. Surprisingly, Nbs1 is not strictly required, indicating separable roles for the MRN subunits. On the basis of these and other data, we propose that Rad32 nuclease has the catalytic site for Rec12-oligonucleotide generation and is activated by Ctp1, which plays an additional role in meiotic recombination.
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Eccleston J, Schrader CE, Yuan K, Stavnezer J, Selsing E. Class switch recombination efficiency and junction microhomology patterns in Msh2-, Mlh1-, and Exo1-deficient mice depend on the presence of mu switch region tandem repeats. THE JOURNAL OF IMMUNOLOGY 2009; 183:1222-8. [PMID: 19553545 DOI: 10.4049/jimmunol.0900135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Msh2 mismatch repair (MMR) protein is critical for class switch recombination (CSR) events that occur in mice that lack the Smu tandem repeat (SmuTR) region (SmuTR(-/-) mice). The pattern of microhomology among switch junction sites in Msh2-deficient mice is also dependent on the presence or absence of SmuTR sequences. It is not known whether these CSR effects reflect an individual function of Msh2 or the function of Msh2 within the MMR machinery. In the absence of the SmuTR sequences, Msh2 deficiency nearly ablates CSR. We now show that Mlh1 or Exo1 deficiencies also eliminate CSR in the absence of the SmuTR. Furthermore, in SmuTR(-/-) mice, deficiencies of Mlh1 or Exo1 result in increased switch junction microhomology as has also been seen with Msh2 deficiency. These results are consistent with a CSR model in which the MMR machinery is important in processing DNA nicks to produce double-stranded breaks, particularly in sequences where nicks are infrequent. We propose that double-stranded break paucity in MMR-deficient mice leads to increased use of an alternative joining pathway where microhomologies are important for CSR break ligation. Interestingly, when the SmuTR region is present, deficiency of Msh2 does not lead to the increased microhomology seen with Mlh1 or Exo1 deficiencies, suggesting that Msh2 might have an additional function in CSR. It is also possible that the inability to initiate MMR in the absence of Msh2 results in CSR junctions with less microhomology than joinings that occur when MMR is initiated but then proceeds abnormally due to Mlh1 or Exo1 deficiencies.
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Affiliation(s)
- Jennifer Eccleston
- Immunology Program and Department of Pathology, Tufts University School of Medicine, Boston, MA 02111, USA
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36
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Ctp1 and Exonuclease 1, alternative nucleases regulated by the MRN complex, are required for efficient meiotic recombination. Proc Natl Acad Sci U S A 2009; 106:9356-61. [PMID: 19470480 DOI: 10.1073/pnas.0902793106] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Double-strand breaks (DSBs) in DNA are lethal unless repaired. Faithful repair requires processing of the DSB ends and interaction with intact homologous DNA, which can produce genetic recombinants. To determine the role of nucleases in DSB end-processing and joint molecule resolution, we studied recombination at the site of a single DSB, generated by induction of the I-SceI endonuclease, during meiosis of fission yeast lacking Rec12 (Spo11 homolog) and, hence, other DSBs. We find that in the presence of the MRN (Rad32-Rad50-Nbs1) complex efficient recombination requires Ctp1, the ortholog of the nuclease Sae2, but not the nuclease activity of MRN. In the absence of MRN, exonuclease 1 (Exo1) becomes the major nuclease required for efficient recombination. Our data indicate that MRN enables access of Ctp1 to the DSB but blocks access of Exo1. In our assay, the Rad16-Swi10 nuclease, required for nucleotide excision-repair, is required for efficient recombination, presumably to remove heterologous DNA at the end of the I-SceI cut site. Another nuclease, the Mus81-Eme1 Holliday junction resolvase, is required to generate crossovers accompanying gene conversion at the I-SceI cut site. Additional, previously published evidence indicates that these 5 nucleases play similar roles in wild-type fission yeast meiotic recombination and in the repair of spontaneous and damage-induced mitotic DSBs. We propose that in wild-type meiosis MRN, in conjunction with Ctp1, removes the covalently attached Rec12 protein from the DNA end, which is then resected by Ctp1 and other activities to produce the single-stranded DNA necessary for further steps of DSB repair.
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37
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Bolderson E, Richard DJ, Edelmann W, Khanna KK. Involvement of Exo1b in DNA damage-induced apoptosis. Nucleic Acids Res 2009; 37:3452-63. [PMID: 19339515 PMCID: PMC2691832 DOI: 10.1093/nar/gkp194] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Apoptosis is essential for the maintenance of inherited genomic integrity. During DNA damage-induced apoptosis, mechanisms of cell survival, such as DNA repair are inactivated to allow cell death to proceed. Here, we describe a role for the mammalian DNA repair enzyme Exonuclease 1 (Exo1) in DNA damage-induced apoptosis. Depletion of Exo1 in human fibroblasts, or mouse embryonic fibroblasts led to a delay in DNA damage-induced apoptosis. Furthermore, we show that Exo1 acts upstream of caspase-3, DNA fragmentation and cytochrome c release. In addition, induction of apoptosis with DNA-damaging agents led to cleavage of both isoforms of Exo1. The cleavage of Exo1 was mapped to Asp514, and shown to be mediated by caspase-3. Expression of a caspase-3 cleavage site mutant form of Exo1, Asp514Ala, prevented formation of the previously observed fragment without any affect on the onset of apoptosis. We conclude that Exo1 has a role in the timely induction of apoptosis and that it is subsequently cleaved and degraded during apoptosis, potentially inhibiting DNA damage repair.
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Affiliation(s)
- Emma Bolderson
- Signal Transduction Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia
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38
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Human exonuclease 1 and BLM helicase interact to resect DNA and initiate DNA repair. Proc Natl Acad Sci U S A 2008; 105:16906-11. [PMID: 18971343 DOI: 10.1073/pnas.0809380105] [Citation(s) in RCA: 248] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The error-free repair of double-stranded DNA breaks by homologous recombination requires processing of broken ends. These processed ends are substrates for assembly of DNA strand exchange proteins that mediate DNA strand invasion. Here, we establish that human BLM helicase, a member of the RecQ family, stimulates the nucleolytic activity of human exonuclease 1 (hExo1), a 5'-->3' double-stranded DNA exonuclease. The stimulation is specific because other RecQ homologs fail to stimulate hExo1. Stimulation of DNA resection by hExo1 is independent of BLM helicase activity and is, instead, mediated by an interaction between the 2 proteins. Finally, we show that DNA ends resected by hExo1 and BLM are used by human Rad51, but not its yeast or bacterial counterparts, to promote homologous DNA pairing. This in vitro system recapitulates initial steps of homologous recombination and provides biochemical evidence for a role of BLM and Exo1 in the initiation of recombinational DNA repair.
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39
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McDowell HD, Carney JP, Wilson TM. Inhibition of the 5' to 3' exonuclease activity of hEXO1 by 8-oxoguanine. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2008; 49:388-398. [PMID: 18418867 DOI: 10.1002/em.20398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The mismatch repair pathway is responsible for maintaining genomic stability by correcting base-base mismatches and insertion/deletion loops that arise mainly via replication errors. Additionally, the mismatch repair pathway performs a central role in the cellular response to both alkylation and reactive oxygen species induced DNA damage. An important step in mismatch processing is the recruitment of hEXO1, a 5' to 3' exonuclease, by hMSH2-hMSH6 to remove the nascent DNA strand. However, very little is currently known about the capacity of hEXO1 to exonucleolytically process damaged DNA bases. Therefore, we examined whether hEXO1 can degrade double-stranded DNA substrates containing alkylated or oxidized nucleotides. Our results demonstrated that hEXO1 is capable of degrading duplex DNA containing an O6-methylguanine (O6-meG) adduct paired with either a C or a T. Additionally, the hMSH2-hMSH6 complex stimulated hEXO1 exonuclease activity on the O6-meG/T and O6-meG/C DNA substrates. In contrast, hEXO1 exonuclease activity was significantly blocked by the presence of an 8-oxoguanine adduct in both single and double stranded DNA substrates. Further, hMSH2-hMSH6 was not able to alleviate the nucleolytic block caused by the 8-oxoguanine adduct in heteroduplex DNA.
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Affiliation(s)
- Heather D McDowell
- Department of Radiation Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
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40
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Ehmsen KT, Heyer WD. Biochemistry of Meiotic Recombination: Formation, Processing, and Resolution of Recombination Intermediates. GENOME DYNAMICS AND STABILITY 2008; 3:91. [PMID: 20098639 PMCID: PMC2809983 DOI: 10.1007/7050_2008_039] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Meiotic recombination ensures accurate chromosome segregation during the first meiotic division and provides a mechanism to increase genetic heterogeneity among the meiotic products. Unlike homologous recombination in somatic (vegetative) cells, where sister chromatid interactions prevail and crossover formation is avoided, meiotic recombination is targeted to involve homologs, resulting in crossovers to connect the homologs before anaphase of the first meiotic division. The mechanisms responsible for homolog choice and crossover control are poorly understood, but likely involve meiosis-specific recombination proteins, as well as meiosis-specific chromosome organization and architecture. Much progress has been made to identify and biochemically characterize many of the proteins acting during meiotic recombination. This review will focus on the proteins that generate and process heteroduplex DNA, as well as those that process DNA junctions during meiotic recombination, with particular attention to how recombination activities promote crossover resolution between homologs.
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Affiliation(s)
- Kirk T. Ehmsen
- Section of Microbiology, University of California, Davis, One Shields Ave, Davis, CA 95616-8665, USA
| | - Wolf-Dietrich Heyer
- Section of Microbiology, University of California, Davis, One Shields Ave, Davis, CA 95616-8665, USA
- Section of Molecular and Cellular Biology, University of California, Davis, One Shields Ave, Davis, CA 95616-8665, USA
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41
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Lam AF, Krogh BO, Symington LS. Unique and overlapping functions of the Exo1, Mre11 and Pso2 nucleases in DNA repair. DNA Repair (Amst) 2008; 7:655-62. [PMID: 18295552 DOI: 10.1016/j.dnarep.2007.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 12/20/2007] [Accepted: 12/20/2007] [Indexed: 12/21/2022]
Abstract
The Mre11 and Pso2 nucleases function in homologous recombination and interstrand cross-link (ICL) repair pathways, respectively, while the Exo1 nuclease is involved in homologous recombination and mismatch repair. Characterization of the sensitivity of single, double and triple mutants for these nucleases in Saccharomyces cerevisiae to various DNA damaging agents reveals complex interactions that depend on the type of DNA damage. The pso2 mutant is uniquely sensitive to agents that generate ICLs and mre11-H125N shows the highest sensitivity of the single mutants for ionizing radiation and methyl methane sulfonate. However, elimination of all three nucleases confers higher sensitivity to IR than any of the single or double mutant combinations indicating a high degree of redundancy and versatility in the response to DNA damage. In response to ICL agents, double-strand breaks are still formed in the triple nuclease mutant indicating that none of these nucleases are responsible for unhooking cross-links.
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Affiliation(s)
- Alicia F Lam
- Department of Microbiology, Columbia University Medical Center, New York, NY 10032, United States
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42
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Furukawa T, Imamura T, Kitamoto HK, Shimada H. Rice exonuclease-1 homologue, OsEXO1, that interacts with DNA polymerase lambda and RPA subunit proteins, is involved in cell proliferation. PLANT MOLECULAR BIOLOGY 2008; 66:519-531. [PMID: 18231866 DOI: 10.1007/s11103-008-9288-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 12/31/2007] [Indexed: 05/25/2023]
Abstract
Exonuclease 1, a class III member of the RAD2 nuclease family, is a structure-specific nuclease involved in DNA metabolism (replication, repair and recombination). We have identified a homologue to Exonuclease-1 from rice (Oryza sativa L. cv. Nipponbare) and have designated it O. sativa Exonuclease-1 (OsEXO1). The open reading frame of OsEXO1 encodes a predicted product of 836 amino acid residues with a molecular weight of 92 kDa. Two highly conserved nuclease domains (XPG-N and XPG-I) are present in the N-terminal region of the protein. OsEXO1-sGFP fusion protein transiently overexpressed in the onion epidermal cells localized to the nucleus. The transcript of OsEXO1 is highly expressed in meristematic tissues and panicles. Inhibition of cell proliferation by removal of sucrose from the medium or by the addition of cell cycle inhibitors decreased OsEXO1 expression. Functional complementation assays using yeast RAD2 member null mutants demonstrates that OsEXO1 is able to substitute for ScEXO1 and ScRAD27 functions. Yeast two-hybrid analysis shows that OsEXO1 interacted with rice DNA polymerase lambda (OsPol lambda), the 70 kDa subunit b of rice replication protein A (OsRPA70b), and the 32 kDa subunit 1 of rice replication protein A (OsRPA32-1). Irradiation of UV-B induces OsEXO1 expression while hydrogen peroxide treatment represses it. These results suggest that OsEXO1 plays an important role in both cell proliferation and UV-damaged nuclear DNA repair pathway under dark conditions.
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Affiliation(s)
- Tomoyuki Furukawa
- Division of Plant Biotechnology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
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43
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El-Shemerly M, Hess D, Pyakurel AK, Moselhy S, Ferrari S. ATR-dependent pathways control hEXO1 stability in response to stalled forks. Nucleic Acids Res 2007; 36:511-9. [PMID: 18048416 PMCID: PMC2241874 DOI: 10.1093/nar/gkm1052] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nucleases play important roles in DNA synthesis, recombination and repair. We have previously shown that human exonuclease 1 (hEXO1) is phosphorylated in response to agents stalling DNA replication and that hEXO1 consequently undergoes ubiquitination and degradation in a proteasome-dependent manner. In the present study, we have addressed the identity of the pathway transducing stalled-replication signals to hEXO1. Using chemical inhibitors, RNA interference, ATM- and ATR-deficient cell lines we have concluded that hEXO1 phosphorylation is ATR-dependent. By means of mass spectrometry, we have identified the sites of phosphorylation in hEXO1 in undamaged cells and in cells treated with hydroxyurea (HU). hEXO1 is phosphorylated at nine basal sites and three additional sites are induced by HU treatment. Analysis of single- and multiple-point mutants revealed that mutation to Ala of the three HU-induced sites of phosphorylation partially rescued HU-dependent degradation of hEXO1 and additionally stabilized the protein in non-treated cells. We have raised an antibody to pS714, an HU-induced site of the S/T-Q type, and we provide evidence that S714 is phosphorylated upon HU but not IR treatment. The antibody may be a useful tool to monitor signal transduction events triggered by stalled DNA replication.
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Affiliation(s)
- Mahmoud El-Shemerly
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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44
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Tran PT, Fey JP, Erdeniz N, Gellon L, Boiteux S, Liskay RM. A mutation in EXO1 defines separable roles in DNA mismatch repair and post-replication repair. DNA Repair (Amst) 2007; 6:1572-83. [PMID: 17602897 PMCID: PMC2447855 DOI: 10.1016/j.dnarep.2007.05.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 05/10/2007] [Accepted: 05/11/2007] [Indexed: 01/27/2023]
Abstract
Replication forks stall at DNA lesions or as a result of an unfavorable replicative environment. These fork stalling events have been associated with recombination and gross chromosomal rearrangements. Recombination and fork bypass pathways are the mechanisms accountable for restart of stalled forks. An important lesion bypass mechanism is the highly conserved post-replication repair (PRR) pathway that is composed of error-prone translesion and error-free bypass branches. EXO1 codes for a Rad2p family member nuclease that has been implicated in a multitude of eukaryotic DNA metabolic pathways that include DNA repair, recombination, replication, and telomere integrity. In this report, we show EXO1 functions in the MMS2 error-free branch of the PRR pathway independent of the role of EXO1 in DNA mismatch repair (MMR). Consistent with the idea that EXO1 functions independently in two separate pathways, we defined a domain of Exo1p required for PRR distinct from those required for interaction with MMR proteins. We then generated a point mutant exo1 allele that was defective for the function of Exo1p in MMR due to disrupted interaction with Mlh1p, but still functional for PRR. Lastly, by using a compound exo1 mutant that was defective for interaction with Mlh1p and deficient for nuclease activity, we provide further evidence that Exo1p plays both structural and catalytic roles during MMR.
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Affiliation(s)
- Phuoc T. Tran
- Department of Radiation Oncology, Stanford Hospital & Clinics, Stanford, CA 94305, USA
- Corresponding Author: Phuoc T. Tran, 875 Blake Wilbur Drive, Stanford, CA 94305, e-mail:
| | - Julien P. Fey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Naz Erdeniz
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lionel Gellon
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Serge Boiteux
- Commissariat à l'Energie Atomique (CEA), Département de Radiobiologie et Radiopathologie, UMR217 CNRS/CEA Radiobiologie Moléculaire et Cellulaire, Fontenay aux Roses 92265, France
| | - R. Michael Liskay
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
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45
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Affiliation(s)
- Ravi R Iyer
- Department of Biochemistry and Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA
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46
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El-Shemerly M, Janscak P, Hess D, Jiricny J, Ferrari S. Degradation of human exonuclease 1b upon DNA synthesis inhibition. Cancer Res 2005; 65:3604-9. [PMID: 15867354 DOI: 10.1158/0008-5472.can-04-4069] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In response to DNA damage, signaling pathways are triggered that either block the cell division cycle at defined transitions (G1-S and G2-M) or slow down progression through the S phase. Nucleases play important roles in DNA synthesis, recombination, repair, and apoptosis. In this study, we have examined the regulation of human exonuclease 1 (hEXO1b). The endogenous hEXO1b protein was only detected upon enrichment by immunoprecipitation. We found that hEXO1b was constantly expressed throughout the cell cycle. However, treatment of cells with agents that cause arrest of DNA replication led to rapid degradation of hEXO1b. This effect was fully reversed upon removal of the block. Analysis of synchronized cells showed that degradation of hEXO1b during the S phase was strictly dependent on DNA synthesis inhibition. DNA damage caused by UV-C radiation, ionizing radiation, cisplatin, or the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine did not affect hEXO1b stability. We show that hEXO1b was phosphorylated in response to inhibition of DNA synthesis and that phosphorylation coincided with rapid protein degradation through ubiquitin-proteasome pathways. Our data support the evidence that control of exonuclease 1 activity may be critical for the maintenance of stalled replication forks.
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Affiliation(s)
- Mahmoud El-Shemerly
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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47
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Moritoh S, Miki D, Akiyama M, Kawahara M, Izawa T, Maki H, Shimamoto K. RNAi-mediated Silencing of OsGEN-L (OsGEN-like), a New Member of the RAD2/XPG Nuclease Family, Causes Male Sterility by Defect of Microspore Development in Rice. ACTA ACUST UNITED AC 2005; 46:699-715. [PMID: 15792960 DOI: 10.1093/pcp/pci090] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We have cloned a new member of the RAD2/XPG nuclease family, OsGEN-L (OsGEN-like), from rice (Oryza sativa L.). OsGEN-L possesses two domains, the N- and I-regions, that are conserved in the RAD2/XPG nuclease family. Database searches and phylogenetic analyses revealed that OsGEN-L belongs to class 4 of the RAD2/XPG nuclease family, and OsGEN-L homologs were found in animals and higher plants. To elucidate the function of OsGEN-L, we generated rice OsGEN-L-RNAi transgenic plants in which OsGEN-L expression was silenced. Most of the OsGEN-L-RNAi plants displayed low fertility, and some of them were male-sterile. OsGEN-L-RNAi plants lacked mature pollen, resulting from a defect in early microspore development. A OsGEN-L-green fluorescent protein (GFP) fusion protein was localized in the nucleus, and the OsGEN-L promoter was specifically active in the anthers. Furthermore, a recombinant OsGEN-L protein possessed flap endonuclease activity and both single-stranded and double-stranded DNA-binding activities. Our results suggest that OsGEN-L plays an essential role in DNA metabolism required for early microspore development in rice.
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Affiliation(s)
- Satoru Moritoh
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192 Japan
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Llorente B, Symington LS. The Mre11 nuclease is not required for 5' to 3' resection at multiple HO-induced double-strand breaks. Mol Cell Biol 2004; 24:9682-94. [PMID: 15485933 PMCID: PMC522228 DOI: 10.1128/mcb.24.21.9682-9694.2004] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Current hypotheses suggest the Mre11 nuclease activity could be directly involved in double-strand break (DSB) resection in the presence of a large number of DSBs or limited to processing abnormal DNA ends. To distinguish between these possibilities, we used two methods to create large numbers of DSBs in Saccharomyces cerevisiae chromosomes, without introducing other substrates for the Mre11 nuclease. Multiple DSBs were created either by expressing the HO endonuclease in strains containing several HO cut sites embedded within randomly dispersed Ty1 elements or by phleomycin treatment. Analysis of resection by single-strand DNA formation in these systems showed no difference between strains containing MRE11 or the mre11-D56N nuclease defective allele, suggesting that the Mre11 nuclease is not involved in the extensive 5' to 3' resection of DSBs. We postulate that the ionizing radiation (IR) sensitivity of mre11 nuclease-defective mutants results from the accumulation of IR-induced DNA damage that is normally processed by the Mre11 nuclease. We also report that the processivity of 5' to 3' DSB resection and the yield of repaired products are affected by the number of DSBs in a dose-dependent manner. Finally, we show that the exonuclease Exo1 is involved in the processivity of 5' to 3' resection of an HO-induced DSB at the MAT locus.
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Affiliation(s)
- Bertrand Llorente
- Department of Microbiology, Columbia University Medical Center, 701 W. 168th St., New York, NY 10032, USA
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49
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Tran PT, Erdeniz N, Symington LS, Liskay RM. EXO1-A multi-tasking eukaryotic nuclease. DNA Repair (Amst) 2004; 3:1549-59. [PMID: 15474417 DOI: 10.1016/j.dnarep.2004.05.015] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 05/26/2004] [Indexed: 12/14/2022]
Abstract
Exo1 was first isolated as a 5' --> 3' exonuclease activity induced during meiosis in fission yeast and since that time has been implicated in a multitude of eukaryotic DNA metabolic pathways that include DNA repair, recombination, replication, and telomere integrity. Involvement in multiple pathways affecting genomic stability makes EXO1 a logical target for mutation during oncogenesis. Here, we review studies in several experimental systems that shed light on the role of Exo1 in these DNA transaction pathways, particularly those that may relate to oncogenesis.
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Affiliation(s)
- Phuoc T Tran
- Graduate Medical Education, St. Mary's Medical Center, San Francisco, CA 94117, USA
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50
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Abstract
One strand of cellular DNA is generated as RNA-initiated discontinuous segments called Okazaki fragments that later are joined. The RNA terminated region is displaced into a 5' single-stranded flap, which is removed by the structure-specific flap endonuclease 1 (FEN1), leaving a nick for ligation. Similarly, in long-patch base excision repair, a damaged nucleotide is displaced into a flap and removed by FEN1. FEN1 is a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. As an endonuclease, FEN1 enters the flap from the 5' end and then tracks to cleave the flap base. Cleavage is oriented by the formation of a double flap. Analyses of FEN1 crystal structures suggest mechanisms for tracking and cleavage. Some flaps can form self-annealed and template bubble structures that interfere with FEN1. FEN1 interacts with other nucleases and helicases that allow it to act efficiently on structured flaps. Genetic and biochemical analyses continue to reveal many roles of FEN1.
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Affiliation(s)
- Yuan Liu
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.
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