1
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Kotenko O, Makovets S. The functional significance of the RPA- and PCNA-dependent recruitment of Pif1 to DNA. EMBO Rep 2024; 25:1734-1751. [PMID: 38480846 PMCID: PMC11014909 DOI: 10.1038/s44319-024-00114-9] [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: 08/19/2023] [Revised: 02/10/2024] [Accepted: 02/26/2024] [Indexed: 04/14/2024] Open
Abstract
Pif1 family helicases are multifunctional proteins conserved in eukaryotes, from yeast to humans. They are important for the genome maintenance in both nuclei and mitochondria, where they have been implicated in Okazaki fragment processing, replication fork progression and termination, telomerase regulation and DNA repair. While the Pif1 helicase activity is readily detectable on naked nucleic acids in vitro, the in vivo functions rely on recruitment to DNA. We identify the single-stranded DNA binding protein complex RPA as the major recruiter of Pif1 in budding yeast, in addition to the previously reported Pif1-PCNA interaction. The two modes of the Pif1 recruitment act independently during telomerase inhibition, as the mutations in the Pif1 motifs disrupting either of the recruitment pathways act additively. In contrast, both recruitment mechanisms are essential for the replication-related roles of Pif1 at conventional forks and during the repair by break-induced replication. We propose a molecular model where RPA and PCNA provide a double anchoring of Pif1 at replication forks, which is essential for the Pif1 functions related to the fork movement.
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Affiliation(s)
- Oleksii Kotenko
- Institute of Cell Biology, University of Edinburgh, King's Buildings, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Svetlana Makovets
- Institute of Cell Biology, University of Edinburgh, King's Buildings, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK.
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2
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Wu Y, Fu W, Zang N, Zhou C. Structural characterization of human RPA70N association with DNA damage response proteins. eLife 2023; 12:e81639. [PMID: 37668474 PMCID: PMC10479964 DOI: 10.7554/elife.81639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/09/2023] [Indexed: 09/06/2023] Open
Abstract
The heterotrimeric Replication protein A (RPA) is the ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein and participates in nearly all aspects of DNA metabolism, especially DNA damage response. The N-terminal OB domain of the RPA70 subunit (RPA70N) is a major protein-protein interaction element for RPA and binds to more than 20 partner proteins. Previous crystallography studies of RPA70N with p53, DNA2 and PrimPol fragments revealed that RPA70N binds to amphipathic peptides that mimic ssDNA. NMR chemical-shift studies also provided valuable information on the interaction of RPA70N residues with target sequences. However, it is still unclear how RPA70N recognizes and distinguishes such a diverse group of target proteins. Here, we present high-resolution crystal structures of RPA70N in complex with peptides from eight DNA damage response proteins. The structures show that, in addition to the ssDNA mimicry mode of interaction, RPA70N employs multiple ways to bind its partners. Our results advance the mechanistic understanding of RPA70N-mediated recruitment of DNA damage response proteins.
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Affiliation(s)
- Yeyao Wu
- School of Public Health & Sir Run Run Shaw Hospital, Zhejiang University School of MedicineZhejiangChina
| | - Wangmi Fu
- School of Public Health & Sir Run Run Shaw Hospital, Zhejiang University School of MedicineZhejiangChina
| | - Ning Zang
- School of Public Health & Sir Run Run Shaw Hospital, Zhejiang University School of MedicineZhejiangChina
| | - Chun Zhou
- School of Public Health & Sir Run Run Shaw Hospital, Zhejiang University School of MedicineZhejiangChina
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3
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Martinez MZ, Olmo F, Taylor MC, Caudron F, Wilkinson SR. Dissecting the interstrand crosslink DNA repair system of Trypanosoma cruzi. DNA Repair (Amst) 2023; 125:103485. [PMID: 36989950 DOI: 10.1016/j.dnarep.2023.103485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
DNA interstrand crosslinks (ICLs) are toxic lesions that can block essential biological processes. Here we show Trypanosoma cruzi, the causative agent of Chagas disease, is susceptible to ICL-inducing compounds including mechlorethamine and novel nitroreductase-activated prodrugs that have potential in treating this infection. To resolve such lesions, cells co-opt enzymes from "classical" DNA repair pathways that alongside dedicated factors operate in replication-dependent and -independent mechanisms. To assess ICL repair in T. cruzi, orthologues of SNM1, MRE11 and CSB were identified and their function assessed. The T. cruzi enzymes could complement the mechlorethamine susceptibility phenotype displayed by corresponding yeast and/or T. brucei null confirming their role as ICL repair factors while GFP-tagged TcSNM1, TcMRE11 and TcCSB were shown to localise to the nuclei of insect and/or intracellular form parasites. Gene disruption demonstrated that while each activity was non-essential for T. cruzi viability, nulls displayed a growth defect in at least one life cycle stage with TcMRE11-deficient trypomastigotes also compromised in mammalian cell infectivity. Phenotyping revealed all nulls were more susceptible to mechlorethamine than controls, a trait complemented by re-expression of the deleted gene. To assess interplay, the gene disruption approach was extended to generate T. cruzi deficient in TcSNM1/TcMRE11 or in TcSNM1/TcCSB. Analysis demonstrated these activities functioned across two ICL repair pathways with TcSNM1 and TcMRE11 postulated to operate in a replication-dependent system while TcCSB helps resolve transcription-blocking lesions. By unravelling how T. cruzi repairs ICL damage, specific inhibitors targeting repair components could be developed and used to increase the potency of trypanocidal ICL-inducing compounds.
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Affiliation(s)
- Monica Zavala Martinez
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Francisco Olmo
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Martin C Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Fabrice Caudron
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Shane R Wilkinson
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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4
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Schuhwerk H, Kleemann J, Gupta P, van Roey R, Armstark I, Kreileder M, Feldker N, Ramesh V, Hajjaj Y, Fuchs K, Mahapatro M, Hribersek M, Volante M, Groenewoud A, Engel FB, Ceppi P, Eckstein M, Hartmann A, Müller F, Kroll T, Stemmler MP, Brabletz S, Brabletz T. The EMT transcription factor ZEB1 governs a fitness-promoting but vulnerable DNA replication stress response. Cell Rep 2022; 41:111819. [PMID: 36516781 DOI: 10.1016/j.celrep.2022.111819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response (DDR) and epithelial-to-mesenchymal transition (EMT) are two crucial cellular programs in cancer biology. While the DDR orchestrates cell-cycle progression, DNA repair, and cell death, EMT promotes invasiveness, cellular plasticity, and intratumor heterogeneity. Therapeutic targeting of EMT transcription factors, such as ZEB1, remains challenging, but tumor-promoting DDR alterations elicit specific vulnerabilities. Using multi-omics, inhibitors, and high-content microscopy, we discover a chemoresistant ZEB1-high-expressing sub-population (ZEB1hi) with co-rewired cell-cycle progression and proficient DDR across tumor entities. ZEB1 stimulates accelerated S-phase entry via CDK6, inflicting endogenous DNA replication stress. However, DDR buildups involving constitutive MRE11-dependent fork resection allow homeostatic cycling and enrichment of ZEB1hi cells during transforming growth factor β (TGF-β)-induced EMT and chemotherapy. Thus, ZEB1 promotes G1/S transition to launch a progressive DDR benefitting stress tolerance, which concurrently manifests a targetable vulnerability in chemoresistant ZEB1hi cells. Our study thus highlights the translationally relevant intercept of the DDR and EMT.
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Affiliation(s)
- Harald Schuhwerk
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
| | - Julia Kleemann
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Pooja Gupta
- Core Unit for Bioinformatics, Data Integration and Analysis, Center for Medical Information and Communication Technology, University Hospital Erlangen, Erlangen Germany
| | - Ruthger van Roey
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Isabell Armstark
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Martina Kreileder
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Nora Feldker
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Vignesh Ramesh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Yussuf Hajjaj
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Kathrin Fuchs
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Mousumi Mahapatro
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Mojca Hribersek
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Marco Volante
- Department of Oncology, University of Turin, Orbassano, Turin, Italy
| | - Arwin Groenewoud
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Felix B Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Paolo Ceppi
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Markus Eckstein
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen- Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen- Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Fabian Müller
- Department of Internal Medicine 5, Haematology and Oncology, University Hospital Erlangen, Erlangen Germany
| | - Torsten Kroll
- Leibniz Institute on Aging - Fritz-Lipmann Institute (FLI), Jena, Germany
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Simone Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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5
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Berger ND, Brownlee PM, Chen MJ, Morrison H, Osz K, Ploquin NP, Chan JA, Goodarzi AA. High replication stress and limited Rad51-mediated DNA repair capacity, but not oxidative stress, underlie oligodendrocyte precursor cell radiosensitivity. NAR Cancer 2022; 4:zcac012. [PMID: 35425901 PMCID: PMC9004414 DOI: 10.1093/narcan/zcac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 02/15/2022] [Accepted: 03/21/2022] [Indexed: 12/29/2022] Open
Abstract
Abstract
Cranial irradiation is part of the standard of care for treating pediatric brain tumors. However, ionizing radiation can trigger serious long-term neurologic sequelae, including oligodendrocyte and brain white matter loss enabling neurocognitive decline in children surviving brain cancer. Oxidative stress-mediated oligodendrocyte precursor cell (OPC) radiosensitivity has been proposed as a possible explanation for this. Here, however, we demonstrate that antioxidants fail to improve OPC viability after irradiation, despite suppressing oxidative stress, suggesting an alternative etiology for OPC radiosensitivity. Using systematic approaches, we find that OPCs have higher irradiation-induced and endogenous γH2AX foci compared to neural stem cells, neurons, astrocytes and mature oligodendrocytes, and these correlate with replication-associated DNA double strand breakage. Furthermore, OPCs are reliant upon ATR kinase and Mre11 nuclease-dependent processes for viability, are more sensitive to drugs increasing replication fork collapse, and display synthetic lethality with PARP inhibitors after irradiation. This suggests an insufficiency for homology-mediated DNA repair in OPCs—a model that is supported by evidence of normal RPA but reduced RAD51 filament formation at resected lesions in irradiated OPCs. We therefore propose a DNA repair-centric mechanism of OPC radiosensitivity, involving chronically-elevated replication stress combined with ‘bottlenecks’ in RAD51-dependent DNA repair that together reduce radiation resilience.
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Affiliation(s)
- N Daniel Berger
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Peter M Brownlee
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Myra J Chen
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Hali Morrison
- Department of Oncology and Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | - Katalin Osz
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Nicolas P Ploquin
- Department of Oncology and Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | - Jennifer A Chan
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Aaron A Goodarzi
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology and Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
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6
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Graziano S, Coll-Bonfill N, Teodoro-Castro B, Kuppa S, Jackson J, Shashkova E, Mahajan U, Vindigni A, Antony E, Gonzalo S. Lamin A/C recruits ssDNA protective proteins RPA and RAD51 to stalled replication forks to maintain fork stability. J Biol Chem 2021; 297:101301. [PMID: 34648766 PMCID: PMC8571089 DOI: 10.1016/j.jbc.2021.101301] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/15/2021] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
Lamin A/C provides a nuclear scaffold for compartmentalization of genome function that is important for genome integrity. Lamin A/C dysfunction is associated with cancer, aging, and degenerative diseases. The mechanisms whereby lamin A/C regulates genome stability remain poorly understood. We demonstrate a crucial role for lamin A/C in DNA replication. Lamin A/C binds to nascent DNA, especially during replication stress (RS), ensuring the recruitment of replication fork protective factors RPA and RAD51. These ssDNA-binding proteins, considered the first and second responders to RS respectively, function in the stabilization, remodeling, and repair of the stalled fork to ensure proper restart and genome stability. Reduced recruitment of RPA and RAD51 upon lamin A/C depletion elicits replication fork instability (RFI) characterized by MRE11 nuclease–mediated degradation of nascent DNA, RS-induced DNA damage, and sensitivity to replication inhibitors. Importantly, unlike homologous recombination–deficient cells, RFI in lamin A/C-depleted cells is not linked to replication fork reversal. Thus, the point of entry of nucleases is not the reversed fork but regions of ssDNA generated during RS that are not protected by RPA and RAD51. Consistently, RFI in lamin A/C-depleted cells is rescued by exogenous overexpression of RPA or RAD51. These data unveil involvement of structural nuclear proteins in the protection of ssDNA from nucleases during RS by promoting recruitment of RPA and RAD51 to stalled forks. Supporting this model, we show physical interaction between RPA and lamin A/C. We suggest that RS is a major source of genomic instability in laminopathies and lamin A/C-deficient tumors.
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Affiliation(s)
- Simona Graziano
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Nuria Coll-Bonfill
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Barbara Teodoro-Castro
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Sahiti Kuppa
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Jessica Jackson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Elena Shashkova
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Urvashi Mahajan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Edwin Antony
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Susana Gonzalo
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, St Louis, Missouri, USA.
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7
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Chowdhury S, Chowdhury AB, Kumar M, Chakraborty S. Revisiting regulatory roles of replication protein A in plant DNA metabolism. PLANTA 2021; 253:130. [PMID: 34047822 DOI: 10.1007/s00425-021-03641-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
This review provides insight into the roles of heterotrimeric RPA protein complexes encompassing all aspects of DNA metabolism in plants along with specific function attributed by individual subunits. It highlights research gaps that need further attention. Replication protein A (RPA), a heterotrimeric protein complex partakes in almost every aspect of DNA metabolism in eukaryotes with its principle role being a single-stranded DNA-binding protein, thereby providing stability to single-stranded (ss) DNA. Although most of our knowledge of RPA structure and its role in DNA metabolism is based on studies in yeast and animal system, in recent years, plants have also been reported to have diverse repertoire of RPA complexes (formed by combination of different RPA subunit homologs arose during course of evolution), expected to be involved in plethora of DNA metabolic activities. Here, we have reviewed all studies regarding role of RPA in DNA metabolism in plants. As combination of plant RPA complexes may vary largely depending on number of homologs of each subunit, next step for plant biologists is to develop specific functional methods for detailed analysis of biological roles of these complexes, which we have tried to formulate in our review. Besides, complete absence of any study regarding regulatory role of posttranslational modification of RPA complexes in DNA metabolism in plants, prompts us to postulate a hypothetical model of same in light of information from animal system. With our review, we envisage to stimulate the RPA research in plants to shift its course from descriptive to functional studies, thereby bringing a new angle of studying dynamic DNA metabolism in plants.
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Affiliation(s)
- Supriyo Chowdhury
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Arpita Basu Chowdhury
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manish Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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8
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Shorrocks AMK, Jones SE, Tsukada K, Morrow CA, Belblidia Z, Shen J, Vendrell I, Fischer R, Kessler BM, Blackford AN. The Bloom syndrome complex senses RPA-coated single-stranded DNA to restart stalled replication forks. Nat Commun 2021; 12:585. [PMID: 33500419 PMCID: PMC7838300 DOI: 10.1038/s41467-020-20818-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
The Bloom syndrome helicase BLM interacts with topoisomerase IIIα (TOP3A), RMI1 and RMI2 to form the BTR complex, which dissolves double Holliday junctions to produce non-crossover homologous recombination (HR) products. BLM also promotes DNA-end resection, restart of stalled replication forks, and processing of ultra-fine DNA bridges in mitosis. How these activities of the BTR complex are regulated in cells is still unclear. Here, we identify multiple conserved motifs within the BTR complex that interact cooperatively with the single-stranded DNA (ssDNA)-binding protein RPA. Furthermore, we demonstrate that RPA-binding is required for stable BLM recruitment to sites of DNA replication stress and for fork restart, but not for its roles in HR or mitosis. Our findings suggest a model in which the BTR complex contains the intrinsic ability to sense levels of RPA-ssDNA at replication forks, which controls BLM recruitment and activation in response to replication stress.
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Affiliation(s)
- Ann-Marie K Shorrocks
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Samuel E Jones
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Kaima Tsukada
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Department of Transdisciplinary Science and Engineering, School of Environment and Society, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Carl A Morrow
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Zoulikha Belblidia
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Johanna Shen
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Iolanda Vendrell
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andrew N Blackford
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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9
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Vitamin D3 Ameliorates DNA Damage Caused by Developmental Exposure to Endocrine Disruptors in the Uterine Myometrial Stem Cells of Eker Rats. Cells 2020; 9:cells9061459. [PMID: 32545544 PMCID: PMC7349254 DOI: 10.3390/cells9061459] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Early-life exposure of the myometrium to endocrine-disrupting chemicals (EDCs) has been shown to increase the risk of uterine fibroid (UF) prevalence in adulthood. Vitamin D3 (VitD3) is an unique, natural compound that may reduce the risk of developing UFs. However, little is known about the role and molecular mechanism of VitD3 on exposed myometrial stem cells (MMSCs). We investigated the role and molecular mechanism underlying VitD3 action on DNA damage response (DDR) defects in rat MMSCs due to developmental exposure to diethylstilbestrol (DES), with the additional goal of understanding how VitD3 decreases the incidence of UFs later in life. Female newborn Eker rats were exposed to DES or a vehicle early in life; they were then sacrificed at 5 months of age (pro-fibroid stage) and subjected to myometrial Stro1+/CD44+ stem cell isolation. Several techniques were performed to determine the effect of VitD3 treatment on the DNA repair pathway in DES-exposed MMSCs (DES-MMSCs). Results showed that there was a significantly reduced expression of RAD50 and MRE11, key DNA repair proteins in DES-exposed myometrial tissues, compared to vehicle (VEH)-exposed tissues (p < 0.01). VitD3 treatment significantly decreased the DNA damage levels in DES-MMSCs. Concomitantly, the levels of key DNA damage repair members, including the MRN complex, increased in DES-MMSCs following treatment with VitD3 (p < 0.01). VitD3 acts on DNA repair via the MRN complex/ATM axis, restores the DNA repair signaling network, and enhances DDR. This study demonstrates, for the first time, that VitD3 treatment attenuated the DNA damage load in MMSCs exposed to DES and classic DNA damage inducers. Moreover, VitD3 targets primed MMSCs, suggesting a novel therapeutic approach for the prevention of UF development.
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10
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Bylicky MA, Mueller GP, Day RM. Radiation resistance of normal human astrocytes: the role of non-homologous end joining DNA repair activity. JOURNAL OF RADIATION RESEARCH 2019; 60:37-50. [PMID: 30423138 PMCID: PMC6373697 DOI: 10.1093/jrr/rry084] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/03/2018] [Indexed: 05/27/2023]
Abstract
Radiotherapy is a common modality for treatment of brain cancers, but it can induce long-term physiological and cognitive deficits. The responses of normal human brain cells to radiation is not well understood. Astrocytes have been shown to have a variety of protective mechanisms against oxidative stress and have been shown to protect neurons. We investigated the response of cultured normal human astrocytes (NHAs) to X-ray irradiation. Following exposure to 10 Gy X-irradiation, NHAs exhibited DNA damage as indicated by the formation of γ-H2AX foci. Western blotting showed that NHAs displayed a robust increase in expression of non-homologous end joining DNA repair enzymes within 15 min post-irradiation and increased expression of homologous recombination DNA repair enzymes ~2 h post-irradiation. The cell cycle checkpoint protein p21/waf1 was upregulated from 6-24 h, and then returned to baseline. Levels of DNA repair enzymes returned to basal ~48 h post-irradiation. NHAs re-entered the cell cycle and proliferation was observed at 6 days. In contrast, normal human mesenchymal stem cells (MSCs) failed to upregulate DNA repair enzymes and instead displayed sustained upregulation of p21/waf1, a cell cycle checkpoint marker for senescence. Ectopic overexpression of Ku70 was sufficient to protect MSCs from sustained upregulation of p21/waf1 induced by 10 Gy X-rays. These findings suggest that increased expression of Ku70 may be a key mechanism for the radioresistance of NHAs, preventing their accelerated senescence from high-dose radiation. These results may have implications for the development of novel targets for radiation countermeasure development.
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Affiliation(s)
- Michelle A Bylicky
- Department of Anatomy, Physiology, and Genetics, The Uniformed Services University of the Health Sciences, Jones Bridge Road, Bethesda, MD, USA
| | - Gregory P Mueller
- Department of Anatomy, Physiology, and Genetics, The Uniformed Services University of the Health Sciences, Jones Bridge Road, Bethesda, MD, USA
| | - Regina M Day
- Department of Pharmacology and Molecular Therapeutics, The Uniformed Services University of the Health Sciences, Jones Bridge Road, Bethesda, MD, USA
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11
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Oh J, Symington LS. Role of the Mre11 Complex in Preserving Genome Integrity. Genes (Basel) 2018; 9:E589. [PMID: 30501098 PMCID: PMC6315862 DOI: 10.3390/genes9120589] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous lesions that threaten genome integrity and cell survival. The DNA damage response (DDR) safeguards the genome by sensing DSBs, halting cell cycle progression and promoting repair through either non-homologous end joining (NHEJ) or homologous recombination (HR). The Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex is central to the DDR through its structural, enzymatic, and signaling roles. The complex tethers DNA ends, activates the Tel1/ATM kinase, resolves protein-bound or hairpin-capped DNA ends, and maintains telomere homeostasis. In addition to its role at DSBs, MRX/N associates with unperturbed replication forks, as well as stalled replication forks, to ensure complete DNA synthesis and to prevent chromosome rearrangements. Here, we summarize the significant progress made in characterizing the MRX/N complex and its various activities in chromosome metabolism.
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Affiliation(s)
- Julyun Oh
- Biological Sciences Program, Columbia University, New York, NY 10027, USA.
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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12
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Chen MY, Hsu WC, Hsu SC, Yang YS, Chuang TH, Lin WJ, Tan TH, Su YW. PP4 deficiency leads to DNA replication stress that impairs immunoglobulin class switch efficiency. Cell Death Differ 2018; 26:1221-1234. [PMID: 30237510 PMCID: PMC6748143 DOI: 10.1038/s41418-018-0199-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/30/2018] [Accepted: 08/27/2018] [Indexed: 01/02/2023] Open
Abstract
The serine/threonine phosphatase PP4 has been implicated in DNA damage repair and cell cycle regulation through its dephosphorylation of specific substrates. We previously showed that PP4 is required for mouse B cell development, germinal center (GC) formation and immunoglobulin (Ig) class switch recombination (CSR). Here, we investigate the mechanisms underlying this requirement and demonstrate that murine PP4-deficient B lymphocytes have a defect in cell proliferation. Strikingly, the DNA damage response pathway that involves ATM/p53 and is linked to cell cycle arrest and impaired cell survival is strongly induced in these mutant B cells. In response to LPS + IL-4, stimuli that trigger IgG1 production, these PP4-deficient B cells show inefficient phosphorylation of ATR, leading to reduced retention of γH2AX-NBS1 complexes at sites of DNA damage, and compromised switching to IgG1. However, beyond the cell proliferation phase, conditional deletion of PP4 under the control of AID/cre completely restores normal IgG1 production in mutant B cell cultures. In vivo, co-deletion of PP4 and p53 by AID/cre partially rescues switching to IgG1 in B cells of mice immunized with TNP-KLH. Our findings establish that PP4 is indispensable for preventing DNA replication stress that could interfere with CSR, thereby promoting antibody switching during the humoral immune response.
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Affiliation(s)
- Ming-Yu Chen
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan
| | - Wei-Chan Hsu
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan
| | - Shu-Ching Hsu
- National Institute of Infectious Diseases and Vaccinology, NHRI, Zhunan, Miaoli County, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Research and Development, Chang Bing Show Chwan Memorial Hospital, Chang Hua, Taiwan
| | - Yu-Shao Yang
- National Institute of Infectious Diseases and Vaccinology, NHRI, Zhunan, Miaoli County, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan
| | - Wen-Jye Lin
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Yu-Wen Su
- Immunology Research Center, National Health Research Institutes (NHRI), Zhunan, Miaoli County, Taiwan.
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13
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The concerted roles of FANCM and Rad52 in the protection of common fragile sites. Nat Commun 2018; 9:2791. [PMID: 30022024 PMCID: PMC6052092 DOI: 10.1038/s41467-018-05066-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/10/2018] [Indexed: 12/18/2022] Open
Abstract
Common fragile sites (CFSs) are prone to chromosomal breakage and are hotspots for chromosomal rearrangements in cancer cells. We uncovered a novel function of Fanconi anemia (FA) protein FANCM in the protection of CFSs that is independent of the FA core complex and the FANCI–FANCD2 complex. FANCM, along with its binding partners FAAP24 and MHF1/2, is recruited to CFS-derived structure-prone AT-rich sequences, where it suppresses DNA double-strand break (DSB) formation and mitotic recombination in a manner dependent on FANCM translocase activity. Interestingly, we also identified an indispensable function of Rad52 in the repair of DSBs at CFS-derived AT-rich sequences, despite its nonessential function in general homologous recombination (HR) in mammalian cells. Suppression of Rad52 expression in combination with FANCM knockout drastically reduces cell and tumor growth, suggesting a synthetic lethality interaction between these two genes, which offers a potential targeted treatment strategy for FANCM-deficient tumors with Rad52 inhibition. Fanconi anemia core proteins have been linked to common fragile site stability. Here the authors shed light into the role of FANCM in common fragile site protection by suppressing double-strand break formation and mitotic recombination.
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14
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Reichman R, Shi Z, Malone R, Smolikove S. Mitotic and Meiotic Functions for the SUMOylation Pathway in the Caenorhabditis elegans Germline. Genetics 2018; 208:1421-1441. [PMID: 29472245 PMCID: PMC5887140 DOI: 10.1534/genetics.118.300787] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/19/2018] [Indexed: 02/07/2023] Open
Abstract
Meiosis is a highly regulated process, partly due to the need to break and then repair DNA as part of the meiotic program. Post-translational modifications are widely used during meiotic events to regulate steps such as protein complex formation, checkpoint activation, and protein attenuation. In this paper, we investigate how proteins that are obligatory components of the SUMO (small ubiquitin-like modifier) pathway, one such post-translational modification, affect the Caenorhabditis elegans germline. We show that UBC-9, the E2 conjugation enzyme, and the C. elegans homolog of SUMO, SMO-1, localize to germline nuclei throughout prophase I. Mutant analysis of smo-1 and ubc-9 revealed increased recombination intermediates throughout the germline, originating during the mitotic divisions. SUMOylation mutants also showed late meiotic defects including defects in the restructuring of oocyte bivalents and endomitotic oocytes. Increased rates of noninterfering crossovers were observed in ubc-9 heterozygotes, even though interfering crossovers were unaffected. We have also identified a physical interaction between UBC-9 and DNA repair protein MRE-11 ubc-9 and mre-11 null mutants exhibited similar phenotypes at germline mitotic nuclei and were synthetically sick. These phenotypes and genetic interactions were specific to MRE-11 null mutants as opposed to RAD-50 or resection-defective MRE-11 We propose that the SUMOylation pathway acts redundantly with MRE-11, and in this process MRE-11 likely plays a structural role.
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Affiliation(s)
- Rachel Reichman
- Department of Biology, The University of Iowa, Iowa City, Iowa 52242
| | - Zhuoyue Shi
- Department of Biology, The University of Iowa, Iowa City, Iowa 52242
| | - Robert Malone
- Department of Biology, The University of Iowa, Iowa City, Iowa 52242
| | - Sarit Smolikove
- Department of Biology, The University of Iowa, Iowa City, Iowa 52242
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15
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BRCA2 suppresses replication stress-induced mitotic and G1 abnormalities through homologous recombination. Nat Commun 2017; 8:525. [PMID: 28904335 PMCID: PMC5597640 DOI: 10.1038/s41467-017-00634-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 07/12/2017] [Indexed: 02/07/2023] Open
Abstract
Mutations in the tumor suppressor BRCA2 predominantly predispose to breast cancer. Paradoxically, while loss of BRCA2 promotes tumor formation, it also causes cell lethality, although how lethality is triggered is unclear. Here, we generate BRCA2 conditional non-transformed human mammary epithelial cell lines using CRISPR-Cas9. Cells are inviable upon BRCA2 loss, which leads to replication stress associated with under replication, causing mitotic abnormalities, 53BP1 nuclear body formation in the ensuing G1 phase, and G1 arrest. Unexpected from other systems, the role of BRCA2 in homologous recombination, but not in stalled replication fork protection, is primarily associated with supporting human mammary epithelial cell viability, and, moreover, preventing replication stress, a hallmark of pre-cancerous lesions. Thus, we uncover a DNA under replication-53BP1 nuclear body formation-G1 arrest axis as an unanticipated outcome of homologous recombination deficiency, which triggers cell lethality and, we propose, serves as a barrier that must be overcome for tumor formation. BRCA2 mutations promote tumour formation while also paradoxically causing cell lethality. Here the authors generate conditional BRCA2 loss in a non-transformed human mammary cell line and see increased replication stress due to under-replication of DNA.
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16
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Morgan MA, Lawrence TS. Molecular Pathways: Overcoming Radiation Resistance by Targeting DNA Damage Response Pathways. Clin Cancer Res 2016; 21:2898-904. [PMID: 26133775 DOI: 10.1158/1078-0432.ccr-13-3229] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
DNA double-strand breaks are the critical lesions responsible for the majority of ionizing radiation-induced cell killing. Thus, the ability of tumor cells to elicit a DNA damage response following radiation, via activation of DNA repair and cell-cycle checkpoints, promotes radiation resistance and tumor cell survival. Consequently, agents that target these DNA damage response pathways are being developed to overcome radiation resistance. Overall, these agents are effective radiosensitizers; however, their mechanisms of tumor cell selectivity are not fully elucidated. In this review, we focus on the crucial radiation-induced DNA damage responses as well as clinical and translational advances with agents designed to inhibit these responses. Importantly, we describe how synthetic lethality can provide tumor cell-selective radiosensitization by these agents and expand the therapeutic window for DNA damage response-targeted agents used in combination with radiotherapy.
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Affiliation(s)
- Meredith A Morgan
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan.
| | - Theodore S Lawrence
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
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17
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Kar A, Kaur M, Ghosh T, Khan MM, Sharma A, Shekhar R, Varshney A, Saxena S. RPA70 depletion induces hSSB1/2-INTS3 complex to initiate ATR signaling. Nucleic Acids Res 2015; 43:4962-74. [PMID: 25916848 PMCID: PMC4446429 DOI: 10.1093/nar/gkv369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/08/2015] [Indexed: 01/12/2023] Open
Abstract
The primary eukaryotic single-stranded DNA-binding protein, Replication protein A (RPA), binds to single-stranded DNA at the sites of DNA damage and recruits the apical checkpoint kinase, ATR via its partner protein, ATRIP. It has been demonstrated that absence of RPA incapacitates the ATR-mediated checkpoint response. We report that in the absence of RPA, human single-stranded DNA-binding protein 1 (hSSB1) and its partner protein INTS3 form sub-nuclear foci, associate with the ATR-ATRIP complex and recruit it to the sites of genomic stress. The ATRIP foci formed after RPA depletion are abrogated in the absence of INTS3, establishing that hSSB-INTS3 complex recruits the ATR-ATRIP checkpoint complex to the sites of genomic stress. Depletion of homologs hSSB1/2 and INTS3 in RPA-deficient cells attenuates Chk1 phosphorylation, indicating that the cells are debilitated in responding to stress. We have identified that TopBP1 and the Rad9-Rad1-Hus1 complex are essential for the alternate mode of ATR activation. In summation, we report that the single-stranded DNA-binding protein complex, hSSB1/2-INTS3 can recruit the checkpoint complex to initiate ATR signaling.
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Affiliation(s)
- Ananya Kar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Manpreet Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Tanushree Ghosh
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Md Muntaz Khan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Aparna Sharma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Ritu Shekhar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Akhil Varshney
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Sandeep Saxena
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
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18
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Bais MV, Ozdener GB, Sonenshein GE, Trackman PC. Effects of tumor-suppressor lysyl oxidase propeptide on prostate cancer xenograft growth and its direct interactions with DNA repair pathways. Oncogene 2015; 34:1928-37. [PMID: 24882580 PMCID: PMC4254378 DOI: 10.1038/onc.2014.147] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 04/01/2014] [Accepted: 04/18/2014] [Indexed: 01/27/2023]
Abstract
Lysyl oxidase (LOX) is a multifunctional protein required for normal collagen and elastin biosynthesis and maturation. In addition, LOX has complex roles in cancer in which the lysyl oxidase propeptide (LOX-PP) domain of secreted pro-LOX has tumor-suppressor activity, while the active enzyme promotes metastasis. In prostate cancer cell lines, recombinant LOX-PP (rLOX-PP) inhibits the growth of PC3 cells in vitro by mechanisms that were not characterized, while in DU145 cells rLOX-PP targeted fibroblast growth factor signaling. Because rLOX-PP can enhance effects of a genotoxic chemotherapeutic on breast cancer cell apoptosis, we reasoned that rLOX-PP could target DNA repair pathways typically elevated in cancer. Here we demonstrate for the first time that rLOX-PP inhibits prostate xenograft growth in vivo and that activating phosphorylations of the key DNA repair molecules ataxia-telangiectasia mutated (ATM) and checkpoint kinase 2 (CHK2) are inhibited by rLOX-PP expression in vivo. In addition, in vitro studies showed that rLOX-PP inhibits radiation-induced activating phosphorylations of ATM and CHK2 and that exogenously added rLOX-PP protein can localize to the nucleus in both DU145 and PC3 cells. rLOX-PP pull-down studies resulted in detection of a protein complex with the nuclear DNA repair regulator MRE11 in both cell lines, and rLOX-PP localized to radiation-induced nuclear DNA repair foci. Finally, rLOX-PP was shown to sensitize both DU145 and PC3 cells to radiation-induced cell death determined in colony-formation assays. These data provide evidence that rLOX-PP has a nuclear mechanism of action in which it directly interacts with DNA repair proteins to sensitize prostate cancer cells to the effects of ionizing radiation.
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Affiliation(s)
- Manish V. Bais
- Boston University Henry M. Goldman School of Dental Medicine, Department of Periodontology and Oral Biology, Boston, MA 02118
| | - Gokhan Baris Ozdener
- Boston University Henry M. Goldman School of Dental Medicine, Department of Periodontology and Oral Biology, Boston, MA 02118
| | - Gail E. Sonenshein
- Tufts University School of Medicine, Department of Biochemistry, Boston, MA 02111
| | - Philip C. Trackman
- Boston University Henry M. Goldman School of Dental Medicine, Department of Periodontology and Oral Biology, Boston, MA 02118
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19
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MR (Mre11-Rad50) complex in Giardia duodenalis: In vitro characterization and its response upon DNA damage. Biochimie 2015; 111:45-57. [DOI: 10.1016/j.biochi.2015.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 01/17/2015] [Indexed: 11/24/2022]
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20
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Ning B, Feldkamp MD, Cortez D, Chazin WJ, Friedman KL, Fanning E. Simian virus Large T antigen interacts with the N-terminal domain of the 70 kD subunit of Replication Protein A in the same mode as multiple DNA damage response factors. PLoS One 2015; 10:e0116093. [PMID: 25706313 PMCID: PMC4337903 DOI: 10.1371/journal.pone.0116093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/04/2014] [Indexed: 11/18/2022] Open
Abstract
Simian virus 40 (SV40) serves as an important model organism for studying eukaryotic DNA replication. Its helicase, Large T-antigen (Tag), is a multi-functional protein that interacts with multiple host proteins, including the ubiquitous ssDNA binding protein Replication Protein A (RPA). Tag recruits RPA, actively loads it onto the unwound DNA, and together they promote priming of the template. Although interactions of Tag with RPA have been mapped, no interaction between Tag and the N-terminal protein interaction domain of the RPA 70kDa subunit (RPA70N) has been reported. Here we provide evidence of direct physical interaction of Tag with RPA70N and map the binding sites using a series of pull-down and mutational experiments. In addition, a monoclonal anti-Tag antibody, the epitope of which overlaps with the binding site, blocks the binding of Tag to RPA70N. We use NMR chemical shift perturbation analysis to show that Tag uses the same basic cleft in RPA70N as multiple of DNA damage response proteins. Mutations in the binding sites of both RPA70N and Tag demonstrate that specific charge reversal substitutions in either binding partner strongly diminish the interaction. These results expand the known repertoire of contacts between Tag and RPA, which mediate the many critical roles of Tag in viral replication.
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Affiliation(s)
- Boting Ning
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Michael D. Feldkamp
- Departments of Biochemistry, Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - David Cortez
- Department of Biochemistry, Vanderbilt University Medical School, Nashville, Tennessee, United States of America
| | - Walter J. Chazin
- Departments of Biochemistry, Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (KLF); (WJC)
| | - Katherine L. Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (KLF); (WJC)
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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21
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Laffitte MCN, Genois MM, Mukherjee A, Légaré D, Masson JY, Ouellette M. Formation of linear amplicons with inverted duplications in Leishmania requires the MRE11 nuclease. PLoS Genet 2014; 10:e1004805. [PMID: 25474106 PMCID: PMC4256157 DOI: 10.1371/journal.pgen.1004805] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 10/06/2014] [Indexed: 11/22/2022] Open
Abstract
Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance. The extrachromosomal amplified DNA is either circular or linear, and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome. The RAD51 recombinase plays an important role in circular amplicons formation, but the mechanism by which linear amplicons are formed is unknown. We hypothesized that the Leishmania infantum DNA repair protein MRE11 is required for linear amplicons following rearrangements at the level of inverted repeats. The purified LiMRE11 protein showed both DNA binding and exonuclease activities. Inactivation of the LiMRE11 gene led to parasites with enhanced sensitivity to DNA damaging agents. The MRE11−/− parasites had a reduced capacity to form linear amplicons after drug selection, and the reintroduction of an MRE11 allele led to parasites regaining their capacity to generate linear amplicons, but only when MRE11 had an active nuclease activity. These results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment. Extrachromosomal DNA amplification is frequent in the human protozoan parasite Leishmania when challenged with drug or other stressful conditions. DNA amplicons, either circular or linear, are formed by recombination between direct or inverted repeats spread throughout the genome of the parasite. The recombinase RAD51 is involved in the formation of circular amplicons, but the mechanism by which linear amplicons are formed is still unknown in this parasite. Studies in other organisms have provided some evidence that a DNA break is required for linear amplifications, and that the DNA repair protein MRE11 can be involved in this process. In this work, we present our biochemical, cellular and molecular characterization of the Leishmania infantum MRE11 orthologue and provide evidence that this nuclease is involved in the formation of linear amplicons in Leishmania. Our results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment.
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Affiliation(s)
| | - Marie-Michelle Genois
- Centre de Recherche en Infectiologie du CHU de Québec, Quebec City, Québec, Canada
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavillon, Oncology Axis, Quebec City, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Québec, Canada
| | - Angana Mukherjee
- Centre de Recherche en Infectiologie du CHU de Québec, Quebec City, Québec, Canada
| | - Danielle Légaré
- Centre de Recherche en Infectiologie du CHU de Québec, Quebec City, Québec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavillon, Oncology Axis, Quebec City, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du CHU de Québec, Quebec City, Québec, Canada
- * E-mail:
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22
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Maréchal A, Zou L. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res 2014; 25:9-23. [PMID: 25403473 DOI: 10.1038/cr.2014.147] [Citation(s) in RCA: 313] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Replication Protein A (RPA) complex is an essential regulator of eukaryotic DNA metabolism. RPA avidly binds to single-stranded DNA (ssDNA) through multiple oligonucleotide/oligosaccharide-binding folds and coordinates the recruitment and exchange of genome maintenance factors to regulate DNA replication, recombination and repair. The RPA-ssDNA platform also constitutes a key physiological signal which activates the master ATR kinase to protect and repair stalled or collapsed replication forks during replication stress. In recent years, the RPA complex has emerged as a key target and an important regulator of post-translational modifications in response to DNA damage, which is critical for its genome guardian functions. Phosphorylation and SUMOylation of the RPA complex, and more recently RPA-regulated ubiquitination, have all been shown to control specific aspects of DNA damage signaling and repair by modulating the interactions between RPA and its partners. Here, we review our current understanding of the critical functions of the RPA-ssDNA platform in the maintenance of genome stability and its regulation through an elaborate network of covalent modifications.
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Affiliation(s)
- Alexandre Maréchal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- 1] Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA [2] Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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23
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Wu CS, Ouyang J, Mori E, Nguyen HD, Maréchal A, Hallet A, Chen DJ, Zou L. SUMOylation of ATRIP potentiates DNA damage signaling by boosting multiple protein interactions in the ATR pathway. Genes Dev 2014; 28:1472-84. [PMID: 24990965 PMCID: PMC4083090 DOI: 10.1101/gad.238535.114] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 06/02/2014] [Indexed: 12/21/2022]
Abstract
The ATR (ATM [ataxia telangiectasia-mutated]- and Rad3-related) checkpoint is a crucial DNA damage signaling pathway. While the ATR pathway is known to transmit DNA damage signals through the ATR-Chk1 kinase cascade, whether post-translational modifications other than phosphorylation are important for this pathway remains largely unknown. Here, we show that protein SUMOylation plays a key role in the ATR pathway. ATRIP, the regulatory partner of ATR, is modified by SUMO2/3 at K234 and K289. An ATRIP mutant lacking the SUMOylation sites fails to localize to DNA damage and support ATR activation efficiently. Surprisingly, the ATRIP SUMOylation mutant is compromised in the interaction with a protein group, rather than a single protein, in the ATR pathway. Multiple ATRIP-interacting proteins, including ATR, RPA70, TopBP1, and the MRE11-RAD50-NBS1 complex, exhibit reduced binding to the ATRIP SUMOylation mutant in cells and display affinity for SUMO2 chains in vitro, suggesting that they bind not only ATRIP but also SUMO. Fusion of a SUMO2 chain to the ATRIP SUMOylation mutant enhances its interaction with the protein group and partially suppresses its localization and functional defects, revealing that ATRIP SUMOylation promotes ATR activation by providing a unique type of protein glue that boosts multiple protein interactions along the ATR pathway.
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Affiliation(s)
- Ching-Shyi Wu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Eiichiro Mori
- Division of Molecular Radiation Biology, Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hai Dang Nguyen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Alexandre Maréchal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Alexander Hallet
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - David J. Chen
- Division of Molecular Radiation Biology, Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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24
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Štorcelová M, Vicián M, Reis R, Zeman M, Herichová I. Expression of cell cycle regulatory factors hus1, gadd45a, rb1, cdkn2a and mre11a correlates with expression of clock gene per2 in human colorectal carcinoma tissue. Mol Biol Rep 2013; 40:6351-61. [PMID: 24062075 DOI: 10.1007/s11033-013-2749-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 09/14/2013] [Indexed: 01/20/2023]
Abstract
Deregulated expression of clock gene per2 has previously been associated with progression of cancer. The aim of the present study was to identify genes related to per2 expression and involved in cell cycle control. Patients surgically treated for colorectal carcinoma with up-regulated and down-regulated per2 expression in cancer versus adjacent tissue were studied. Total RNA from cancer tissue of these patients was used to specify genes associated with altered per2 expression using the Human Cell Cycle RT(2) profiler PCR array system. We identified seven genes positively correlated (hus1, gadd45α, rb1, cdkn2a, cdk5rp1, mre11a, sumo1) and two genes negatively correlated (cdc20, birc5) with per2 expression. Expression of these seven genes was subsequently measured by real time PCR in all patients of the cohort. Patients were divided into three groups according to TNM classification. We observed an increase in gene expression in cancer tissue compared to adjacent tissue in the first group of patients in all genes measured. Expression of genes positively associated with per2 gene expression was dependent on tumor staging and changes were observed preferentially in cancer tissue. For genes negatively associated with per2 expression we also detected changes in expression dependent on tumor staging. Expression of cdc20 and birc5 was increasing in the proximal tissue and decreasing in the cancer tissue. These results implicate functional involvement of per2 in the process of carcinogenesis via newly uncovered genes. The relevancy of gene expression for determination of diagnosis and prognosis should be considered in relation to tumor staging.
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Affiliation(s)
- Mária Štorcelová
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University Bratislava, Mlynska dolina B-2, 842 15, Bratislava, Slovak Republic
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25
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Duursma AM, Driscoll R, Elias JE, Cimprich KA. A role for the MRN complex in ATR activation via TOPBP1 recruitment. Mol Cell 2013; 50:116-22. [PMID: 23582259 DOI: 10.1016/j.molcel.2013.03.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 02/11/2013] [Accepted: 03/05/2013] [Indexed: 12/17/2022]
Abstract
The MRN (MRE11-RAD50-NBS1) complex has been implicated in many aspects of the DNA damage response. It has key roles in sensing and processing DNA double-strand breaks, as well as in activation of ATM (ataxia telangiectasia mutated). We reveal a function for MRN in ATR (ATM- and RAD3-related) activation by using defined ATR-activating DNA structures in Xenopus egg extracts. Strikingly, we demonstrate that MRN is required for recruitment of TOPBP1 to an ATR-activating structure that contains a single-stranded DNA (ssDNA) and a double-stranded DNA (dsDNA) junction and that this recruitment is necessary for phosphorylation of CHK1. We also show that the 911 (RAD9-RAD1-HUS1) complex is not required for TOPBP1 recruitment but is essential for TOPBP1 function. Thus, whereas MRN is required for TOPBP1 recruitment at an ssDNA-to-dsDNA junction, 911 is required for TOPBP1 "activation." These findings provide molecular insights into how ATR is activated.
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Affiliation(s)
- Anja M Duursma
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
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26
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Shiotani B, Nguyen HD, Håkansson P, Maréchal A, Tse A, Tahara H, Zou L. Two distinct modes of ATR activation orchestrated by Rad17 and Nbs1. Cell Rep 2013; 3:1651-62. [PMID: 23684611 DOI: 10.1016/j.celrep.2013.04.018] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 04/05/2013] [Accepted: 04/19/2013] [Indexed: 11/15/2022] Open
Abstract
The ATM- and Rad3-related (ATR) kinase is a master regulator of the DNA damage response, yet how ATR is activated toward different substrates is still poorly understood. Here, we show that ATR phosphorylates Chk1 and RPA32 through distinct mechanisms at replication-associated DNA double-stranded breaks (DSBs). In contrast to the rapid phosphorylation of Chk1, RPA32 is progressively phosphorylated by ATR at Ser33 during DSB resection prior to the phosphorylation of Ser4/Ser8 by DNA-PKcs. Surprisingly, despite its reliance on ATR and TopBP1, substantial RPA32 Ser33 phosphorylation occurs in a Rad17-independent but Nbs1-dependent manner in vivo and in vitro. Importantly, the role of Nbs1 in RPA32 phosphorylation can be separated from ATM activation and DSB resection, and it is dependent upon the interaction of Nbs1 with RPA. An Nbs1 mutant that is unable to bind RPA fails to support proper recovery of collapsed replication forks, suggesting that the Nbs1-mediated mode of ATR activation is important for the repair of replication-associated DSBs.
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Affiliation(s)
- Bunsyo Shiotani
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.
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27
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Ashton NW, Bolderson E, Cubeddu L, O'Byrne KJ, Richard DJ. Human single-stranded DNA binding proteins are essential for maintaining genomic stability. BMC Mol Biol 2013; 14:9. [PMID: 23548139 PMCID: PMC3626794 DOI: 10.1186/1471-2199-14-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/20/2013] [Indexed: 12/25/2022] Open
Abstract
The double-stranded conformation of cellular DNA is a central aspect of DNA stabilisation and protection. The helix preserves the genetic code against chemical and enzymatic degradation, metabolic activation, and formation of secondary structures. However, there are various instances where single-stranded DNA is exposed, such as during replication or transcription, in the synthesis of chromosome ends, and following DNA damage. In these instances, single-stranded DNA binding proteins are essential for the sequestration and processing of single-stranded DNA. In order to bind single-stranded DNA, these proteins utilise a characteristic and evolutionary conserved single-stranded DNA-binding domain, the oligonucleotide/oligosaccharide-binding (OB)-fold. In the current review we discuss a subset of these proteins involved in the direct maintenance of genomic stability, an important cellular process in the conservation of cellular viability and prevention of malignant transformation. We discuss the central roles of single-stranded DNA binding proteins from the OB-fold domain family in DNA replication, the restart of stalled replication forks, DNA damage repair, cell cycle-checkpoint activation, and telomere maintenance.
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Affiliation(s)
- Nicholas W Ashton
- Genome Stability Laboratory, Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, 4102, Australia
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28
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Wang H, Shi LZ, Wong CCL, Han X, Hwang PYH, Truong LN, Zhu Q, Shao Z, Chen DJ, Berns MW, Yates JR, Chen L, Wu X. The interaction of CtIP and Nbs1 connects CDK and ATM to regulate HR-mediated double-strand break repair. PLoS Genet 2013; 9:e1003277. [PMID: 23468639 PMCID: PMC3585124 DOI: 10.1371/journal.pgen.1003277] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/12/2012] [Indexed: 11/19/2022] Open
Abstract
CtIP plays an important role in homologous recombination (HR)-mediated DNA double-stranded break (DSB) repair and interacts with Nbs1 and BRCA1, which are linked to Nijmegen breakage syndrome (NBS) and familial breast cancer, respectively. We identified new CDK phosphorylation sites on CtIP and found that phosphorylation of these newly identified CDK sites induces association of CtIP with the N-terminus FHA and BRCT domains of Nbs1. We further showed that these CDK-dependent phosphorylation events are a prerequisite for ATM to phosphorylate CtIP upon DNA damage, which is important for end resection to activate HR by promoting recruitment of BLM and Exo1 to DSBs. Most notably, this CDK-dependent CtIP and Nbs1 interaction facilitates ATM to phosphorylate CtIP in a substrate-specific manner. These studies reveal one important mechanism to regulate cell-cycle-dependent activation of HR upon DNA damage by coupling CDK- and ATM-mediated phosphorylation of CtIP through modulating the interaction of CtIP with Nbs1, which significantly helps to understand how DSB repair is regulated in mammalian cells to maintain genome stability.
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Affiliation(s)
- Hailong Wang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Linda Z. Shi
- The Institute of Engineering in Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Catherine C. L. Wong
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Xuemei Han
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patty Yi-Hwa Hwang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lan N. Truong
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Qingyuan Zhu
- The Institute of Engineering in Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Zhengping Shao
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - David J. Chen
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michael W. Berns
- The Institute of Engineering in Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Longchuan Chen
- Department of Pathology, Veterans Affairs Medical Center, Long Beach, California, United States of America
| | - Xiaohua Wu
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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29
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Glanzer JG, Carnes KA, Soto P, Liu S, Parkhurst LJ, Oakley GG. A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A. Nucleic Acids Res 2012; 41:2047-59. [PMID: 23267009 PMCID: PMC3561959 DOI: 10.1093/nar/gks1291] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Replication protein A (RPA), essential for DNA replication, repair and DNA damage signalling, possesses six ssDNA-binding domains (DBDs), including DBD-F on the N-terminus of the largest subunit, RPA70. This domain functions as a binding site for p53 and other DNA damage and repair proteins that contain amphipathic alpha helical domains. Here, we demonstrate direct binding of both ssDNA and the transactivation domain 2 of p53 (p53TAD2) to DBD-F, as well as DBD-F-directed dsDNA strand separation by RPA, all of which are inhibited by fumaropimaric acid (FPA). FPA binds directly to RPA, resulting in a conformational shift as determined through quenching of intrinsic tryptophan fluorescence in full length RPA. Structural analogues of FPA provide insight on chemical properties that are required for inhibition. Finally, we confirm the inability of RPA possessing R41E and R43E mutations to bind to p53, destabilize dsDNA and quench tryptophan fluorescence by FPA, suggesting that protein binding, DNA modulation and inhibitor binding all occur within the same site on DBD-F. The disruption of p53–RPA interactions by FPA may disturb the regulatory functions of p53 and RPA, thereby inhibiting cellular pathways that control the cell cycle and maintain the integrity of the human genome.
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Affiliation(s)
- Jason G Glanzer
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
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30
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Lu CS, Truong LN, Aslanian A, Shi LZ, Li Y, Hwang PYH, Koh KH, Hunter T, Yates JR, Berns MW, Wu X. The RING finger protein RNF8 ubiquitinates Nbs1 to promote DNA double-strand break repair by homologous recombination. J Biol Chem 2012; 287:43984-94. [PMID: 23115235 DOI: 10.1074/jbc.m112.421545] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ubiquitination plays an important role in the DNA damage response. We identified a novel interaction of the E3 ubiquitin ligase RNF8 with Nbs1, a key regulator of DNA double-strand break (DSB) repair. We found that Nbs1 is ubiquitinated both before and after DNA damage and is a direct ubiquitination substrate of RNF8. We also identified key residues on Nbs1 that are ubiquitinated by RNF8. By using laser microirradiation and live-cell imaging, we observed that RNF8 and its ubiquitination activity are important for promoting optimal binding of Nbs1 to DSB-containing chromatin. We also demonstrated that RNF8-mediated ubiquitination of Nbs1 contributes to the efficient and stable binding of Nbs1 to DSBs and is important for HR-mediated DSB repair. Taken together, these studies suggest that Nbs1 is one important target of RNF8 to regulate DNA DSB repair.
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Affiliation(s)
- Chi-Sheng Lu
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California 92037, USA
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31
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He J, Shi LZ, Truong LN, Lu CS, Razavian N, Li Y, Negrete A, Shiloach J, Berns MW, Wu X. Rad50 zinc hook is important for the Mre11 complex to bind chromosomal DNA double-stranded breaks and initiate various DNA damage responses. J Biol Chem 2012; 287:31747-56. [PMID: 22833675 PMCID: PMC3442509 DOI: 10.1074/jbc.m112.384750] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/24/2012] [Indexed: 11/06/2022] Open
Abstract
The Mre11-Rad50-Nbs1 (MRN) complex plays critical roles in checkpoint activation and double-stranded break (DSB) repair. The Rad50 zinc hook domain mediates zinc-dependent intercomplex associations of MRN, which is important for DNA tethering. Studies in yeast suggest that the Rad50 zinc hook domain is essential for MRN functions, but its role in mammalian cells is not clear. We demonstrated that the human Rad50 hook mutants are severely defective in various DNA damage responses including ATM (Ataxia telangiectasia mutated) activation, homologous recombination, sensitivity to IR, and activation of the ATR pathway. By using live cell imaging, we observed that the Rad50 hook mutants fail to be recruited to chromosomal DSBs, suggesting a novel mechanism underlying the severe defects observed for the Rad50 hook mutants. In vitro analysis showed that Zn(2+) promotes wild type but not the hook mutant of MR to bind double-stranded DNA. In vivo, the Rad50 hook mutants are defective in being recruited to chromosomal DSBs in both H2AX-proficient and -deficient cells, suggesting that the Rad50 hook mutants are impaired in direct binding to chromosomal DSB ends. We propose that the Rad50 zinc hook domain is important for the initial binding of MRN to DSBs, leading to ATM activation to phosphorylate H2AX, which recruits more MRN to the DSB-flanking chromosomal regions. Our studies reveal a critical role for the Rad50 zinc hook domain in establishing and maintaining MRN recruitment to chromosomal DSBs and suggest an important mechanism of how the Rad50 zinc hook domain contributes to DNA repair and checkpoint activation.
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Affiliation(s)
- Jing He
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Linda Z. Shi
- the Institute of Engineering in Medicine, University of California San Diego, La Jolla, California 92093, and
| | - Lan N. Truong
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Chi-Sheng Lu
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Niema Razavian
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Yongjiang Li
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
| | - Alejandro Negrete
- the Biotechnology Core Laboratory, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Joseph Shiloach
- the Biotechnology Core Laboratory, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael W. Berns
- the Institute of Engineering in Medicine, University of California San Diego, La Jolla, California 92093, and
| | - Xiaohua Wu
- From the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La, Jolla, California 92037
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32
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Agyeman A, Mazumdar T, Houghton JA. Regulation of DNA damage following termination of Hedgehog (HH) survival signaling at the level of the GLI genes in human colon cancer. Oncotarget 2012; 3:854-68. [PMID: 23097684 PMCID: PMC3478462 DOI: 10.18632/oncotarget.586] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 08/18/2012] [Indexed: 01/23/2023] Open
Abstract
Transcriptional regulation of the Hedgehog (HH) signaling response is mediated by GLI genes (GLI1, GLI2) downstream of SMO, that are also activated by oncogenic signaling pathways. We have demonstrated the importance of targeting GLI downstream of SMO in the induction of cell death in human colon carcinoma cells. In HT29 cells inhibition of GLI1/GLI2 by the small molecule inhibitor GANT61 induced DNA double strand breaks (DSBs) and activation of ATM, MDC1 and NBS1; γH2AX and MDC1, NBS1 and MDC1 co-localized in nuclear foci. Early activation of ATM was decreased by 24 hr, when p-NBS1Ser343, activated by ATM, was significantly reduced in cell extracts. Bound γH2AX was detected in isolated chromatin fractions or nuclei during DNA damage but not during DNA repair. MDC1 was tightly bound to chromatin at 32 hr as cells accumulated in early S-phase prior to becoming subG1, and during DNA repair. Limited binding of NBS1 was detected at all times during DNA damage but was strongly bound during DNA repair. Transient overexpression of NBS1 protected HT29 cells from GANT61-induced cell death, while knockdown of H2AX by H2AXshRNA delayed DNA damage signaling. Data demonstrate following GLI1/GLI2 inhibition: 1) induction of DNA damage in cells that are also resistant to SMO inhibitors, 2) dynamic interactions between γH2AX, MDC1 and NBS1 in single cell nuclei and in isolated chromatin fractions, 3) expression and chromatin binding properties of key mediator proteins that mark DNA damage or DNA repair, and 4) the importance of NBS1 in the DNA damage response mechanism.
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Affiliation(s)
- Akwasi Agyeman
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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33
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Wang H, Shao Z, Shi LZ, Hwang PYH, Truong LN, Berns MW, Chen DJ, Wu X. CtIP protein dimerization is critical for its recruitment to chromosomal DNA double-stranded breaks. J Biol Chem 2012; 287:21471-80. [PMID: 22544744 DOI: 10.1074/jbc.m112.355354] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CtIP (CtBP-interacting protein) associates with BRCA1 and the Mre11-Rad50-Nbs1 (MRN) complex and plays an essential role in homologous recombination (HR)-mediated DNA double-stranded break (DSB) repair. It has been described that CtIP forms dimers in mammalian cells, but the biological significance is not clear. In this study, we identified a conserved motif in the N terminus of CtIP, which is required for dimer formation. We further showed that CtIP mutants impaired in forming dimers are strongly defective in HR, end resection, and activation of the ataxia telangiectasia and Rad3-related pathway, without notable change of CtIP interactions with BRCA1 or Nbs1. In addition to HR, CtIP dimerization is also required for microhomology-mediated end joining. Live cell imaging of enhanced GFP-tagged CtIP demonstrates that the CtIP dimerization mutant fails to be localized to DSBs, whereas placing a heterologous dimerization motif to the dimerization mutant restores CtIP recruitment to DSBs. These studies suggest that CtIP dimer formation is essential for its recruitment to DSBs on chromatin upon DNA damage. Furthermore, DNA damage-induced phosphorylation of CtIP is significantly reduced in the CtIP dimerization mutants. Therefore, in addition to the C-terminal conserved domains critical for CtIP function, the dimerization motif on the N terminus of CtIP is also conserved and essential for its function in DNA damage responses. The severe repair defects of CtIP dimerization mutants are likely due to the failure in localization to chromosomal DSBs upon DNA damage.
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Affiliation(s)
- Hailong Wang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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34
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Errico A, Costanzo V. Mechanisms of replication fork protection: a safeguard for genome stability. Crit Rev Biochem Mol Biol 2012; 47:222-35. [DOI: 10.3109/10409238.2012.655374] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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35
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Guler GD, Liu H, Vaithiyalingam S, Arnett DR, Kremmer E, Chazin WJ, Fanning E. Human DNA helicase B (HDHB) binds to replication protein A and facilitates cellular recovery from replication stress. J Biol Chem 2011; 287:6469-81. [PMID: 22194613 DOI: 10.1074/jbc.m111.324582] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Maintenance of genomic stability in proliferating cells depends on a network of proteins that coordinate chromosomal replication with DNA damage responses. Human DNA helicase B (HELB or HDHB) has been implicated in chromosomal replication, but its role in this coordinated network remains undefined. Here we report that cellular exposure to UV irradiation, camptothecin, or hydroxyurea induces accumulation of HDHB on chromatin in a dose- and time-dependent manner, preferentially in S phase cells. Replication stress-induced recruitment of HDHB to chromatin is independent of checkpoint signaling but correlates with the level of replication protein A (RPA) recruited to chromatin. We show using purified proteins that HDHB physically interacts with the N-terminal domain of the RPA 70-kDa subunit (RPA70N). NMR spectroscopy and site-directed mutagenesis reveal that HDHB docks on the same RPA70N surface that recruits S phase checkpoint signaling proteins to chromatin. Consistent with this pattern of recruitment, cells depleted of HDHB display reduced recovery from replication stress.
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Affiliation(s)
- Gulfem Dilek Guler
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
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36
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Abstract
Replication protein A (RPA), the major eukaryotic single-strand DNA (ssDNA)-binding protein, is essential for replication, repair, recombination, and checkpoint activation. Defects in RPA-associated cellular activities lead to genomic instability, a major factor in the pathogenesis of cancer and other diseases. ssDNA binding activity is primarily mediated by two domains in the 70-kDa subunit of the RPA complex. These ssDNA interactions are mediated by a combination of polar residues and four conserved aromatic residues. Mutation of the aromatic residues causes a modest decrease in binding to long (30-nucleotide) ssDNA fragments but results in checkpoint activation and cell cycle arrest in cells. We have used a combination of biochemical analysis and knockdown replacement studies in cells to determine the contribution of these aromatic residues to RPA function. Cells containing the aromatic residue mutants were able to progress normally through S-phase but were defective in DNA repair. Biochemical characterization revealed that mutation of the aromatic residues severely decreased binding to short ssDNA fragments less than 20 nucleotides long. These data indicate that altered binding of RPA to short ssDNA intermediates causes a defect in DNA repair but not in DNA replication. These studies show that cells require different RPA functions in DNA replication and DNA repair.
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Affiliation(s)
- Cathy S Hass
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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37
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Dzikiewicz-Krawczyk A, Mosor M, Januszkiewicz D, Nowak J. Impact of heterozygous c.657-661del, p.I171V and p.R215W mutations in NBN on nibrin functions. Mutagenesis 2011; 27:337-43. [PMID: 22131123 DOI: 10.1093/mutage/ger084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nibrin, product of the NBN gene, together with MRE11 and RAD50 is involved in DNA double-strand breaks (DSBs) sensing and repair, induction of apoptosis and cell cycle control. Biallelic NBN mutations cause the Nijmegen breakage syndrome, a chromosomal instability disorder characterised by, among other things, radiosensitivity, immunodeficiency and an increased cancer risk. Several studies have shown an association of heterozygous c.657-661del, p.I171V and p.R215W mutations in the NBN gene with a variety of malignancies but the data are controversial. Little is known, however, whether and to what extent do these mutations in heterozygous state affect nibrin functions. We examined frequency of chromatid breaks, DSB repair, defects in S-phase checkpoint and radiosensitivity in X-ray-irradiated cells from control individuals, NBS patients and heterozygous carriers of the c.657-661del, p.I171V and p.R215W mutations. While cells homozygous for c.657-661del displayed a significantly increased number of chromatid breaks and residual γ-H2AX foci, as well as abrogation of the intra-S-phase checkpoint following irradiation, which resulted in increased radiosensitivity, cells with heterozygous c.657-661del, p.I171V and p.R215W mutations behaved similarly to control cells. Significant differences in the frequency of spontaneous and ionising radiation-induced chromatid breaks and the level of persistent γ-H2AX foci were observed when comparing control and mutant cells heterozygous for c.657-661del. However, it is still possible that heterozygous NBN mutations may contribute to cancer development.
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Lee AYL, Chiba T, Truong LN, Cheng AN, Do J, Cho MJ, Chen L, Wu X. Dbf4 is direct downstream target of ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) protein to regulate intra-S-phase checkpoint. J Biol Chem 2011; 287:2531-43. [PMID: 22123827 DOI: 10.1074/jbc.m111.291104] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dbf4/Cdc7 (Dbf4-dependent kinase (DDK)) is activated at the onset of S-phase, and its kinase activity is required for DNA replication initiation from each origin. We showed that DDK is an important target for the S-phase checkpoint in mammalian cells to suppress replication initiation and to protect replication forks. We demonstrated that ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) proteins directly phosphorylate Dbf4 in response to ionizing radiation and replication stress. We identified novel ATM/ATR phosphorylation sites on Dbf4 and showed that ATM/ATR-mediated phosphorylation of Dbf4 is critical for the intra-S-phase checkpoint to inhibit DNA replication. The kinase activity of DDK, which is not suppressed upon DNA damage, is required for fork protection under replication stress. We further demonstrated that ATM/ATR-mediated phosphorylation of Dbf4 is important for preventing DNA rereplication upon loss of replication licensing through the activation of the S-phase checkpoint. These studies indicate that DDK is a direct substrate of ATM and ATR to mediate the intra-S-phase checkpoint in mammalian cells.
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Affiliation(s)
- Alan Yueh-Luen Lee
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.
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Langerak P, Mejia-Ramirez E, Limbo O, Russell P. Release of Ku and MRN from DNA ends by Mre11 nuclease activity and Ctp1 is required for homologous recombination repair of double-strand breaks. PLoS Genet 2011; 7:e1002271. [PMID: 21931565 PMCID: PMC3169521 DOI: 10.1371/journal.pgen.1002271] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 07/15/2011] [Indexed: 02/07/2023] Open
Abstract
The multifunctional Mre11-Rad50-Nbs1 (MRN) protein complex recruits ATM/Tel1 checkpoint kinase and CtIP/Ctp1 homologous recombination (HR) repair factor to double-strand breaks (DSBs). HR repair commences with the 5'-to-3' resection of DNA ends, generating 3' single-strand DNA (ssDNA) overhangs that bind Replication Protein A (RPA) complex, followed by Rad51 recombinase. In Saccharomyces cerevisiae, the Mre11-Rad50-Xrs2 (MRX) complex is critical for DSB resection, although the enigmatic ssDNA endonuclease activity of Mre11 and the DNA-end processing factor Sae2 (CtIP/Ctp1 ortholog) are largely unnecessary unless the resection activities of Exo1 and Sgs1-Dna2 are also eliminated. Mre11 nuclease activity and Ctp1/CtIP are essential for DSB repair in Schizosaccharomyces pombe and mammals. To investigate DNA end resection in Schizo. pombe, we adapted an assay that directly measures ssDNA formation at a defined DSB. We found that Mre11 and Ctp1 are essential for the efficient initiation of resection, consistent with their equally crucial roles in DSB repair. Exo1 is largely responsible for extended resection up to 3.1 kb from a DSB, with an activity dependent on Rqh1 (Sgs1) DNA helicase having a minor role. Despite its critical function in DSB repair, Mre11 nuclease activity is not required for resection in fission yeast. However, Mre11 nuclease and Ctp1 are required to disassociate the MRN complex and the Ku70-Ku80 nonhomologous end-joining (NHEJ) complex from DSBs, which is required for efficient RPA localization. Eliminating Ku makes Mre11 nuclease activity dispensable for MRN disassociation and RPA localization, while improving repair of a one-ended DSB formed by replication fork collapse. From these data we propose that release of the MRN complex and Ku from DNA ends by Mre11 nuclease activity and Ctp1 is a critical step required to expose ssDNA for RPA localization and ensuing HR repair.
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Affiliation(s)
- Petra Langerak
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Eva Mejia-Ramirez
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Oliver Limbo
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Paul Russell
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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40
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Bhatti S, Kozlov S, Farooqi AA, Naqi A, Lavin M, Khanna KK. ATM protein kinase: the linchpin of cellular defenses to stress. Cell Mol Life Sci 2011; 68:2977-3006. [PMID: 21533982 PMCID: PMC11115042 DOI: 10.1007/s00018-011-0683-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/24/2011] [Accepted: 03/29/2011] [Indexed: 01/23/2023]
Abstract
ATM is the most significant molecule involved in monitoring the genomic integrity of the cell. Any damage done to DNA relentlessly challenges the cellular machinery involved in recognition, processing and repair of these insults. ATM kinase is activated early to detect and signal lesions in DNA, arrest the cell cycle, establish DNA repair signaling and faithfully restore the damaged chromatin. ATM activation plays an important role as a barrier to tumorigenesis, metabolic syndrome and neurodegeneration. Therefore, studies of ATM-dependent DNA damage signaling pathways hold promise for treatment of a variety of debilitating diseases through the development of new therapeutics capable of modulating cellular responses to stress. In this review, we have tried to untangle the complex web of ATM signaling pathways with the purpose of pinpointing multiple roles of ATM underlying the complex phenotypes observed in AT patients.
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Affiliation(s)
- Shahzad Bhatti
- Institute of Molecular Biology and Biotechnology, The University of Lahore, 1 Km Raiwind Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Sergei Kozlov
- Queensland Institute of Medical Research, QIMR, 300 Herston Rd, Herston, Brisbane, 4029 Australia
| | - Ammad Ahmad Farooqi
- Institute of Molecular Biology and Biotechnology, The University of Lahore, 1 Km Raiwind Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Ali Naqi
- Institute of Molecular Biology and Biotechnology, The University of Lahore, 1 Km Raiwind Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Martin Lavin
- Queensland Institute of Medical Research, QIMR, 300 Herston Rd, Herston, Brisbane, 4029 Australia
| | - Kum Kum Khanna
- Queensland Institute of Medical Research, QIMR, 300 Herston Rd, Herston, Brisbane, 4029 Australia
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41
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Grach AA. Alternative telomere-lengthening mechanisms. CYTOL GENET+ 2011. [DOI: 10.3103/s0095452711020046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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EMSY overexpression disrupts the BRCA2/RAD51 pathway in the DNA-damage response: implications for chromosomal instability/recombination syndromes as checkpoint diseases. Mol Genet Genomics 2011; 285:325-40. [PMID: 21409565 PMCID: PMC3064890 DOI: 10.1007/s00438-011-0612-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 02/27/2011] [Indexed: 11/05/2022]
Abstract
EMSY links the BRCA2 pathway to sporadic breast/ovarian cancer. It encodes a nuclear protein that binds to the BRCA2 N-terminal domain implicated in chromatin/transcription regulation, but when sporadically amplified/overexpressed, increased EMSY level represses BRCA2 transactivation potential and induces chromosomal instability, mimicking the activity of BRCA2 mutations in the development of hereditary breast/ovarian cancer. In addition to chromatin/transcription regulation, EMSY may also play a role in the DNA-damage response, suggested by its ability to localize at chromatin sites of DNA damage/repair. This implies that EMSY overexpression may also repress BRCA2 in DNA-damage replication/checkpoint and recombination/repair, coordinated processes that also require its interacting proteins: PALB2, the partner and localizer of BRCA2; RPA, replication/checkpoint protein A; and RAD51, the inseparable recombination/repair enzyme. Here, using a well-characterized recombination/repair assay system, we demonstrate that a slight increase in EMSY level can indeed repress these two processes independently of transcriptional interference/repression. Since EMSY, RPA and PALB2 all bind to the same BRCA2 region, these findings further support a scenario wherein: (a) EMSY amplification may mimic BRCA2 deficiency, at least by overriding RPA and PALB2, crippling the BRCA2/RAD51 complex at DNA-damage and replication/transcription sites; and (b) BRCA2/RAD51 may coordinate these processes by employing at least EMSY, PALB2 and RPA. We extensively discuss the molecular details of how this can happen to ascertain its implications for a novel recombination mechanism apparently conceived as checkpoint rather than a DNA repair system for cell division, survival, death, and human diseases, including the tissue specificity of cancer predisposition, which may renew our thinking about targeted therapy and prevention.
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43
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Glanzer JG, Liu S, Oakley GG. Small molecule inhibitor of the RPA70 N-terminal protein interaction domain discovered using in silico and in vitro methods. Bioorg Med Chem 2011; 19:2589-95. [PMID: 21459001 DOI: 10.1016/j.bmc.2011.03.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 02/25/2011] [Accepted: 03/06/2011] [Indexed: 01/26/2023]
Abstract
The pharmacological suppression of the DNA damage response and DNA repair can increase the therapeutic indices of conventional chemotherapeutics. Replication Protein A (RPA), the major single-stranded DNA binding protein in eukaryotes, is required for DNA replication, DNA repair, DNA recombination, and DNA damage response signaling. Through the use of high-throughput screening of 1500 compounds, we have identified a small molecule inhibitor, 15-carboxy-13-isopropylatis-13-ene-17,18-dioic acid (NSC15520), that inhibited both the binding of Rad9-GST and p53-GST fusion proteins to the RPA N-terminal DNA binding domain (DBD), interactions that are essential for robust DNA damage signaling. NSC15520 competitively inhibited the binding of p53-GST peptide with an IC(50) of 10 μM. NSC15520 also inhibited helix destabilization of a duplex DNA (dsDNA) oligonucleotide, an activity dependent on the N-terminal domain of RPA70. NSC15520 did not inhibit RPA from binding single-stranded oligonucleotides, suggesting that the action of this inhibitor is specific for the N-terminal DBD of RPA, and does not bind to DBDs essential for single-strand DNA binding. Computer modeling implicates direct competition between NSC15520 and Rad9 for the same binding surface on RPA. Inhibitors of protein-protein interactions within the N-terminus of RPA are predicted to act synergistically with DNA damaging agents and inhibitors of DNA repair. Novel compounds such as NSC15520 have the potential to serve as chemosensitizing agents.
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Affiliation(s)
- Jason G Glanzer
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, United States.
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44
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Horton JK, Stefanick DF, Zeng JY, Carrozza MJ, Wilson SH. Requirement for NBS1 in the S phase checkpoint response to DNA methylation combined with PARP inhibition. DNA Repair (Amst) 2010; 10:225-34. [PMID: 21130714 DOI: 10.1016/j.dnarep.2010.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 11/03/2010] [Accepted: 11/08/2010] [Indexed: 11/19/2022]
Abstract
Treatment of PARP-1-expressing cells with the combination of a DNA methylating agent (MMS) and the PARP inhibitor 4-amino-1,8-naphthalimide (4-AN) leads to an ATR/Chk1-dependent S phase checkpoint and cell death by apoptosis. Activation of ATM/Chk2 is involved in sustaining the S phase checkpoint, and double strand break (DSB) accumulation was demonstrated. NBS1, part of the MRN complex that responds to DSBs, is known to modulate ATR- and ATM-dependent checkpoint responses to UV and IR, but a role in the response to PARP inhibition has not been addressed. Here we show that the S phase checkpoint observed 4-8h after MMS+4-AN treatment was absent in cells deficient in NBS1, but was present in NBS1-complemented (i.e., functionally wild-type) cells, indicating a critical role for NBS1 in this checkpoint response. NBS1 was phosphorylated in response to MMS+4-AN treatment, and this was partially ATR- and ATM-dependent, suggesting involvement of both upstream kinases. NBS1 expression had little effect on ATR-mediated phosphorylation of Chk1 and ATM-mediated phosphorylation of Chk2 in response to MMS+4-AN. Phosphorylation of SMC1 was also observed in response to MMS+4-AN treatment. In the absence of ATM and NBS1, phosphorylation of SMC1 was weak, especially at early times after MMS+4-AN treatment. In the absence of ATR activation, reduced SMC1 phosphorylation was seen over a 24h time course. These results suggested that both ATR and ATM phosphorylate SMC1 in response to MMS+4-AN and that this phosphorylation is enhanced by phospho-NBS1. The loss of the MMS+4-AN-induced S phase checkpoint in NBS1-deficient cells may be due to a reduced cellular level of the critical downstream effector, phospho-SMC1.
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Affiliation(s)
- Julie K Horton
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
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45
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Flynn RL, Zou L. Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians. Crit Rev Biochem Mol Biol 2010; 45:266-75. [PMID: 20515430 DOI: 10.3109/10409238.2010.488216] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The maintenance of genomic stability relies on the coordinated action of a number of cellular processes, including activation of the DNA-damage checkpoint, DNA replication, DNA repair, and telomere homeostasis. Many proteins involved in these cellular processes use different types of functional modules to regulate and execute their functions. Recent studies have revealed that many DNA-damage checkpoint and DNA repair proteins in human cells possess the oligonucleotide/oligosaccharide-binding (OB) fold domains, which are known to bind single-stranded DNA in both prokaryotes and eukaryotes. Furthermore, during the DNA damage response, the OB folds of the human checkpoint and DNA repair proteins play critical roles in DNA binding, protein complex assembly, and regulating protein-protein interactions. These findings suggest that the OB fold is an evolutionarily conserved functional module that is widely used by genome guardians. In this review, we will highlight the functions of several well-characterized or newly discovered eukaryotic OB-fold proteins in the DNA damage response.
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Affiliation(s)
- Rachel Litman Flynn
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
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46
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Oakley GG, Patrick SM. Replication protein A: directing traffic at the intersection of replication and repair. FRONT BIOSCI-LANDMRK 2010; 15:883-900. [PMID: 20515732 DOI: 10.2741/3652] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the initial discovery of replication protein A (RPA) as a DNA replication factor, much progress has been made on elucidating critical roles for RPA in other DNA metabolic pathways. RPA has been shown to be required for DNA replication, DNA repair, DNA recombination, and the DNA damage response pathway with roles in checkpoint activation. This review summarizes the current understanding of RPA structure, phosphorylation and protein-protein interactions in mediating these DNA metabolic processes.
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Affiliation(s)
- Greg G Oakley
- College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583, USA
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47
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Yuan J, Chen J. MRE11-RAD50-NBS1 complex dictates DNA repair independent of H2AX. J Biol Chem 2010; 285:1097-104. [PMID: 19910469 PMCID: PMC2801237 DOI: 10.1074/jbc.m109.078436] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 11/11/2009] [Indexed: 11/06/2022] Open
Abstract
DNA double-strand breaks (DSBs) represent one of the most serious forms of DNA damage that can occur in the genome. Here, we show that the DSB-induced signaling cascade and homologous recombination (HR)-mediated DSB repair pathway can be genetically separated. We demonstrate that the MRE11-RAD50-NBS1 (MRN) complex acts to promote DNA end resection and the generation of single-stranded DNA, which is critically important for HR repair. These functions of the MRN complex can occur independently of the H2AX-mediated DNA damage signaling cascade, which promotes stable accumulation of other signaling and repair proteins such as 53BP1 and BRCA1 to sites of DNA damage. Nevertheless, mild defects in HR repair are observed in H2AX-deficient cells, suggesting that the H2AX-dependent DNA damage-signaling cascade assists DNA repair. We propose that the MRN complex is responsible for the initial recognition of DSBs and works together with both CtIP and the H2AX-dependent DNA damage-signaling cascade to facilitate repair by HR and regulate DNA damage checkpoints.
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Affiliation(s)
- Jingsong Yuan
- From the Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Junjie Chen
- From the Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520
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48
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Yuan J, Chen J. N terminus of CtIP is critical for homologous recombination-mediated double-strand break repair. J Biol Chem 2009; 284:31746-52. [PMID: 19759395 PMCID: PMC2797245 DOI: 10.1074/jbc.m109.023424] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/31/2009] [Indexed: 12/16/2022] Open
Abstract
DNA double-strand breaks (DSBs) represent one of the most lethal types of DNA damage cells encounter. CtIP (also known as RBBP8) acts together with the MRN (MRE11-RAD50-NBS1) complex to promote DNA end resection and the generation of single-stranded DNA, which is critically important for homologous recombination repair. However, it is not yet clear exactly how CtIP participates in this process. Here, we demonstrate that besides the known conserved C terminus, the N terminus of CtIP protein is also required in DSB end resection and DNA damage-induced G(2)/M checkpoint control. We further show that both termini of CtIP can interact with the MRN complex and that the N terminus of CtIP, especially residues 22-45, binds to MRN and plays a critical role in targeting CtIP to sites of DNA breaks. Collectively, our results highlight the importance of the N terminus of CtIP in directing its localization and function in DSB repair.
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Affiliation(s)
- Jingsong Yuan
- From the Department of Experimental Radiation Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Junjie Chen
- From the Department of Experimental Radiation Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
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49
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Yuan J, Ghosal G, Chen J. The annealing helicase HARP protects stalled replication forks. Genes Dev 2009; 23:2394-9. [PMID: 19793864 DOI: 10.1101/gad.1836409] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mutations in HepA-related protein (HARP) are the only identified causes of Schimke immunoosseous dysplasia (SIOD). HARP has a unique annealing helicase activity in vitro, but the in vivo functional significance remains unknown. Here, we demonstrated that HARP is recruited to stalled replication forks via its direct interaction with Replication protein A (RPA). Cells with HARP depletion displayed increased spontaneous DNA damage and G2/M arrest, suggesting that HARP normally acts to stabilize stalled replication forks. Our data place the annealing helicase activity of HARP at replication forks and propose that SIOD syndrome may be caused by the destabilization of replication forks during cell proliferation.
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Affiliation(s)
- Jingsong Yuan
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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50
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Oakley GG, Tillison K, Opiyo SA, Glanzer JG, Horn JM, Patrick SM. Physical interaction between replication protein A (RPA) and MRN: involvement of RPA2 phosphorylation and the N-terminus of RPA1. Biochemistry 2009; 48:7473-81. [PMID: 19586055 DOI: 10.1021/bi900694p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Replication protein A (RPA) is a heterotrimeric protein consisting of RPA1, RPA2, and RPA3 subunits that binds to single-stranded DNA (ssDNA) with high affinity. The response to replication stress requires the recruitment of RPA and the MRE11-RAD50-NBS1 (MRN) complex. RPA bound to ssDNA stabilizes stalled replication forks by recruiting checkpoint proteins involved in fork stabilization. MRN can bind DNA structures encountered at stalled or collapsed replication forks, such as ssDNA-double-stranded DNA (dsDNA) junctions or breaks, and promote the restart of DNA replication. Here, we demonstrate that RPA2 phosphorylation regulates the assembly of DNA damage-induced RPA and MRN foci. Using purified proteins, we observe a direct interaction between RPA with both NBS1 and MRE11. By utilizing RPA bound to ssDNA, we demonstrate that substituting RPA with phosphorylated RPA or a phosphomimetic weakens the interaction with the MRN complex. Also, the N-terminus of RPA1 is a critical component of the RPA-MRN protein-protein interaction. Deletion of the N-terminal oligonucleotide-oligosaccharide binding fold (OB-fold) of RPA1 abrogates interactions of RPA with MRN and individual proteins of the MRN complex. Further identification of residues critical for MRN binding in the N-terminus of RPA1 shows that substitution of Arg31 and Arg41 with alanines disrupts the RPA-MRN interaction and alters cell cycle progression in response to DNA damage. Thus, the N-terminus of RPA1 and phosphorylation of RPA2 regulate RPA-MRN interactions and are important in the response to DNA damage.
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Affiliation(s)
- Greg G Oakley
- College of Dentistry, University of Nebraska Medical Center, Lincoln, Nebraska 68583, USA
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