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Plugged into the Ku-DNA hub: The NHEJ network. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:62-76. [PMID: 30851288 DOI: 10.1016/j.pbiomolbio.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Abstract
In vertebrates, double-strand breaks in DNA are primarily repaired by Non-Homologous End-Joining (NHEJ). The ring-shaped Ku heterodimer rapidly senses and threads onto broken DNA ends forming a recruiting hub. Through protein-protein contacts eventually reinforced by protein-DNA interactions, the Ku-DNA hub attracts a series of specialized proteins with scaffolding and/or enzymatic properties. To shed light on these dynamic interplays, we review here current knowledge on proteins directly interacting with Ku and on the contact points involved, with a particular accent on the different classes of Ku-binding motifs identified in several Ku partners. An integrated structural model of the core NHEJ network at the synapsis step is proposed.
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Mitra J, Guerrero EN, Hegde PM, Liachko NF, Wang H, Vasquez V, Gao J, Pandey A, Taylor JP, Kraemer BC, Wu P, Boldogh I, Garruto RM, Mitra S, Rao KS, Hegde ML. Motor neuron disease-associated loss of nuclear TDP-43 is linked to DNA double-strand break repair defects. Proc Natl Acad Sci U S A 2019; 116:4696-4705. [PMID: 30770445 PMCID: PMC6410842 DOI: 10.1073/pnas.1818415116] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome damage and their defective repair have been etiologically linked to degenerating neurons in many subtypes of amyotrophic lateral sclerosis (ALS) patients; however, the specific mechanisms remain enigmatic. The majority of sporadic ALS patients feature abnormalities in the transactivation response DNA-binding protein of 43 kDa (TDP-43), whose nucleo-cytoplasmic mislocalization is characteristically observed in spinal motor neurons. While emerging evidence suggests involvement of other RNA/DNA binding proteins, like FUS in DNA damage response (DDR), the role of TDP-43 in DDR has not been investigated. Here, we report that TDP-43 is a critical component of the nonhomologous end joining (NHEJ)-mediated DNA double-strand break (DSB) repair pathway. TDP-43 is rapidly recruited at DSB sites to stably interact with DDR and NHEJ factors, specifically acting as a scaffold for the recruitment of break-sealing XRCC4-DNA ligase 4 complex at DSB sites in induced pluripotent stem cell-derived motor neurons. shRNA or CRISPR/Cas9-mediated conditional depletion of TDP-43 markedly increases accumulation of genomic DSBs by impairing NHEJ repair, and thereby, sensitizing neurons to DSB stress. Finally, TDP-43 pathology strongly correlates with DSB repair defects, and damage accumulation in the neuronal genomes of sporadic ALS patients and in Caenorhabditis elegans mutant with TDP-1 loss-of-function. Our findings thus link TDP-43 pathology to impaired DSB repair and persistent DDR signaling in motor neuron disease, and suggest that DSB repair-targeted therapies may ameliorate TDP-43 toxicity-induced genome instability in motor neuron disease.
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Affiliation(s)
- Joy Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030
| | - Erika N Guerrero
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030
- Center for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, City of Knowledge, Panama, Republic of Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur 522510, India
| | - Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030
| | - Nicole F Liachko
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA 98104
| | - Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030
- Institute of Academic Medicine, Houston Methodist Research Institute, Houston, TX 77030
| | - Velmarini Vasquez
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030
- Center for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, City of Knowledge, Panama, Republic of Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur 522510, India
| | - Junling Gao
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Arvind Pandey
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Chevy Chase, MD 20815
| | - Brian C Kraemer
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA 98104
| | - Ping Wu
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555
| | - Ralph M Garruto
- Department of Anthropology, Binghamton University, State University of New York, Binghamton, NY 13902;
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030
- Department of Radiation Oncology, Weill Medical College, New York, NY 10065
| | - K S Rao
- Center for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, City of Knowledge, Panama, Republic of Panama
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030;
- Institute of Academic Medicine, Houston Methodist Research Institute, Houston, TX 77030
- Department of Radiation Oncology, Weill Medical College, New York, NY 10065
- Houston Methodist Neurological Institute, Houston Methodist Research Institute, Houston, TX 77030
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Hecox-Lea BJ, Mark Welch DB. Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers. BMC Evol Biol 2018; 18:177. [PMID: 30486781 PMCID: PMC6264785 DOI: 10.1186/s12862-018-1288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/02/2018] [Indexed: 11/26/2022] Open
Abstract
Background Bdelloid rotifers are the oldest, most diverse and successful animal taxon for which males, hermaphrodites, and traditional meiosis are unknown. Their degenerate tetraploid genome, with 2–4 copies of most loci, includes thousands of genes acquired from all domains of life by horizontal transfer. Many bdelloid species thrive in ephemerally aquatic habitats by surviving desiccation at any life stage with no loss of fecundity or lifespan. Their unique genomic diversity and the intense selective pressure of desiccation provide an exceptional opportunity to study the evolution of diversity and novelty in genes involved in DNA repair. Results We used genomic data and RNA-Seq of the desiccation process in the bdelloid Adineta vaga to characterize DNA damage reversal, translesion synthesis, and the major DNA repair pathways: base, nucleotide, and alternate excision repair, mismatch repair (MMR), and double strand break repair by homologous recombination (HR) and classical non-homologous end joining (NHEJ). We identify multiple horizontally transferred DNA damage response genes otherwise unknown in animals (AlkD, Fpg, LigK UVDE), and the presence of genes often considered vertebrate specific, particularly in the NHEJ complex and X family polymerases. While 75–100% of genes involved in MMR and HR are present in 0–2 copies, genes involved in NHEJ, which are present in only a single copy in nearly all other animals, are retained in 3–8 copies. We present structural predictions and expression evidence of neo- or sub-functionalization of multiple copy genes involved in NHEJ and other repair processes. Conclusion The horizontally-acquired genes and duplicated genes in BER and NHEJ suggest resilience to oxidative damage is conferred in part by increased DNA damage recognition and efficient end repair capabilities. The pattern of gene loss and retention in MMR and HR may facilitate recombination and gene conversion between divergent sequences, thus providing at least some of the benefits of sex. The unique retention and divergence of duplicates genes in NHEJ may be facilitated by the lack of efficient selection in the absence of meiotic recombination and independent assortment, and may contribute to the evolutionary success of bdelloids. Electronic supplementary material The online version of this article (10.1186/s12862-018-1288-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bette J Hecox-Lea
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.,Department of Biology, Northeastern University, Boston, MA, USA
| | - David B Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
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The Role for the DSB Response Pathway in Regulating Chromosome Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:65-87. [PMID: 29956292 DOI: 10.1007/978-981-13-0593-1_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In response to DNA double strand breaks (DSB), mammalian cells activate the DNA Damage Response (DDR), a network of factors that coordinate their detection, signaling and repair. Central to this network is the ATM kinase and its substrates at chromatin surrounding DSBs H2AX, MDC1 and 53BP1. In humans, germline inactivation of ATM causes Ataxia Telangiectasia (A-T), an autosomal recessive syndrome of increased proneness to hematological malignancies driven by clonal chromosomal translocations. Studies of cancers arising in A-T patients and in genetically engineered mouse models (GEMM) deficient for ATM and its substrates have revealed complex, multilayered roles for ATM in translocation suppression and identified functional redundancies between ATM and its substrates in this context. "Programmed" DSBs at antigen receptor loci in developing lymphocytes employ ubiquitous DDR factors for signaling and repair and have been particularly useful for mechanistic studies because they are region-specific and can be monitored in vitro and in vivo. In this context, murine thymocytes deficient for ATM recapitulate the molecular events that lead to transformation in T cells from A-T patients and provide a widely used model to study the mechanisms that suppress RAG recombinase-dependent translocations. Similarly, analyses of the fate of Activation induced Cytidine Deaminase (AID)-dependent DSBs during mature B cell Class Switch Recombination (CSR) have defined the genetic requirements for end-joining and translocation suppression in this setting. Moreover, a unique role for 53BP1 in the promotion of synapsis of distant DSBs has emerged from these studies.
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A single XLF dimer bridges DNA ends during nonhomologous end joining. Nat Struct Mol Biol 2018; 25:877-884. [PMID: 30177755 PMCID: PMC6128732 DOI: 10.1038/s41594-018-0120-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/05/2018] [Indexed: 01/09/2023]
Abstract
Non-homologous end joining (NHEJ) is the primary pathway of DNA double-strand break repair in vertebrate cells, yet it remains unclear how NHEJ factors assemble a synaptic complex that bridges DNA ends. To address the role of XRCC4-like factor (XLF) in synaptic complex assembly, we employed single-molecule fluorescence imaging in Xenopus laevis egg extract, a system that efficiently joins DNA ends. We find that a single XLF dimer binds to DNA substrates just prior to formation of a ligation-competent synaptic complex between DNA ends. The interaction of both globular head domains of the XLF dimer with XRCC4 is required for efficient formation of this synaptic complex. In contrast to a model in which filaments of XLF and XRCC4 bridge DNA ends, our results indicate that binding of a single XLF dimer facilitates the assembly of a stoichiometrically well-defined synaptic complex.
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Sawicka M, Aramayo R, Ayala R, Glyde R, Zhang X. Single-Particle Electron Microscopy Analysis of DNA Repair Complexes. Methods Enzymol 2018; 592:159-186. [PMID: 28668120 DOI: 10.1016/bs.mie.2017.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA repair complexes play crucial roles in maintaining genome integrity, which is essential for the survival of an organism. The understanding of their modes of action is often obscure due to limited structural knowledge. Structural characterizations of these complexes are often challenging due to a poor protein production yield, a conformational flexibility, and a relatively high molecular mass. Single-particle electron microscopy (EM) has been successfully applied to study some of these complexes as it requires low amount of samples, is not limited by the high molecular mass of a protein or a complex, and can separate heterogeneous assemblies. Recently, near-atomic resolution structures have been obtained with EM owing to the advances in technology and image processing algorithms. In this chapter, we review the EM methodology of obtaining three-dimensional reconstructions of macromolecular complexes and provide a workflow that can be applied to DNA repair complex assemblies.
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Affiliation(s)
- Marta Sawicka
- Section of Structural Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Ricardo Aramayo
- Section of Structural Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Rafael Ayala
- Section of Structural Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Robert Glyde
- Section of Structural Biology, Imperial College London, South Kensington, London, United Kingdom
| | - Xiaodong Zhang
- Section of Structural Biology, Imperial College London, South Kensington, London, United Kingdom.
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57
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Torrecilla I, Oehler J, Ramadan K. The role of ubiquitin-dependent segregase p97 (VCP or Cdc48) in chromatin dynamics after DNA double strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0282. [PMID: 28847819 PMCID: PMC5577460 DOI: 10.1098/rstb.2016.0282] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/27/2022] Open
Abstract
DNA double strand breaks (DSBs) are the most cytotoxic DNA lesions and, if not repaired, lead to chromosomal rearrangement, genomic instability and cell death. Cells have evolved a complex network of DNA repair and signalling molecules which promptly detect and repair DSBs, commonly known as the DNA damage response (DDR). The DDR is orchestrated by various post-translational modifications such as phosphorylation, methylation, ubiquitination or SUMOylation. As DSBs are located in complex chromatin structures, the repair of DSBs is engineered at two levels: (i) at sites of broken DNA and (ii) at chromatin structures that surround DNA lesions. Thus, DNA repair and chromatin remodelling machineries must work together to efficiently repair DSBs. Here, we summarize the current knowledge of the ubiquitin-dependent molecular unfoldase/segregase p97 (VCP in vertebrates and Cdc48 in worms and lower eukaryotes) in DSB repair. We identify p97 as an essential factor that regulates DSB repair. p97-dependent extraction of ubiquitinated substrates mediates spatio-temporal protein turnover at and around the sites of DSBs, thus orchestrating chromatin remodelling and DSB repair. As p97 is a druggable target, p97 inhibition in the context of DDR has great potential for cancer therapy, as shown for other DDR components such as PARP, ATR and CHK1.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Judith Oehler
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
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Wang X, Liu H, Shi L, Yu X, Gu Y, Sun X. LINP1 facilitates DNA damage repair through non-homologous end joining (NHEJ) pathway and subsequently decreases the sensitivity of cervical cancer cells to ionizing radiation. Cell Cycle 2018. [PMID: 29527968 PMCID: PMC5927633 DOI: 10.1080/15384101.2018.1442625] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
LncRNA in non-homologous end joining (NHEJ) pathway 1 (LINP1) is an lncRNA which promotes therapeutic resistance in triple-negative breast cancer (TNBC). However, the expression and function of LINP1 in cervical cancer is not yet well-understood. In this study, we evaluated the expression levels of LINP1 in tumor tissues and cell lines of cervical cancer. We found that LINP1 associates with NHEJ proteins (Ku80 and DNA-PKcs). LINP1 translocates from cytosol to nucleus in response to irradiation. In addition, LINP1 knockdown significantly increases the levels of cleaved caspase3 and PARP, leading to enhanced cell apoptosis after ionizing radiation (IR). LINP1-knockdown cells showed delayed repairs of DNA double-strand breaks (DSBs) after IR. Finally, LINP1 knockdown increases radiosensitivity of Hela S3 cells. These results suggest that LINP1 facilitates DSBs repair through NHEJ pathway and may thus serve as a prognostic marker and a potential target for the therapy of cervical cancer.
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Affiliation(s)
- Xuanxuan Wang
- a Department of Radiation Oncology , Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou , China
| | - Hai Liu
- a Department of Radiation Oncology , Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou , China
| | - Liming Shi
- a Department of Radiation Oncology , Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou , China
| | - Xiaoli Yu
- b Department of Pathology , Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou , China
| | - Yanjun Gu
- a Department of Radiation Oncology , Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou , China
| | - Xiaonan Sun
- a Department of Radiation Oncology , Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou , China
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Ku DNA End-Binding Activity Promotes Repair Fidelity and Influences End-Processing During Nonhomologous End-Joining in Saccharomyces cerevisiae. Genetics 2018; 209:115-128. [PMID: 29500182 DOI: 10.1534/genetics.117.300672] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/25/2018] [Indexed: 12/21/2022] Open
Abstract
The Ku heterodimer acts centrally in nonhomologous end-joining (NHEJ) of DNA double-strand breaks (DSB). Saccharomyces cerevisiae Ku, like mammalian Ku, binds and recruits NHEJ factors to DSB ends. Consequently, NHEJ is virtually absent in yeast Ku null (yku70∆ or yku80∆) strains. Previously, we unexpectedly observed imprecise NHEJ proficiency in a yeast Ku mutant with impaired DNA end-binding (DEB). However, how DEB impairment supported imprecise NHEJ was unknown. Here, we found imprecise NHEJ proficiency to be a feature of a panel of DEB-impaired Ku mutants and that DEB impairment resulted in a deficiency in precise NHEJ. These results suggest that DEB-impaired Ku specifically promotes error-prone NHEJ. Epistasis analysis showed that classical NHEJ factors, as well as novel and previously characterized NHEJ-specific residues of Ku, are required for the distinct error-prone repair in a Ku DEB mutant. However, sequencing of repair junctions revealed that imprecise repair in Ku DEB mutants was almost exclusively characterized by small deletions, in contrast to the majority of insertions that define imprecise repair in wild-type strains. Notably, while sequencing indicated a lack of Pol4-dependent insertions at the site of repair, Pol2 exonuclease activity, which mediates small deletions in NHEJ, contributed to imprecise NHEJ in a Ku DEB mutant. The deletions were smaller than in Ku-independent microhomology-mediated end-joining (MMEJ) and were neither promoted by Mre11 nuclease activity nor Sae2 Thus, the quality of Ku's engagement at the DNA end influences end-processing during NHEJ and DEB impairment unmasks a Ku-dependent error-prone pathway of end-joining distinct from MMEJ.
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60
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Jin Y, Xu X, Wang X, Kuang H, Osterman M, Feng S, Han D, Wu Y, Li M, Guo H. Increasing sensitivity to DNA damage is a potential driver for human ovarian cancer. Oncotarget 2018; 7:49710-49721. [PMID: 27391345 PMCID: PMC5226541 DOI: 10.18632/oncotarget.10436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/29/2016] [Indexed: 12/11/2022] Open
Abstract
Ovarian cancer is one of the most common cancers among women, accounting for more deaths than any other gynecological diseases. However, the survival rate for ovarian cancer has not essentially improved over the past thirty years. Thus, to understand the molecular mechanism of ovarian tumorigenesis is important for optimizing the early diagnosis and treating this disease. In this study, we observed obvious DNA lesions, especially DNA double strand breaks (DSBs) accompanying cell cycle checkpoint activation, in the human epithelial ovarian cancer samples, which could be due to the impaired DNA response machinery. Following this line, we found that these DNA damage response-deficient primary cancer cells were hypersensitive to DNA damage and lost their ability to repair the DNA breaks, leading to genomic instability. Of note, three key DNA damage response factors, RNF8, Ku70, and FEN1 exhibited dramatically decreased expression level, implying the dysfunctional DNA repair pathways. Re-expression of wild type RNF8, Ku70, or FEN1 in these cells restored the DNA lesions and also partially rescued the cells from death. Our current study therefore proposes that accumulated DNA lesions might be a potential driver of ovarian cancer and the impaired DNA damage responders could be the targets for clinical treatment.
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Affiliation(s)
- Yimei Jin
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Xin Xu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Xuemeng Wang
- Department of Molecular and Medical pharmacology, University of California, Los Angeles, 90095, USA
| | - Henry Kuang
- Medical School and University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Michael Osterman
- School of Public Health, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Shi Feng
- Education Department, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Deqiang Han
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Yu Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Mo Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, P.R. China
| | - Hongyan Guo
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, P.R. China
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Schuler N, Timm S, Rübe CE. Hair Follicle Stem Cell Faith Is Dependent on Chromatin Remodeling Capacity Following Low-Dose Radiation. Stem Cells 2018; 36:574-588. [PMID: 29282803 DOI: 10.1002/stem.2768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/21/2017] [Accepted: 12/03/2017] [Indexed: 12/17/2022]
Abstract
The main function of the skin, to protect against the environment, is supported by the activity of different stem cell populations. The main focus of this study was elucidating the coping mechanisms of stem cells against the stimulation of constant exposure to genotoxic stresses, both endogenous and exogenous, to ensure long-term function. Investigation of various mouse strains, differing in their DNA repair capacity, enables us to clarify fractionated low-dose irradiation (LDR)-induced consequences for different stem cell populations of the murine hair follicle (HF) in their physiological stem cell niche. Using microscopic techniques combined with flow cytometry, we could show that LDR induces accumulation of persisting; pKu70-independent 53BP1-foci ("chromatin-alterations") in heterochromatic regions of the HF stem cells (HFSCs). These remaining chromatin-alterations result in varying stem cell consequences. CD34-positive HFSCs react by ataxia telangiectasia mutated-dependent, premature senescence, which correlates with global chromatin compaction, whereby apoptosis is prevented by the activity of DNA-dependent protein kinase catalytic subunit. However, distinctively highly damaged HFSCs seem to be sorted out of the niche by differentiation, transferring their chromatin-alterations to more proliferative G protein-coupled receptor 5-positive stem cells. Consequentially, the loss of basal HFSCs is compensated by increased proliferation within the stem cell pool. Despite the initial success of these mechanisms in stem cell population maintenance, the combined effect of the chromatin-alterations and the modification in stem cell pool composition may lead to downstream long-term functional loss of tissue or organs. Stem Cells 2018;36:574-588.
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Affiliation(s)
- Nadine Schuler
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Sara Timm
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Claudia E Rübe
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
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Liu J, Liu Q, Wang H, Li C, Wen T, An G, Qian H. NuRD subunit MTA1 interacts with the DNA non-homologous end joining Ku complex in cancer cells. RSC Adv 2018; 8:35218-35225. [PMID: 35547075 PMCID: PMC9087872 DOI: 10.1039/c8ra06907g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 10/10/2018] [Indexed: 11/29/2022] Open
Abstract
Metastasis-associated antigen 1 (MTA1) is a chromatin modifier mediating DNA modification and gene expression. Ku70/Ku80 complex has been reported to be essential in DNA damage response. In an effort to explore the MTA1 interactome, we captured the Ku70/Ku80 complex with two specific MTA1 antibodies in a colon cancer cell line. We first validated the in vitro interaction between MTA1 and the Ku complex by co-immunoprecipitation (co-IP) analyses in cell lysate, showing that the interaction occurred mainly at the nucleus, but also existed in the cytoplasm at a lower level. We further visualized and confirmed their in vivo interaction using proximity ligation assay (PLA), which, in line with the in vitro analysis, also demonstrated a vast majority of interaction plots in the nucleus and a small number in the cytoplasm. We previously demonstrated that MTA1 distributed dynamically and periodically during the cell cycle. Here, through fluorescent colocalization, we found that MTA1 and Ku proteins colocalized well in the nucleus at interphase and moved synchronously from prophase to anaphase. Interestingly, at the time of telophase, when MTA1 was reported to re-enter the nucleus, they were separated and moved non-synchronously. Moreover, using in situ PLA, we visualized that the interaction occurred at both interphase and mitosis. At interphase, they interacted mainly in the nucleus, but during mitosis, they interact at the periphery of chromosomes. We also showed that MTA1 correlated well with Ku in both the cancerous and normal tissues, and that they cooperated in UV-induced DNA damage response. Collectively, our data uncover a specific interaction between MTA1 and Ku complex at both the nucleus and cytoplasm, and across the whole cell cycle. We therefore propose a potential functional crosstalk between NuRD and Ku complexes, the two most fundamental function units in cells, via physical interaction. MTA1 interacts with Ku complex mainly in the nucleus at interphase and surrounding the chromosome during mitosis.![]()
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Affiliation(s)
- Jian Liu
- Medical Research Center
- Beijing Chao-Yang Hospital
- Capital Medical University
- Beijing
- China
| | - Qun Liu
- Department of Obstetrics and Gynecology
- Beijing Anzhen Hospital
- Capital Medical University
- Beijing
- China
| | - Haijuan Wang
- State Key Laboratory of Molecular Oncology
- National Cancer Center/Cancer Hospital
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
- China
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology
- National Cancer Center/Cancer Hospital
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
- China
| | - Tao Wen
- Medical Research Center
- Beijing Chao-Yang Hospital
- Capital Medical University
- Beijing
- China
| | - Guangyu An
- Department of Oncology
- Beijing Chao-Yang Hospital
- Capital Medical University
- Beijing
- China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology
- National Cancer Center/Cancer Hospital
- Chinese Academy of Medical Sciences & Peking Union Medical College
- Beijing
- China
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Baird DM, Hendrickson EA. Telomeres and Chromosomal Translocations : There's a Ligase at the End of the Translocation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:89-112. [PMID: 29956293 DOI: 10.1007/978-981-13-0593-1_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chromosomal translocations are now well understood to not only constitute signature molecular markers for certain human cancers but often also to be causative in the genesis of that tumor. Despite the obvious importance of such events, the molecular mechanism of chromosomal translocations in human cells remains poorly understood. Part of the explanation for this dearth of knowledge is due to the complexity of the reaction and the need to archaeologically work backwards from the final product (a translocation) to the original unrearranged chromosomes to infer mechanism. Although not definitive, these studies have indicated that the aberrant usage of endogenous DNA repair pathways likely lies at the heart of the problem. An equally obfuscating aspect of this field, however, has also originated from the unfortunate species-specific differences that appear to exist in the relevant model systems that have been utilized to investigate this process. Specifically, yeast and murine systems (which are often used by basic science investigators) rely on different DNA repair pathways to promote chromosomal translocations than human somatic cells. In this chapter, we will review some of the basic concepts of chromosomal translocations and the DNA repair systems thought to be responsible for their genesis with an emphasis on underscoring the differences between other species and human cells. In addition, we will focus on a specific subset of translocations that involve the very end of a chromosome (a telomere). A better understanding of the relationship between DNA repair pathways and chromosomal translocations is guaranteed to lead to improved therapeutic treatments for cancer.
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Affiliation(s)
- Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA.
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64
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Pannunzio NR, Watanabe G, Lieber MR. Nonhomologous DNA end-joining for repair of DNA double-strand breaks. J Biol Chem 2017; 293:10512-10523. [PMID: 29247009 DOI: 10.1074/jbc.tm117.000374] [Citation(s) in RCA: 326] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Nonhomologous DNA end-joining (NHEJ) is the predominant double-strand break (DSB) repair pathway throughout the cell cycle and accounts for nearly all DSB repair outside of the S and G2 phases. NHEJ relies on Ku to thread onto DNA termini and thereby improve the affinity of the NHEJ enzymatic components consisting of polymerases (Pol μ and Pol λ), a nuclease (the Artemis·DNA-PKcs complex), and a ligase (XLF·XRCC4·Lig4 complex). Each of the enzymatic components is distinctive for its versatility in acting on diverse incompatible DNA end configurations coupled with a flexibility in loading order, resulting in many possible junctional outcomes from one DSB. DNA ends can either be directly ligated or, if the ends are incompatible, processed until a ligatable configuration is achieved that is often stabilized by up to 4 bp of terminal microhomology. Processing of DNA ends results in nucleotide loss or addition, explaining why DSBs repaired by NHEJ are rarely restored to their original DNA sequence. Thus, NHEJ is a single pathway with multiple enzymes at its disposal to repair DSBs, resulting in a diversity of repair outcomes.
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Affiliation(s)
- Nicholas R Pannunzio
- From the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology, Section of Molecular and Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
| | - Go Watanabe
- From the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology, Section of Molecular and Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
| | - Michael R Lieber
- From the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology, Section of Molecular and Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
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65
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Yan Q, Zhu H, Lan L, Yi J, Yang J. Cleavage of Ku80 by caspase-2 promotes non-homologous end joining-mediated DNA repair. DNA Repair (Amst) 2017; 60:18-28. [DOI: 10.1016/j.dnarep.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 12/12/2022]
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66
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Jaafar L, Li Z, Li S, Dynan WS. SFPQ•NONO and XLF function separately and together to promote DNA double-strand break repair via canonical nonhomologous end joining. Nucleic Acids Res 2017; 45:1848-1859. [PMID: 27924002 PMCID: PMC5605232 DOI: 10.1093/nar/gkw1209] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/28/2016] [Indexed: 01/10/2023] Open
Abstract
A complex of two related mammalian proteins, SFPQ and NONO, promotes DNA double-strand break repair via the canonical nonhomologous end joining (c-NHEJ) pathway. However, its mechanism of action is not fully understood. Here we describe an improved SFPQ•NONO-dependent in vitro end joining assay. We use this system to demonstrate that the SFPQ•NONO complex substitutes in vitro for the core c-NHEJ factor, XLF. Results are consistent with a model where SFPQ•NONO promotes sequence-independent pairing of DNA substrates, albeit in a way that differs in detail from XLF. Although SFPQ•NONO and XLF function redundantly in vitro, shRNA-mediated knockdown experiments indicate that NONO and XLF are both required for efficient end joining and radioresistance in cell-based assays. In addition, knockdown of NONO sensitizes cells to the interstrand crosslinking agent, cisplatin, whereas knockdown of XLF does not, and indeed suppresses the effect of NONO deficiency. These findings suggest that each protein has one or more unique activities, in addition to the DNA pairing revealed in vitro, that contribute to DNA repair in the more complex cellular milieu. The SFPQ•NONO complex contains an RNA binding domain, and prior work has demonstrated diverse roles in RNA metabolism. It is thus plausible that the additional repair function of NONO, revealed in cell-based assays, could involve RNA interaction.
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Affiliation(s)
- Lahcen Jaafar
- Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Zhentian Li
- Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Shuyi Li
- Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - William S Dynan
- Departments of Radiation Oncology and Biochemistry, Emory University, Atlanta, GA 30322, USA
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67
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Abstract
In a recent paper published in Cell Research, a cryo-EM structure reveals the interface between DNA-PKcs and the Ku70/80:DNA complex, together forming the DNA-dependent protein kinase holoenzyme in non-homologous DNA end joining. Insight from this structure suggests how an allosteric rearrangement of DNA-PKcs driven by Ku70/80:DNA binding regulates kinase activity in this largest member of a family of structurally homologous phosphoinositide 3-kinase-related protein kinases that includes mTOR, ATR, and ATM.
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68
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Cryo-EM structure of human DNA-PK holoenzyme. Cell Res 2017; 27:1341-1350. [PMID: 28840859 DOI: 10.1038/cr.2017.110] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/22/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023] Open
Abstract
DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ), the major DNA repair pathway. Here, we determined cryo-electron microscopy structure of human DNA-PK holoenzyme at 6.6 Å resolution. In the complex structure, DNA-PKcs, KU70, KU80 and DNA duplex form a 650-kDa heterotetramer with 1:1:1:1 stoichiometry. The N-terminal α-solenoid (∼2 800 residues) of DNA-PKcs adopts a double-ring fold and connects the catalytic core domain of DNA-PKcs and KU70/80-DNA. DNA-PKcs and KU70/80 together form a DNA-binding tunnel, which cradles ∼30-bp DNA and prevents sliding inward of DNA-PKcs along with DNA duplex, suggesting a mechanism by which the broken DNA end is protected from unnecessary processing. Structural and biochemical analyses indicate that KU70/80 and DNA coordinately induce conformational changes of DNA-PKcs and allosterically stimulate its kinase activity. We propose a model for activation of DNA-PKcs in which allosteric signals are generated upon DNA-PK holoenzyme formation and transmitted to the kinase domain through N-terminal HEAT repeats and FAT domain of DNA-PKcs. Our studies suggest a mechanism for recognition and protection of broken DNA ends and provide a structural basis for understanding the activation of DNA-PKcs and DNA-PK-mediated NHEJ pathway.
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69
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Abstract
DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer of DNA-binding proteins Ku70 and Ku80. Here, we report the cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs at 4.4-Å resolution and the DNA-PK holoenzyme at 5.8-Å resolution. The DNA-PKcs structure contains three distinct segments: the N-terminal region with an arm and a bridge, the circular cradle, and the head that includes the kinase domain. Two perpendicular apertures exist in the structure, which are sufficiently large for the passage of dsDNA. The DNA-PK holoenzyme cryo-EM map reveals density for the C-terminal globular domain of Ku80 that interacts with the arm of DNA-PKcs. The Ku80-binding site is adjacent to the previously identified density for the DNA-binding region of the Ku70/Ku80 complex, suggesting concerted DNA interaction by DNA-PKcs and the Ku complex.
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70
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Blackford AN, Jackson SP. ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response. Mol Cell 2017; 66:801-817. [PMID: 28622525 DOI: 10.1016/j.molcel.2017.05.015] [Citation(s) in RCA: 1184] [Impact Index Per Article: 169.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/09/2023]
Abstract
In vertebrate cells, the DNA damage response is controlled by three related kinases: ATM, ATR, and DNA-PK. It has been 20 years since the cloning of ATR, the last of the three to be identified. During this time, our understanding of how these kinases regulate DNA repair and associated events has grown profoundly, although major questions remain unanswered. Here, we provide a historical perspective of their discovery and discuss their established functions in sensing and responding to genotoxic stress. We also highlight what is known regarding their structural similarities and common mechanisms of regulation, as well as emerging non-canonical roles and how our knowledge of ATM, ATR, and DNA-PK is being translated to benefit human health.
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Affiliation(s)
- Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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71
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Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 2017; 18:495-506. [PMID: 28512351 DOI: 10.1038/nrm.2017.48] [Citation(s) in RCA: 1006] [Impact Index Per Article: 143.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks (DSBs) are the most dangerous type of DNA damage because they can result in the loss of large chromosomal regions. In all mammalian cells, DSBs that occur throughout the cell cycle are repaired predominantly by the non-homologous DNA end joining (NHEJ) pathway. Defects in NHEJ result in sensitivity to ionizing radiation and the ablation of lymphocytes. The NHEJ pathway utilizes proteins that recognize, resect, polymerize and ligate the DNA ends in a flexible manner. This flexibility permits NHEJ to function on a wide range of DNA-end configurations, with the resulting repaired DNA junctions often containing mutations. In this Review, we discuss the most recent findings regarding the relative involvement of the different NHEJ proteins in the repair of various DNA-end configurations. We also discuss the shunting of DNA-end repair to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA) and the relevance of these different pathways to human disease.
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72
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Chirgadze DY, Ascher DB, Blundell TL, Sibanda BL. DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage. Methods Enzymol 2017; 592:145-157. [PMID: 28668119 DOI: 10.1016/bs.mie.2017.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is central to the regulation of the DNA damage response and repair through nonhomologous end joining. The structure has proved challenging due to its large size and multiple HEAT repeats. We have recently reported crystals of selenomethionine-labeled DNA-PKcs complexed with native KU80ct194 (KU80 residues 539-732) diffracting to 4.3Å resolution. The novel use of crystals of selenomethionine-labeled protein expressed in HeLa cells has facilitated the use of single anomalous X-ray scattering of this 4128 amino acid, multiple HEAT-repeat structure. The monitoring of the selenomethionines in the anomalous-difference density map has allowed the checking of the amino acid residue registration in the electron density, and the labeling of the Ku-C-terminal moiety with selenomethionine has further allowed its identification in the structure of the complex with DNA-PKcs. The crystal structure defines a stage on which many of the components assemble and regulate the kinase activity through modulating the conformation and allosteric regulation of kinase activity.
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73
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Sibanda BL, Chirgadze DY, Ascher DB, Blundell TL. DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair. Science 2017; 355:520-524. [DOI: 10.1126/science.aak9654] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/05/2017] [Indexed: 12/15/2022]
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74
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Landuzzi F, Palla PL, Cleri F. Stability of radiation-damaged DNA after multiple strand breaks. Phys Chem Chem Phys 2017; 19:14641-14651. [DOI: 10.1039/c7cp02266b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Radiation induced double-strand breaks in DNA are more stable against thermal and mechanical stress than usually thought.
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Affiliation(s)
- Fabio Landuzzi
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
| | - Pier Luca Palla
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
| | - Fabrizio Cleri
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
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75
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Chang HHY, Watanabe G, Gerodimos CA, Ochi T, Blundell TL, Jackson SP, Lieber MR. Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency. J Biol Chem 2016; 291:24377-24389. [PMID: 27703001 PMCID: PMC5114395 DOI: 10.1074/jbc.m116.752329] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/26/2016] [Indexed: 02/02/2023] Open
Abstract
The nonhomologous DNA end-joining (NHEJ) pathway is a key mechanism for repairing dsDNA breaks that occur often in eukaryotic cells. In the simplest model, these breaks are first recognized by Ku, which then interacts with other NHEJ proteins to improve their affinity at DNA ends. These include DNA-PKcs and Artemis for trimming the DNA ends; DNA polymerase μ and λ to add nucleotides; and the DNA ligase IV complex to ligate the ends with the additional factors, XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor/Cernunos), and PAXX (paralog of XRCC4 and XLF). In vivo studies have demonstrated the degrees of importance of these NHEJ proteins in the mechanism of repair of dsDNA breaks, but interpretations can be confounded by other cellular processes. In vitro studies with NHEJ proteins have been performed to evaluate the nucleolytic resection, polymerization, and ligation steps, but a complete system has been elusive. Here we have developed a NHEJ reconstitution system that includes the nuclease, polymerase, and ligase components to evaluate relative NHEJ efficiency and analyze ligated junctional sequences for various types of DNA ends, including blunt, 5' overhangs, and 3' overhangs. We find that different dsDNA end structures have differential dependence on these enzymatic components. The dependence of some end joining on only Ku and XRCC4·DNA ligase IV allows us to formulate a physical model that incorporates nuclease and polymerase components as needed.
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Affiliation(s)
- Howard H Y Chang
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Go Watanabe
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Christina A Gerodimos
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Takashi Ochi
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Tom L Blundell
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Stephen P Jackson
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Michael R Lieber
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and.
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76
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Fell VL, Walden EA, Hoffer SM, Rogers SR, Aitken AS, Salemi LM, Schild-Poulter C. Ku70 Serine 155 mediates Aurora B inhibition and activation of the DNA damage response. Sci Rep 2016; 6:37194. [PMID: 27849008 PMCID: PMC5111114 DOI: 10.1038/srep37194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/25/2016] [Indexed: 11/17/2022] Open
Abstract
The Ku heterodimer (Ku70/Ku80) is the central DNA binding component of the classical non-homologous end joining (NHEJ) pathway that repairs DNA double-stranded breaks (DSBs), serving as the scaffold for the formation of the NHEJ complex. Here we show that Ku70 is phosphorylated on Serine 155 in response to DNA damage. Expression of Ku70 bearing a S155 phosphomimetic substitution (Ku70 S155D) in Ku70-deficient mouse embryonic fibroblasts (MEFs) triggered cell cycle arrest at multiple checkpoints and altered expression of several cell cycle regulators in absence of DNA damage. Cells expressing Ku70 S155D exhibited a constitutive DNA damage response, including ATM activation, H2AX phosphorylation and 53BP1 foci formation. Ku70 S155D was found to interact with Aurora B and to have an inhibitory effect on Aurora B kinase activity. Lastly, we demonstrate that Ku and Aurora B interact following ionizing radiation treatment and that Aurora B inhibition in response to DNA damage is dependent upon Ku70 S155 phosphorylation. This uncovers a new pathway where Ku may relay signaling to Aurora B to enforce cell cycle arrest in response to DNA damage.
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Affiliation(s)
- Victoria L Fell
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine &Dentistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Elizabeth A Walden
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine &Dentistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Sarah M Hoffer
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine &Dentistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Stephanie R Rogers
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine &Dentistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Amelia S Aitken
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine &Dentistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Louisa M Salemi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine &Dentistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine &Dentistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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77
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Hammel M, Yu Y, Radhakrishnan SK, Chokshi C, Tsai MS, Matsumoto Y, Kuzdovich M, Remesh SG, Fang S, Tomkinson AE, Lees-Miller SP, Tainer JA. An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex. J Biol Chem 2016; 291:26987-27006. [PMID: 27875301 PMCID: PMC5207133 DOI: 10.1074/jbc.m116.751867] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/03/2016] [Indexed: 11/29/2022] Open
Abstract
DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). Yet, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcs (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.
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Affiliation(s)
- Michal Hammel
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720,
| | - Yaping Yu
- the Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Sarvan K Radhakrishnan
- the Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Chirayu Chokshi
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Miaw-Sheue Tsai
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Yoshihiro Matsumoto
- the University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico 87131, and
| | - Monica Kuzdovich
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Soumya G Remesh
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Shujuan Fang
- the Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Alan E Tomkinson
- the University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico 87131, and
| | - Susan P Lees-Miller
- the Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada,
| | - John A Tainer
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, .,the Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
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78
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Liang S, Esswein SR, Ochi T, Wu Q, Ascher DB, Chirgadze D, Sibanda BL, Blundell TL. Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached. Struct Chem 2016. [DOI: 10.1007/s11224-016-0841-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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79
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Graham TGW, Walter JC, Loparo JJ. Two-Stage Synapsis of DNA Ends during Non-homologous End Joining. Mol Cell 2016; 61:850-8. [PMID: 26990988 DOI: 10.1016/j.molcel.2016.02.010] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/21/2015] [Accepted: 02/07/2016] [Indexed: 11/28/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) is essential for genomic stability. The most common DSB repair mechanism in human cells, non-homologous end joining (NHEJ), rejoins broken DNA ends by direct ligation. It remains unclear how components of the NHEJ machinery assemble a synaptic complex that bridges DNA ends. Here, we use single-molecule imaging in a vertebrate cell-free extract to show that synapsis of DNA ends occurs in at least two stages that are controlled by different NHEJ factors. DNA ends are initially tethered in a long-range complex whose formation requires the Ku70/80 heterodimer and the DNA-dependent protein kinase catalytic subunit. The ends are then closely aligned, which requires XLF, a non-catalytic function of XRCC4-LIG4, and DNA-PK activity. These results reveal a structural transition in the synaptic complex that governs alignment of DNA ends. Our approach provides a means of studying physiological DNA DSB repair at single-molecule resolution.
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Affiliation(s)
- Thomas G W Graham
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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80
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Lysines 3241 and 3260 of DNA-PKcs are important for genomic stability and radioresistance. Biochem Biophys Res Commun 2016; 477:235-40. [PMID: 27297111 DOI: 10.1016/j.bbrc.2016.06.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 11/22/2022]
Abstract
DNA-dependent protein kinase (DNA-PK) is a serine/threonine kinase that plays an essential role in the repair of DNA double-strand breaks (DSBs) in the non-homologous end-joining (NHEJ) pathway. The DNA-PK holoenzyme consists of a catalytic subunit (DNA-PKcs) and DNA-binding subunit (Ku70/80, Ku). Ku is a molecular sensor for double-stranded DNA and once bound to DSB ends it recruits DNA-PKcs to the DSB site. Subsequently, DNA-PKcs is activated and heavily phosphorylated, with these phosphorylations modulating DNA-PKcs. Although phosphorylation of DNA-PKcs is well studied, other post-translational modifications of DNA-PKcs are not. In this study, we aimed to determine if acetylation of DNA-PKcs regulates DNA-PKcs-dependent DSB repair. We report that DNA-PKcs is acetylated in vivo and identified two putative acetylation sites, lysine residues 3241 and 3260. Mutating these sites to block potential acetylation results in increased radiosensitive, a slight decrease in DSB repair capacity as assessed by γH2AX resolution, and increased chromosomal aberrations, especially quadriradial chromosomes. Together, our results provide evidence that acetylation potentially regulates DNA-PKcs.
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81
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Di Domenico EG, Toma L, Bordignon V, Trento E, D'Agosto G, Cordiali-Fei P, Ensoli F. Activation of DNA Damage Response Induced by the Kaposi's Sarcoma-Associated Herpes Virus. Int J Mol Sci 2016; 17:ijms17060854. [PMID: 27258263 PMCID: PMC4926388 DOI: 10.3390/ijms17060854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/23/2016] [Accepted: 05/27/2016] [Indexed: 01/24/2023] Open
Abstract
The human herpes virus 8 (HHV-8), also known as Kaposi sarcoma-associated herpes virus (KSHV), can infect endothelial cells often leading to cell transformation and to the development of tumors, namely Kaposi’s sarcoma (KS), primary effusion lymphoma (PEL), and the plasmablastic variant of multicentric Castleman’s disease. KSHV is prevalent in areas such as sub-Saharan Africa and the Mediterranean region presenting distinct genotypes, which appear to be associated with differences in disease manifestation, according to geographical areas. In infected cells, KSHV persists in a latent episomal form. However, in a limited number of cells, it undergoes spontaneous lytic reactivation to ensure the production of new virions. During both the latent and the lytic cycle, KSHV is programmed to express genes which selectively modulate the DNA damage response (DDR) through the activation of the ataxia telangiectasia mutated (ATM) pathway and by phosphorylating factors associated with the DDR, including the major tumor suppressor protein p53 tumor suppressor p53. This review will focus on the interplay between the KSHV and the DDR response pathway throughout the viral lifecycle, exploring the putative molecular mechanism/s that may contribute to malignant transformation of host cells.
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Affiliation(s)
- Enea Gino Di Domenico
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Luigi Toma
- Infectious Disease Consultant, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Valentina Bordignon
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Elisabetta Trento
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Giovanna D'Agosto
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Paola Cordiali-Fei
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
| | - Fabrizio Ensoli
- Clinical Pathology and Microbiology Department, San Gallicano Institute, IRCCS, Rome 00144, Italy.
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82
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Wang Q, Ma S, Song N, Li X, Liu L, Yang S, Ding X, Shan L, Zhou X, Su D, Wang Y, Zhang Q, Liu X, Yu N, Zhang K, Shang Y, Yao Z, Shi L. Stabilization of histone demethylase PHF8 by USP7 promotes breast carcinogenesis. J Clin Invest 2016; 126:2205-20. [PMID: 27183383 DOI: 10.1172/jci85747] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/31/2016] [Indexed: 01/26/2023] Open
Abstract
The histone demethylase PHF8 has been implicated in multiple pathological disorders, including X-linked mental retardation and tumorigenesis. However, it is not clear how the abundance and function of PHF8 are regulated. Here, we report that PHF8 physically associates with the deubiquitinase USP7. Specifically, we demonstrated that USP7 promotes deubiquitination and stabilization of PHF8, leading to the upregulation of a group of genes, including cyclin A2, that are critical for cell growth and proliferation. The USP7-encoding gene was also transcriptionally regulated by PHF8, via positive feedback. USP7 was overexpressed in breast carcinomas, and the level of expression positively correlated with expression of PHF8 and cyclin A2 and with the histological grade of breast cancer. We showed that USP7 promotes breast carcinogenesis by stabilizing PHF8 and upregulating cyclin A2 and that the interaction between USP7 and PHF8 is augmented during DNA damage. Moreover, USP7-promoted PHF8 stabilization conferred cellular resistance to genotoxic insults and was required for the recruitment of BLM and KU70, which are both essential for DNA double-strand break repair. Our study mechanistically links USP7 to epigenetic regulation and DNA repair. Moreover, these data support the pursuit of USP7 and PHF8 as potential targets for breast cancer intervention, especially in combination with chemo- or radiotherapies.
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83
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Sawicka M, Wanrooij PH, Darbari VC, Tannous E, Hailemariam S, Bose D, Makarova AV, Burgers PM, Zhang X. The Dimeric Architecture of Checkpoint Kinases Mec1ATR and Tel1ATM Reveal a Common Structural Organization. J Biol Chem 2016; 291:13436-47. [PMID: 27129217 PMCID: PMC4919432 DOI: 10.1074/jbc.m115.708263] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 12/21/2022] Open
Abstract
The phosphatidylinositol 3-kinase-related protein kinases are key regulators controlling a wide range of cellular events. The yeast Tel1 and Mec1·Ddc2 complex (ATM and ATR-ATRIP in humans) play pivotal roles in DNA replication, DNA damage signaling, and repair. Here, we present the first structural insight for dimers of Mec1·Ddc2 and Tel1 using single-particle electron microscopy. Both kinases reveal a head to head dimer with one major dimeric interface through the N-terminal HEAT (named after Huntingtin, elongation factor 3, protein phosphatase 2A, and yeast kinase TOR1) repeat. Their dimeric interface is significantly distinct from the interface of mTOR complex 1 dimer, which oligomerizes through two spatially separate interfaces. We also observe different structural organizations of kinase domains of Mec1 and Tel1. The kinase domains in the Mec1·Ddc2 dimer are located in close proximity to each other. However, in the Tel1 dimer they are fully separated, providing potential access of substrates to this kinase, even in its dimeric form.
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Affiliation(s)
- Marta Sawicka
- From the Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Paulina H Wanrooij
- the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Vidya C Darbari
- From the Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Elias Tannous
- the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Sarem Hailemariam
- the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Daniel Bose
- From the Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
| | - Alena V Makarova
- the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Peter M Burgers
- the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Xiaodong Zhang
- From the Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom and
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84
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Dickreuter E, Eke I, Krause M, Borgmann K, van Vugt MA, Cordes N. Targeting of β1 integrins impairs DNA repair for radiosensitization of head and neck cancer cells. Oncogene 2016; 35:1353-62. [PMID: 26073085 DOI: 10.1038/onc.2015.212] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 04/08/2015] [Accepted: 04/12/2015] [Indexed: 11/09/2022]
Abstract
β1 Integrin-mediated cell-extracellular matrix interactions allow cancer cell survival and confer therapy resistance. It was shown that inhibition of β1 integrins sensitizes cells to radiotherapy. Here, we examined the impact of β1 integrin targeting on the repair of radiation-induced DNA double-strand breaks (DSBs). β1 Integrin inhibition was accomplished using the monoclonal antibody AIIB2 and experiments were performed in three-dimensional cell cultures and tumor xenografts of human head and neck squamous cell carcinoma (HNSCC) cell lines. AIIB2, X-ray irradiation, small interfering RNA-mediated knockdown and Olaparib treatment were performed and residual DSB number, protein and gene expression, non-homologous end joining (NHEJ) activity as well as clonogenic survival were determined. β1 Integrin targeting impaired repair of radiogenic DSB (γH2AX/53BP1, pDNA-PKcs T2609 foci) in vitro and in vivo and reduced the protein expression of Ku70, Rad50 and Nbs1. Further, we identified Ku70, Ku80 and DNA-PKcs but not poly(ADP-ribose) polymerase (PARP)-1 to reside in the β1 integrin pathway. Intriguingly, combined inhibition of β1 integrin and PARP using Olaparib was significantly more effective than either treatment alone in non-irradiated and irradiated HNSCC cells. Here, we support β1 integrins as potential cancer targets and highlight a regulatory role for β1 integrins in the repair of radiogenic DNA damage via classical NHEJ. Further, the data suggest combined targeting of β1 integrin and PARP as promising approach for radiosensitization of HNSCC.
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Affiliation(s)
- E Dickreuter
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - I Eke
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- Department of Radiation Oncology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - M Krause
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- Department of Radiation Oncology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Radiooncology, Dresden, Germany
- German Cancer Consortium (DKTK), 01307 Dresden, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - K Borgmann
- Laboratory of Radiobiology and Experimental Radiooncology, Clinic of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - M A van Vugt
- Department of Medical Oncology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - N Cordes
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
- Department of Radiation Oncology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden - Rossendorf, Institute of Radiooncology, Dresden, Germany
- German Cancer Consortium (DKTK), 01307 Dresden, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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85
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Sakasai R, Iwabuchi K. The distinctive cellular responses to DNA strand breaks caused by a DNA topoisomerase I poison in conjunction with DNA replication and RNA transcription. Genes Genet Syst 2015; 90:187-94. [PMID: 26616758 DOI: 10.1266/ggs.15-00023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Camptothecin (CPT) inhibits DNA topoisomerase I (Top1) through a non-catalytic mechanism that stabilizes the Top1-DNA cleavage complex (Top1cc) and blocks the DNA re-ligation step, resulting in the accumulation in the genome of DNA single-strand breaks (SSBs), which are converted to secondary strand breaks when they collide with the DNA replication and RNA transcription machinery. DNA strand breaks mediated by replication, which have one DNA end, are distinct in repair from the DNA double-strand breaks (DSBs) that have two ends and are caused by ionizing radiation and other agents. In contrast to two-ended DSBs, such one-ended DSBs are preferentially repaired through the homologous recombination pathway. Conversely, the repair of one-ended DSBs by the non-homologous end-joining pathway is harmful for cells and leads to cell death. The choice of repair pathway has a crucial impact on cell fate and influences the efficacy of anticancer drugs such as CPT derivatives. In addition to replication-mediated one-ended DSBs, transcription also generates DNA strand breaks upon collision with the Top1cc. Some reports suggest that transcription-mediated DNA strand breaks correlate with neurodegenerative diseases. However, the details of the repair mechanisms of, and cellular responses to, transcription-mediated DNA strand breaks still remain unclear. In this review, combining our recent results and those of previous reports, we introduce and discuss the responses to CPT-induced DNA damage mediated by DNA replication and RNA transcription.
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Affiliation(s)
- Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University
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86
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Spratt DE, Evans MJ, Davis BJ, Doran MG, Lee MX, Shah N, Wongvipat J, Carnazza KE, Klee GG, Polkinghorn W, Tindall DJ, Lewis JS, Sawyers CL. Androgen Receptor Upregulation Mediates Radioresistance after Ionizing Radiation. Cancer Res 2015; 75:4688-96. [PMID: 26432404 DOI: 10.1158/0008-5472.can-15-0892] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 08/11/2015] [Indexed: 12/19/2022]
Abstract
Clinical trials have established the benefit of androgen deprivation therapy (ADT) combined with radiotherapy in prostate cancer. ADT sensitizes prostate cancer to radiotherapy-induced death at least in part through inhibition of DNA repair machinery, but for unknown reasons, adjuvant ADT provides further survival benefits. Here, we show that androgen receptor (AR) expression and activity are durably upregulated following radiotherapy in multiple human prostate cancer models in vitro and in vivo. Moreover, the degree of AR upregulation correlates with survival in vitro and time to tumor progression in animal models. We also provide evidence of AR pathway upregulation, measured by a rise in serum levels of AR-regulated hK2 protein, in nearly 20% of patients after radiotherapy. Furthermore, these men were three-fold more likely to experience subsequent biochemical failure. Collectively, these data demonstrate that radiotherapy can upregulate AR signaling after therapy to an extent that negatively affects disease progression and/or survival.
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Affiliation(s)
- Daniel E Spratt
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Radiology and Molecular the Molecular Pharmacology & Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael J Evans
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian J Davis
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Michael G Doran
- Department of Radiology and Molecular the Molecular Pharmacology & Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Man Xia Lee
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neel Shah
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John Wongvipat
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kathryn E Carnazza
- Department of Radiology and Molecular the Molecular Pharmacology & Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - George G Klee
- Departments of Urology and Biochemistry/Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - William Polkinghorn
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Donald J Tindall
- Departments of Urology and Biochemistry/Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jason S Lewis
- Department of Radiology and Molecular the Molecular Pharmacology & Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Charles L Sawyers
- Human Oncology Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
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87
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Liu P, Gan W, Chin YR, Ogura K, Guo J, Zhang J, Wang B, Blenis J, Cantley LC, Toker A, Su B, Wei W. PtdIns(3,4,5)P3-Dependent Activation of the mTORC2 Kinase Complex. Cancer Discov 2015; 5:1194-209. [PMID: 26293922 DOI: 10.1158/2159-8290.cd-15-0460] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 08/18/2015] [Indexed: 12/15/2022]
Abstract
UNLABELLED mTOR serves as a central regulator of cell growth and metabolism by forming two distinct complexes, mTORC1 and mTORC2. Although mechanisms of mTORC1 activation by growth factors and amino acids have been extensively studied, the upstream regulatory mechanisms leading to mTORC2 activation remain largely elusive. Here, we report that the pleckstrin homology (PH) domain of SIN1, an essential and unique component of mTORC2, interacts with the mTOR kinase domain to suppress mTOR activity. More importantly, PtdIns(3,4,5)P3, but not other PtdInsPn species, interacts with SIN1-PH to release its inhibition on the mTOR kinase domain, thereby triggering mTORC2 activation. Mutating critical SIN1 residues that mediate PtdIns(3,4,5)P3 interaction inactivates mTORC2, whereas mTORC2 activity is pathologically increased by patient-derived mutations in the SIN1-PH domain, promoting cell growth and tumor formation. Together, our study unravels a PI3K-dependent mechanism for mTORC2 activation, allowing mTORC2 to activate AKT in a manner that is regulated temporally and spatially by PtdIns(3,4,5)P3. SIGNIFICANCE The SIN1-PH domain interacts with the mTOR kinase domain to suppress mTOR activity, and PtdIns(3,4,5)P3 binds the SIN1-PH domain to release its inhibition on the mTOR kinase domain, leading to mTORC2 activation. Cancer patient-derived SIN1-PH domain mutations gain oncogenicity by loss of suppressing mTOR activity as a means to facilitate tumorigenesis.
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Affiliation(s)
- Pengda Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Wenjian Gan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Y Rebecca Chin
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Kohei Ogura
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Bin Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - John Blenis
- Cancer Center at Weill Cornell Medical College and New York-Presbyterian Hospital, New York, New York
| | - Lewis C Cantley
- Cancer Center at Weill Cornell Medical College and New York-Presbyterian Hospital, New York, New York
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Bing Su
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China. Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University, New Haven, Connecticut.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
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88
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Glucocorticoid Receptor Transcriptional Activation via the BRG1-Dependent Recruitment of TOP2β and Ku70/86. Mol Cell Biol 2015; 35:2799-817. [PMID: 26055322 DOI: 10.1128/mcb.00230-15] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/27/2015] [Indexed: 12/20/2022] Open
Abstract
BRG1, the central ATPase of the human SWI/SNF complex, is critical for biological functions, including nuclear receptor (NR)-regulated transcription. Analysis of BRG1 mutants demonstrated that functional motifs outside the ATPase domain are important for transcriptional activity. In the course of experiments examining protein interactions mediated through these domains, Ku70 (XRCC6) was found to associate with a BRG1 fragment encompassing the conserved helicase-SANT-associated (HSA) and BRK domains of BRG1. Subsequent transcriptional activation assays and chromatin immunoprecipitation studies showed that Ku70/86 and components of the topoisomerase IIβ (TOP2β)/poly(ADP ribose) polymerase 1 (PARP1) complex are necessary for NR-mediated SWI/SNF-dependent transcriptional activation from endogenous promoters. In addition to establishing Ku-BRG1 binding and TOP2β/PARP1 recruitment by nuclear receptor transactivation, we demonstrate that the transient appearance of glucocorticoid receptor (GR)/BRG1-dependent, TOP2β-mediated double-strand DNA breaks is required for efficient GR-stimulated transcription. Taken together, these results suggest that a direct interaction between Ku70/86 and BRG1 brings together SWI/SNF remodeling capabilities and TOP2β activity to enhance the transcriptional response to hormone stimulation.
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89
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Woods DS, Sears CR, Turchi JJ. Recognition of DNA Termini by the C-Terminal Region of the Ku80 and the DNA-Dependent Protein Kinase Catalytic Subunit. PLoS One 2015; 10:e0127321. [PMID: 25978375 PMCID: PMC4433226 DOI: 10.1371/journal.pone.0127321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/13/2015] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) can be generated by endogenous cellular processes or exogenous agents in mammalian cells. These breaks are highly variable with respect to DNA sequence and structure and all are recognized in some context by the DNA-dependent protein kinase (DNA-PK). DNA-PK is a critical component necessary for the recognition and repair of DSBs via non-homologous end joining (NHEJ). Previously studies have shown that DNA-PK responds differentially to variations in DSB structure, but how DNA-PK senses differences in DNA substrate sequence and structure is unknown. Here we explore the enzymatic mechanisms by which DNA-PK is activated by various DNA substrates and provide evidence that the DNA-PK is differentially activated by DNA structural variations as a function of the C-terminal region of Ku80. Discrimination based on terminal DNA sequence variations, on the other hand, is independent of the Ku80 C-terminal interactions and likely results exclusively from DNA-dependent protein kinase catalytic subunit interactions with the DNA. We also show that sequence differences in DNA termini can drastically influence DNA repair through altered DNA-PK activation. These results indicate that even subtle differences in DNA substrates influence DNA-PK activation and ultimately the efficiency of DSB repair.
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Affiliation(s)
- Derek S. Woods
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Catherine R. Sears
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - John J. Turchi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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90
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Maeshima K, Kaizu K, Tamura S, Nozaki T, Kokubo T, Takahashi K. The physical size of transcription factors is key to transcriptional regulation in chromatin domains. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064116. [PMID: 25563431 DOI: 10.1088/0953-8984/27/6/064116] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Genetic information, which is stored in the long strand of genomic DNA as chromatin, must be scanned and read out by various transcription factors. First, gene-specific transcription factors, which are relatively small (∼50 kDa), scan the genome and bind regulatory elements. Such factors then recruit general transcription factors, Mediators, RNA polymerases, nucleosome remodellers, and histone modifiers, most of which are large protein complexes of 1-3 MDa in size. Here, we propose a new model for the functional significance of the size of transcription factors (or complexes) for gene regulation of chromatin domains. Recent findings suggest that chromatin consists of irregularly folded nucleosome fibres (10 nm fibres) and forms numerous condensed domains (e.g., topologically associating domains). Although the flexibility and dynamics of chromatin allow repositioning of genes within the condensed domains, the size exclusion effect of the domain may limit accessibility of DNA sequences by transcription factors. We used Monte Carlo computer simulations to determine the physical size limit of transcription factors that can enter condensed chromatin domains. Small gene-specific transcription factors can penetrate into the chromatin domains and search their target sequences, whereas large transcription complexes cannot enter the domain. Due to this property, once a large complex binds its target site via gene-specific factors it can act as a 'buoy' to keep the target region on the surface of the condensed domain and maintain transcriptional competency. This size-dependent specialization of target-scanning and surface-tethering functions could provide novel insight into the mechanisms of various DNA transactions, such as DNA replication and repair/recombination.
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Affiliation(s)
- Kazuhiro Maeshima
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan. Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
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91
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Ascher DB, Jubb HC, Pires DEV, Ochi T, Higueruelo A, Blundell TL. Protein-Protein Interactions: Structures and Druggability. MULTIFACETED ROLES OF CRYSTALLOGRAPHY IN MODERN DRUG DISCOVERY 2015. [DOI: 10.1007/978-94-017-9719-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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92
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Rivera-Calzada A, López-Perrote A, Melero R, Boskovic J, Muñoz-Hernández H, Martino F, Llorca O. Structure and Assembly of the PI3K-like Protein Kinases (PIKKs) Revealed by Electron Microscopy. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.2.36] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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The DNA-dependent protein kinase: A multifunctional protein kinase with roles in DNA double strand break repair and mitosis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 117:194-205. [PMID: 25550082 DOI: 10.1016/j.pbiomolbio.2014.12.003] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 11/21/2022]
Abstract
The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemistry, structure and function of DNA-PK, its roles in DNA double strand break repair and its newly described roles in mitosis and other cellular processes.
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94
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Jain A, Arauz E, Aggarwal V, Ikon N, Chen J, Ha T. Stoichiometry and assembly of mTOR complexes revealed by single-molecule pulldown. Proc Natl Acad Sci U S A 2014; 111:17833-8. [PMID: 25453101 PMCID: PMC4273350 DOI: 10.1073/pnas.1419425111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) kinase is a master regulator of cellular, developmental, and metabolic processes. Deregulation of mTOR signaling is implicated in numerous human diseases including cancer and diabetes. mTOR functions as part of either of the two multisubunit complexes, mTORC1 and mTORC2, but molecular details about the assembly and oligomerization of mTORCs are currently lacking. We use the single-molecule pulldown (SiMPull) assay that combines principles of conventional pulldown assays with single-molecule fluorescence microscopy to investigate the stoichiometry and assembly of mTORCs. After validating our approach with mTORC1, confirming a dimeric assembly as previously reported, we show that all major components of mTORC2 exist in two copies per complex, indicating that mTORC2 assembles as a homodimer. Interestingly, each mTORC component, when free from the complexes, is present as a monomer and no single subunit serves as the dimerizing component. Instead, our data suggest that dimerization of mTORCs is the result of multiple subunits forming a composite surface. SiMPull also allowed us to distinguish complex disassembly from stoichiometry changes. Physiological conditions that abrogate mTOR signaling such as nutrient deprivation or energy stress did not alter the stoichiometry of mTORCs. On the other hand, rapamycin treatment leads to transient appearance of monomeric mTORC1 before complete disruption of the mTOR-raptor interaction, whereas mTORC2 stoichiometry is unaffected. These insights into assembly of mTORCs may guide future mechanistic studies and exploration of therapeutic potential.
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Affiliation(s)
- Ankur Jain
- Center for Biophysics and Computational Biology, Institute for Genomic Biology
| | - Edwin Arauz
- Department of Cell and Developmental Biology
| | - Vasudha Aggarwal
- Center for Biophysics and Computational Biology, Institute for Genomic Biology
| | - Nikita Ikon
- Department of Cell and Developmental Biology
| | - Jie Chen
- Department of Cell and Developmental Biology,
| | - Taekjip Ha
- Center for Biophysics and Computational Biology, Institute for Genomic Biology, Department of Physics, and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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95
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Baretić D, Williams RL. PIKKs--the solenoid nest where partners and kinases meet. Curr Opin Struct Biol 2014; 29:134-42. [PMID: 25460276 DOI: 10.1016/j.sbi.2014.11.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 11/15/2014] [Accepted: 11/18/2014] [Indexed: 11/29/2022]
Abstract
The recent structure of a truncated mTOR in a complex with mLST8 has provided a basic framework for understanding all of the phosphoinositide 3-kinase (PI3K)-related kinases (PIKKs): mTOR, ATM, ATR, SMG-1, TRRAP and DNA-PK. The PIKK kinase domain is encircled by the FAT domain, a helical solenoid that is present in all PIKKs. PIKKs also have an extensive helical solenoid N-terminal to the FAT domain for which there is limited structural information. This N-terminal helical solenoid is essential for binding proteins that associate with the PIKKs to regulate their activity and cellular localization.
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Affiliation(s)
- Domagoj Baretić
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Roger L Williams
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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96
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Han J, Won EJ, Kim IC, Yim JH, Lee SJ, Lee JS. Sublethal gamma irradiation affects reproductive impairment and elevates antioxidant enzyme and DNA repair activities in the monogonont rotifer Brachionus koreanus. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 155:101-109. [PMID: 25000471 DOI: 10.1016/j.aquatox.2014.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 06/03/2023]
Abstract
To examine the effects of gamma radiation on marine organisms, we irradiated several doses of gamma ray to the microzooplankton Brachionus koreanus, and measured in vivo and in vitro endpoints including the survival rate, lifespan, fecundity, population growth, gamma ray-induced oxidative stress, and modulated patterns of enzyme activities and gene expressions after DNA damage. After gamma radiation, no individuals showed any mortality within 96 h even at a high intensity (1200 Gy). However, a reduced fecundity (e.g. cumulated number of offspring) of B. koreanus at over 150 Gy was observed along with a slight decrease in lifespan. At 150 Gy and 200 Gy, the reduced fecundity of the rotifers led to a significant decrease in population growth, although in the second generation the population growth pattern was not affected even at 200 Gy when compared to the control group. At sub-lethal doses, reactive oxygen species (ROS) levels dose-dependently increased with GST enzyme activity. In addition, up-regulations of the antioxidant and chaperoning genes in response to gamma radiation were able to recover cellular damages, and life table parameters were significantly influenced, particularly with regard to fecundity. DNA repair-associated genes showed significantly up-regulated expression patterns in response to sublethal doses (150 and 200 Gy), as shown in the expression of the gamma-irradiated B. koreanus p53 gene, suggesting that these sublethal doses were not significantly fatal to B. koreanus but induced DNA damages leading to a decrease of the population size.
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Affiliation(s)
- Jeonghoon Han
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Eun-Ji Won
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Il-Chan Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon 406-840, South Korea
| | - Joung Han Yim
- Division of Life Sciences, Korea Polar Research Institute, Incheon 406-840, South Korea
| | - Su-Jae Lee
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
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97
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Multifunctional role of ATM/Tel1 kinase in genome stability: from the DNA damage response to telomere maintenance. BIOMED RESEARCH INTERNATIONAL 2014; 2014:787404. [PMID: 25247188 PMCID: PMC4163350 DOI: 10.1155/2014/787404] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/28/2014] [Accepted: 08/07/2014] [Indexed: 12/19/2022]
Abstract
The mammalian protein kinase ataxia telangiectasia mutated (ATM) is a key regulator of the DNA double-strand-break response and belongs to the evolutionary conserved phosphatidylinositol-3-kinase-related protein kinases. ATM deficiency causes ataxia telangiectasia (AT), a genetic disorder that is characterized by premature aging, cerebellar neuropathy, immunodeficiency, and predisposition to cancer. AT cells show defects in the DNA damage-response pathway, cell-cycle control, and telomere maintenance and length regulation. Likewise, in Saccharomyces cerevisiae, haploid strains defective in the TEL1 gene, the ATM ortholog, show chromosomal aberrations and short telomeres. In this review, we outline the complex role of ATM/Tel1 in maintaining genomic stability through its control of numerous aspects of cellular survival. In particular, we describe how ATM/Tel1 participates in the signal transduction pathways elicited by DNA damage and in telomere homeostasis and its importance as a barrier to cancer development.
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98
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Abstract
SIGNIFICANCE Ionizing radiation (IR) is an effective and commonly employed treatment in the management of more than half of human malignancies. Because IR's ability to control tumors mainly relies on DNA damage, the cell's DNA damage response and repair (DRR) processes may hold the key to determining tumor responses. IR-induced DNA damage activates a number of DRR signaling cascades that control cell cycle arrest, DNA repair, and the cell's fate. DNA double-strand breaks (DSBs) generated by IR are the most lethal form of damage, and are mainly repaired via either homologous recombination (HR) or nonhomologous end-joining (NHEJ) pathways. RECENT ADVANCES In recent years, immense effort to understand and exploit the differences in the use of these repair pathways between tumors and normal cells will allow for an increase in tumor cell killing and a decrease in normal tissue injury. CRITICAL ISSUES Regulation of the two major DSB repair mechanisms (HR and NHEJ) and new strategies, which may improve the therapeutic ratio of radiation by differentially targeting HR and NHEJ function in tumor and normal tissues, is of intense interest currently, and is the focus of this article. FUTURE DIRECTIONS By utilizing the strategies outlined above, it may be possible to exploit differences between tumor and somatic cell DRR pathways, specifically their DSB repair mechanisms, to improve the therapeutic ratio of IR.
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Affiliation(s)
- Wil L Santivasi
- Department of Radiation Oncology, The Ohio State University College of Medicine , Columbus, Ohio
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99
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Villarreal SA, Stewart PL. CryoEM and image sorting for flexible protein/DNA complexes. J Struct Biol 2014; 187:76-83. [DOI: 10.1016/j.jsb.2013.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/13/2013] [Accepted: 12/05/2013] [Indexed: 12/11/2022]
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100
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Liu C, Srihari S, Cao KAL, Chenevix-Trench G, Simpson PT, Ragan MA, Khanna KK. A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy. Nucleic Acids Res 2014; 42:6106-27. [PMID: 24792170 PMCID: PMC4041457 DOI: 10.1093/nar/gku284] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 02/06/2023] Open
Abstract
DNA-damage response machinery is crucial to maintain the genomic integrity of cells, by enabling effective repair of even highly lethal lesions such as DNA double-strand breaks (DSBs). Defects in specific genes acquired through mutations, copy-number alterations or epigenetic changes can alter the balance of these pathways, triggering cancerous potential in cells. Selective killing of cancer cells by sensitizing them to further DNA damage, especially by induction of DSBs, therefore requires careful modulation of DSB-repair pathways. Here, we review the latest knowledge on the two DSB-repair pathways, homologous recombination and non-homologous end joining in human, describing in detail the functions of their components and the key mechanisms contributing to the repair. Such an in-depth characterization of these pathways enables a more mechanistic understanding of how cells respond to therapies, and suggests molecules and processes that can be explored as potential therapeutic targets. One such avenue that has shown immense promise is via the exploitation of synthetic lethal relationships, for which the BRCA1-PARP1 relationship is particularly notable. Here, we describe how this relationship functions and the manner in which cancer cells acquire therapy resistance by restoring their DSB repair potential.
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Affiliation(s)
- Chao Liu
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Kim-Anh Lê Cao
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia Queensland Facility for Advanced Bioinformatics, The University of Queensland, St. Lucia 4072, Australia
| | | | - Peter T Simpson
- The University of Queensland Centre for Clinical Research, Herston, Brisbane, QLD 4029, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Kum Kum Khanna
- Queensland Facility for Advanced Bioinformatics, The University of Queensland, St. Lucia 4072, Australia
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