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Hou J, Lu M, Guo J, Wu J, Wang C, Zhou PK, Ma T. DNA-PKcs, a player winding and dancing with RNA metabolism and diseases. Cell Mol Biol Lett 2025; 30:25. [PMID: 40038612 PMCID: PMC11877767 DOI: 10.1186/s11658-025-00703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 02/11/2025] [Indexed: 03/06/2025] Open
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key kinase in the DNA repair process that responds to DNA damage caused by various factors and maintains genomic stability. However, DNA-PKcs is overexpressed in some solid tumors and is frequently associated with poor prognosis. DNA-PKcs was initially identified as a part of the transcription complex. In recent years, many studies have focused on its nonclassical functions, including transcriptional regulation, metabolism, innate immunity, and inflammatory response. Given the pleiotropic roles of DNA-PKcs in tumors, pharmacological inhibition of DNA-PK can exert antitumor effects and may serve as a potential target for tumor therapy in the future. This review summarizes several aspects of DNA-PKcs regulation of RNA metabolism, including its impact on transcriptional machinery, alternative splicing, and interaction with noncoding RNAs, and provides insights into DNA-PKcs beyond its DNA damage repair function.
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Affiliation(s)
- Jiabao Hou
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Mingjun Lu
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Jingwei Guo
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Jinghong Wu
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Chenyang Wang
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China
| | - Ping-Kun Zhou
- Beijing Key Laboratory for Radiobiology Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Teng Ma
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, 101149, China.
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2
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Goff NJ, Mikhova M, Schmidt JC, Meek K. DNA-PK: A synopsis beyond synapsis. DNA Repair (Amst) 2024; 141:103716. [PMID: 38996771 PMCID: PMC11369974 DOI: 10.1016/j.dnarep.2024.103716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024]
Abstract
Given its central role in life, DNA is remarkably easy to damage. Double strand breaks (DSBs) are the most toxic form of DNA damage, and DSBs pose the greatest danger to genomic integrity. In higher vertebrates, the non-homologous end joining pathway (NHEJ) is the predominate pathway that repairs DSBs. NHEJ has three steps: 1) DNA end recognition by the DNA dependent protein kinase [DNA-PK], 2) DNA end-processing by numerous NHEJ accessory factors, and 3) DNA end ligation by the DNA ligase IV complex (LX4). Although this would appear to be a relatively simple mechanism, it has become increasingly apparent that it is not. Recently, much insight has been derived regarding the mechanism of non-homologous end joining through a proliferation of cryo-EM studies, structure-function mutational experiments informed by these new structural data, and novel single-molecule imaging approaches. An emerging consensus in the field is that NHEJ progresses from initial DSB end recognition by DNA-PK to synapsis of the two DNA ends in a long-range synaptic complex where ends are held too far apart (115 Å) for ligation, and then progress to a short-range synaptic complex where ends are positioned close enough for ligation. What was surprising from these structural studies was the observation of two distinct types of DNA-PK dimers that represent NHEJ long-range complexes. In this review, we summarize current knowledge about the function of the distinct NHEJ synaptic complexes and align this new information with emerging cellular single-molecule microscopy studies as well as with previous studies of DNA-PK's function in repair.
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Affiliation(s)
- Noah J Goff
- College of Veterinary Medicine, Department of Microbiology Genetics & Immunology, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Mariia Mikhova
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jens C Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA; Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA
| | - Katheryn Meek
- College of Veterinary Medicine, Department of Microbiology Genetics & Immunology, Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
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3
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Han Y, Zhao H, Li G, Jia J, Guo H, Tan J, Sun X, Li S, Ran Q, Bai C, Gu Y, Li Z, Guan H, Gao S, Zhou PK. GCN5 mediates DNA-PKcs crotonylation for DNA double-strand break repair and determining cancer radiosensitivity. Br J Cancer 2024; 130:1621-1634. [PMID: 38575732 PMCID: PMC11091118 DOI: 10.1038/s41416-024-02636-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND DNA double-strand break (DSB) induction and repair are important events for determining cell survival and the outcome of cancer radiotherapy. The DNA-dependent protein kinase (DNA-PK) complex functions at the apex of DSBs repair, and its assembly and activity are strictly regulated by post-translation modifications (PTMs)-associated interactions. However, the PTMs of the catalytic subunit DNA-PKcs and how they affect DNA-PKcs's functions are not fully understood. METHODS Mass spectrometry analyses were performed to identify the crotonylation sites of DNA-PKcs in response to γ-ray irradiation. Co-immunoprecipitation (Co-IP), western blotting, in vitro crotonylation assays, laser microirradiation assays, in vitro DNA binding assays, in vitro DNA-PK assembly assays and IF assays were employed to confirm the crotonylation, identify the crotonylase and decrotonylase, and elucidate how crotonylation regulates the activity and function of DNA-PKcs. Subcutaneous xenografts of human HeLa GCN5 WT or HeLa GCN5 siRNA cells in BALB/c nude mice were generated and utilized to assess tumor proliferation in vivo after radiotherapy. RESULTS Here, we reveal that K525 is an important site of DNA-PKcs for crotonylation, and whose level is sharply increased by irradiation. The histone acetyltransferase GCN5 functions as the crotonylase for K525-Kcr, while HDAC3 serves as its dedicated decrotonylase. K525 crotonylation enhances DNA binding activity of DNA-PKcs, and facilitates assembly of the DNA-PK complex. Furthermore, GCN5-mediated K525 crotonylation is indispensable for DNA-PKcs autophosphorylation and the repair of double-strand breaks in the NHEJ pathway. GCN5 suppression significantly sensitizes xenograft tumors of mice to radiotherapy. CONCLUSIONS Our study defines K525 crotonylation of DNA-PKcs is important for the DNA-PK complex assembly and DSBs repair activity via NHEJ pathway. Targeting GCN5-mediated K525 Kcr of DNA-PKcs may be a promising therapeutic strategy for improving the outcome of cancer radiotherapy.
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Affiliation(s)
- Yang Han
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Hongling Zhao
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Gang Li
- School of Public Health, Institute for Environmental Medicine and Radiation Hygiene, University of South China, Hengyang, China
- Department of Hospital Infection Control, Shenzhen Luohu Peoples Hospital, Shenzhen, China
| | - Jin Jia
- School of Medicine, University of South China, Hengyang, China
| | - Hejiang Guo
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jinpeng Tan
- School of Medicine, University of South China, Hengyang, China
| | - Xingyao Sun
- School of Medicine, University of South China, Hengyang, China
| | - Saiyu Li
- School of life Sciences, Hebei University, Baoding, China
| | - Qian Ran
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China
| | - Chenjun Bai
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yongqing Gu
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - ZhongJun Li
- Laboratory of Radiation Biology, Laboratory Medicine Center, Department of Blood Transfusion, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China.
| | - Hua Guan
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Shanshan Gao
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.
- School of Public Health, Institute for Environmental Medicine and Radiation Hygiene, University of South China, Hengyang, China.
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4
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Vogt A, He Y. Structure and mechanism in non-homologous end joining. DNA Repair (Amst) 2023; 130:103547. [PMID: 37556875 PMCID: PMC10528545 DOI: 10.1016/j.dnarep.2023.103547] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023]
Abstract
DNA double-stranded breaks (DSBs) are a particularly challenging form of DNA damage to repair because the damaged DNA must not only undergo the chemical reactions responsible for returning it to its original state, but, additionally, the two free ends can become physically separated in the nucleus and must be bridged prior to repair. In nonhomologous end joining (NHEJ), one of the major pathways of DSB repair, repair is carried out by a number of repair factors capable of binding to and directly joining DNA ends. It has been unclear how these processes are carried out at a molecular level, owing in part to the lack of structural evidence describing the coordination of the NHEJ factors with each other and a DNA substrate. Advances in cryo-Electron Microscopy (cryo-EM), allowing for the structural characterization of large protein complexes that would be intractable using other techniques, have led to the visualization several key steps of the NHEJ process, which support a model of sequential assembly of repair factors at the DSB, followed by end-bridging mediated by protein-protein complexes and transition to full synapsis. Here we examine the structural evidence for these models, devoting particular attention to recent work identifying a new NHEJ intermediate state and incorporating new NHEJ factors into the general mechanism. We also discuss the evolving understanding of end-bridging mechanisms in NHEJ and DNA-PKcs's role in mediating DSB repair.
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Affiliation(s)
- Alex Vogt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, USA.
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5
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Sakasai R, Matsui T, Sunatani Y, Iwabuchi K. UbcH5c-dependent activation of DNA-dependent protein kinase in response to replication-mediated DNA double-strand breaks. Biochem Biophys Res Commun 2023; 668:42-48. [PMID: 37244033 DOI: 10.1016/j.bbrc.2023.05.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/29/2023]
Abstract
Camptothecin (CPT) exhibits strong cytotoxicity by inducing DNA double-strand breaks (DSBs) through DNA replication. Unlike radiation-induced DSBs, which have two DNA ends, CPT-induced DSBs are considered to have only one DNA end. However, the differences in cellular responses to one-ended and two-ended DSBs are not well understood. Our previous study showed that proteasome inhibitor treatment suppressed CPT-induced activation of DNA-PK, a factor required for non-homologous end-joining in DSB repair, suggesting that the ubiquitin-proteasome pathway is involved in DNA-PK activation in response to one-ended DSBs. To identify the ubiquitination factors required for DNA-PK activation, we screened an siRNA library against E2 ubiquitin-conjugating enzymes and identified UbcH5c. Knockdown of UbcH5c suppressed DNA-PK activation caused by CPT, but not by the radio-mimetic drug neocarzinostatin. UbcH5c-dependent DNA-PK activation occurred independent of DNA end resection. Furthermore, loss of UbcH5c reduced DNA-PK-dependent chromosomal aberrations and suppressed the activation of cell cycle checkpoint in response to CPT. These results suggest that UbcH5c regulates DNA-PK activation in response to one-ended DSBs caused by replication fork collapse. To our knowledge, this is the first report of a DSB repair-related factor that is differentially involved in the response to one- and two-ended DSBs.
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Affiliation(s)
- Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Tadashi Matsui
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Yumi Sunatani
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan.
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6
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Taffoni C, Marines J, Chamma H, Guha S, Saccas M, Bouzid A, Valadao AC, Maghe C, Jardine J, Park MK, Polak K, De Martino M, Vanpouille‐Box C, Del Rio M, Gongora C, Gavard J, Bidère N, Song MS, Pineau D, Hugnot J, Kissa K, Fontenille L, Blanchet FP, Vila IK, Laguette N. DNA damage repair kinase DNA-PK and cGAS synergize to induce cancer-related inflammation in glioblastoma. EMBO J 2023; 42:e111961. [PMID: 36574362 PMCID: PMC10068334 DOI: 10.15252/embj.2022111961] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
Cytosolic DNA promotes inflammatory responses upon detection by the cyclic GMP-AMP (cGAMP) synthase (cGAS). It has been suggested that cGAS downregulation is an immune escape strategy harnessed by tumor cells. Here, we used glioblastoma cells that show undetectable cGAS levels to address if alternative DNA detection pathways can promote pro-inflammatory signaling. We show that the DNA-PK DNA repair complex (i) drives cGAS-independent IRF3-mediated type I Interferon responses and (ii) that its catalytic activity is required for cGAS-dependent cGAMP production and optimal downstream signaling. We further show that the cooperation between DNA-PK and cGAS favors the expression of chemokines that promote macrophage recruitment in the tumor microenvironment in a glioblastoma model, a process that impairs early tumorigenesis but correlates with poor outcome in glioblastoma patients. Thus, our study supports that cGAS-dependent signaling is acquired during tumorigenesis and that cGAS and DNA-PK activities should be analyzed concertedly to predict the impact of strategies aiming to boost tumor immunogenicity.
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Affiliation(s)
- Clara Taffoni
- IGH, Université de Montpellier, CNRSMontpellierFrance
| | - Johanna Marines
- IGH, Université de Montpellier, CNRSMontpellierFrance
- Azelead©MontpellierFrance
| | - Hanane Chamma
- IGH, Université de Montpellier, CNRSMontpellierFrance
| | | | | | - Amel Bouzid
- IGH, Université de Montpellier, CNRSMontpellierFrance
| | | | - Clément Maghe
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'AngersNantesFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Jane Jardine
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'AngersNantesFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Mi Kyung Park
- Department of Molecular and Cellular OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | | | - Mara De Martino
- Department of Radiation Oncology, Weill Cornell MedicineNew YorkNYUSA
| | | | - Maguy Del Rio
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, ICMMontpellierFrance
| | - Celine Gongora
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, ICMMontpellierFrance
| | - Julie Gavard
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'AngersNantesFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
- Institut de Cancérologie de l'Ouest (ICO)Saint‐HerblainFrance
| | - Nicolas Bidère
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'AngersNantesFrance
- Equipe Labellisée Ligue Contre le CancerParisFrance
| | - Min Sup Song
- Department of Molecular and Cellular OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Donovan Pineau
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERMMontpellierFrance
| | - Jean‐Philippe Hugnot
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERMMontpellierFrance
| | - Karima Kissa
- Université de Montpellier, CNRS UMR 5235MontpellierFrance
| | | | - Fabien P Blanchet
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRSMontpellierFrance
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7
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Tao X, Song J, Song Y, Zhang Y, Yang J, Zhang P, Zhang D, Chen D, Sun Q. Ku proteins promote DNA binding and condensation of cyclic GMP-AMP synthase. Cell Rep 2022; 40:111310. [PMID: 36070696 DOI: 10.1016/j.celrep.2022.111310] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/30/2022] [Accepted: 08/12/2022] [Indexed: 11/03/2022] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that plays a critical role in regulating antiviral signaling. cGAS binds to DNA and catalyzes the synthesis of cyclic GMP-AMP (cGAMP), which is essential for downstream signal transduction. The antiviral response is a rapid biological process; however, cGAS itself has relatively low DNA binding affinity, implying that formation of the cGAS-DNA complex requires an additional factor(s) that promotes cGAS-DNA binding, allowing efficient antiviral signal transduction. Here, we report that the Ku proteins (Ku80 and Ku70) directly interact with cGAS and positively regulate cGAS-mediated antiviral signaling. Mechanistically, we find that the interaction of the Ku proteins with cGAS significantly increases the DNA-binding affinity of cGAS and promotes cGAS condensation in the cytosol, thereby enhancing cGAS catalytic activity. Our results show that the Ku proteins are critical partners of cGAS in sensing DNA virus infection and ensuring efficient innate immune signal transduction.
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Affiliation(s)
- Xinyue Tao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Jia #3 Datun Road, Chaoyang District, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiali Song
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Ying Song
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Yao Zhang
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Jing Yang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Jia #3 Datun Road, Chaoyang District, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengfei Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Jia #3 Datun Road, Chaoyang District, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Dechong Zhang
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China.
| | - Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Jia #3 Datun Road, Chaoyang District, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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8
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Fowler FC, Chen BR, Zolnerowich N, Wu W, Pavani R, Paiano J, Peart C, Chen Z, Nussenzweig A, Sleckman BP, Tyler JK. DNA-PK promotes DNA end resection at DNA double strand breaks in G 0 cells. eLife 2022; 11:e74700. [PMID: 35575473 PMCID: PMC9122494 DOI: 10.7554/elife.74700] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/06/2022] [Indexed: 11/16/2022] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs are predominately repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 murine and human cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in proliferating cells at the G1 or G2 phase of the cell cycle was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, which has important implications for DNA DSB repair in quiescent cells.
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Affiliation(s)
- Faith C Fowler
- Weill Cornell Medicine Pharmacology Graduate ProgramNew YorkUnited States
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - Bo-Ruei Chen
- Department of Medicine, Division of Hematology and Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | | | - Wei Wu
- Laboratory of Genome Integrity, National Cancer InstituteBethesdaUnited States
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer InstituteBethesdaUnited States
| | - Jacob Paiano
- Laboratory of Genome Integrity, National Cancer InstituteBethesdaUnited States
| | - Chelsea Peart
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - Zulong Chen
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer InstituteBethesdaUnited States
| | - Barry P Sleckman
- Department of Medicine, Division of Hematology and Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at BirminghamBirminghamUnited States
| | - Jessica K Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
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9
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Sui H, Hao M, Chang W, Imamichi T. The Role of Ku70 as a Cytosolic DNA Sensor in Innate Immunity and Beyond. Front Cell Infect Microbiol 2021; 11:761983. [PMID: 34746031 PMCID: PMC8566972 DOI: 10.3389/fcimb.2021.761983] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/06/2021] [Indexed: 12/24/2022] Open
Abstract
Human Ku70 is a well-known endogenous nuclear protein involved in the non-homologous end joining pathway to repair double-stranded breaks in DNA. However, Ku70 has been studied in multiple contexts and grown into a multifunctional protein. In addition to the extensive functional study of Ku70 in DNA repair process, many studies have emphasized the role of Ku70 in various other cellular processes, including apoptosis, aging, and HIV replication. In this review, we focus on discussing the role of Ku70 in inducing interferons and proinflammatory cytokines as a cytosolic DNA sensor. We explored the unique structure of Ku70 binding with DNA; illustrated, with evidence, how Ku70, as a nuclear protein, responds to extracellular DNA stimulation; and summarized the mechanisms of the Ku70-involved innate immune response pathway. Finally, we discussed several new strategies to modulate Ku70-mediated innate immune response and highlighted some potential physiological insights based on the role of Ku70 in innate immunity.
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Affiliation(s)
- Hongyan Sui
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | | | | | - Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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10
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Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W. Structure of an activated DNA-PK and its implications for NHEJ. Mol Cell 2020; 81:801-810.e3. [PMID: 33385326 DOI: 10.1016/j.molcel.2020.12.015] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/17/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of HEAT repeats. These kinases are activated in response to cellular stress signals, but the mechanisms governing activation and regulation remain unresolved. For DNA-PK, all existing structures represent inactive states with resolution limited to 4.3 Å at best. Here, we report the cryoelectron microscopy (cryo-EM) structures of DNA-PKcs (DNA-PK catalytic subunit) bound to a DNA end or complexed with Ku70/80 and DNA in both inactive and activated forms at resolutions of 3.7 Å overall and 3.2 Å for FATKINs. These structures reveal the sequential transition of DNA-PK from inactive to activated forms. Most notably, activation of the kinase involves previously unknown stretching and twisting within individual solenoid segments and loosens DNA-end binding. This unprecedented structural plasticity of helical repeats may be a general regulatory mechanism of HEAT-repeat proteins.
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Affiliation(s)
- Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiang Xu
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yun Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joyce C Cheung
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiansen Jiang
- Laboratory of Membrane Proteins and Structural Biology, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Natalia de Val
- Cancer Research Technology Program Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Tara Fox
- Cancer Research Technology Program Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Martin Gellert
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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11
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Sui J, Zhang S, Chen BPC. DNA-dependent protein kinase in telomere maintenance and protection. Cell Mol Biol Lett 2020; 25:2. [PMID: 31988640 PMCID: PMC6969447 DOI: 10.1186/s11658-020-0199-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/02/2020] [Indexed: 12/12/2022] Open
Abstract
This review focuses on DNA-dependent protein kinase (DNA-PK), which is the key regulator of canonical non-homologous end-joining (NHEJ), the predominant mechanism of DNA double-strand break (DSB) repair in mammals. DNA-PK consists of the DNA-binding Ku70/80 heterodimer and the catalytic subunit DNA-PKcs. They assemble at DNA ends, forming the active DNA-PK complex, which initiates NHEJ-mediated DSB repair. Paradoxically, both Ku and DNA-PKcs are associated with telomeres, and they play crucial roles in protecting the telomere against fusions. Herein, we discuss possible mechanisms and contributions of Ku and DNA-PKcs in telomere regulation.
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Affiliation(s)
- Jiangdong Sui
- 1Radiation Oncology Center, Chongqing University Cancer Hospital, Chongqing, 400030 China
| | - Shichuan Zhang
- 2Department of Radiation Oncology, Sichuan Cancer Hospital, Chengdu, China
| | - Benjamin P C Chen
- 3Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Rd., Dallas, TX 75390-9187 USA
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12
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New insights into the evolutionary conservation of the sole PIKK pseudokinase Tra1/TRRAP. Biochem Soc Trans 2019; 47:1597-1608. [DOI: 10.1042/bst20180496] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/25/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
Abstract
Phosphorylation by protein kinases is a fundamental mechanism of signal transduction. Many kinase families contain one or several members that, although evolutionarily conserved, lack the residues required for catalytic activity. Studies combining structural, biochemical, and functional approaches revealed that these pseudokinases have crucial roles in vivo and may even represent attractive targets for pharmacological intervention. Pseudokinases mediate signal transduction by a diversity of mechanisms, including allosteric regulation of their active counterparts, assembly of signaling hubs, or modulation of protein localization. One such pseudokinase, named Tra1 in yeast and transformation/transcription domain-associated protein (TRRAP) in mammals, is the only member lacking all catalytic residues within the phosphatidylinositol 3-kinase related kinase (PIKK) family of kinases. PIKKs are related to the PI3K family of lipid kinases, but function as Serine/Threonine protein kinases and have pivotal roles in diverse processes such as DNA damage sensing and repair, metabolic control of cell growth, nonsense-mediated decay, or transcription initiation. Tra1/TRRAP is the largest subunit of two distinct transcriptional co-activator complexes, SAGA and NuA4/TIP60, which it recruits to promoters upon transcription factor binding. Here, we review our current knowledge on the Tra1/TRRAP pseudokinase, focusing on its role as a scaffold for SAGA and NuA4/TIP60 complex assembly and recruitment to chromatin. We further discuss its evolutionary history within the PIKK family and highlight recent findings that reveal the importance of molecular chaperones in pseudokinase folding, function, and conservation.
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13
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Geng W, Tian D, Wang Q, Shan S, Zhou J, Xu W, Shan H. DNA‑PKcs inhibitor increases the sensitivity of gastric cancer cells to radiotherapy. Oncol Rep 2019; 42:561-570. [PMID: 31173270 PMCID: PMC6610038 DOI: 10.3892/or.2019.7187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 05/23/2019] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer (GC) is a severe public health problem worldwide, particularly in China. Radiotherapy is the main locoregional treatment for various types of unresectable tumor, including GC. However, many patients fail to respond to radiotherapy due to the intrinsic radioresistance of cancer cells. This study was designed to investigate the effects and potential mechanism of radiosensitization associated with DNA-dependent protein kinase catalytic subunit (DNA-PKcs) inhibitor in human GC cell lines in vitro. Among the six GC cell lines (SGC7901, HGC-27, MKN45, MKN74, BGC823 and MGC803) that were exposed to increasing doses of IR (0, 2, 4, 6 and 8 Gy), the mean lethal dose and quasi-threshold dose measurements indicated that BGC823 and MGC803 were relatively insensitive to ionizing radiation (IR). IR induced significant elevation of γ H2A histone family member X (γH2AX) in MKN45 cells compared with BGC823 cells. DNA-PKcs and phospho-DNA-PKcs protein levels were increased in BGC823 and MGC803 cells compared with other GC cell lines (SGC7901, HGC-27, MKN45 and MKN74). DNA-PKcs inhibition led to increased sensitivity of BGC823 and MGC803 cells to IR. NU7441 increased γH2AX expression in the nuclei of BGC823 cells following IR. Combination of DNA-PKcs and CK2 inhibition further increased the sensitivity of GC cells to IR. The combination of NU7441 and CX4945 increased γH2AX expression in the nucleus of BGC823 cells following IR compared with treatment with NU7441 alone. Taken together, the findings suggest that DNA-PKcs inhibitor increased the sensitivity of radioresistant BGC823 and MGC803 cells to radiotherapy through the cleaved-caspase3/γH2AX signaling pathway, thus presenting a potential treatment method for GC.
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Affiliation(s)
- Wei Geng
- Yancheng City No. 1 People's Hospital, Yancheng, Jiangsu 224005, P.R. China
| | - Dalong Tian
- Yancheng City No. 1 People's Hospital, Yancheng, Jiangsu 224005, P.R. China
| | - Qiang Wang
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Shunlin Shan
- Yancheng City No. 1 People's Hospital, Yancheng, Jiangsu 224005, P.R. China
| | - Jianwei Zhou
- Cancer Center of The 82nd Hospital of PLA, Huaian, Jiangsu 223001, P.R. China
| | - Wenxia Xu
- Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Husheng Shan
- Cancer Center of The 82nd Hospital of PLA, Huaian, Jiangsu 223001, P.R. China
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14
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Wang JL, Duboc C, Wu Q, Ochi T, Liang S, Tsutakawa SE, Lees-Miller SP, Nadal M, Tainer JA, Blundell TL, Strick TR. Dissection of DNA double-strand-break repair using novel single-molecule forceps. Nat Struct Mol Biol 2018; 25:482-487. [PMID: 29786079 PMCID: PMC5990469 DOI: 10.1038/s41594-018-0065-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/13/2018] [Indexed: 02/02/2023]
Abstract
Repairing DNA double-strand breaks (DSBs) by nonhomologous end joining (NHEJ) requires multiple proteins to recognize and bind DNA ends, process them for compatibility, and ligate them together. We constructed novel DNA substrates for single-molecule nanomanipulation, allowing us to mechanically detect, probe, and rupture in real-time DSB synapsis by specific human NHEJ components. DNA-PKcs and Ku allow DNA end synapsis on the 100 ms timescale, and the addition of PAXX extends this lifetime to ~2 s. Further addition of XRCC4, XLF and ligase IV results in minute-scale synapsis and leads to robust repair of both strands of the nanomanipulated DNA. The energetic contribution of the different components to synaptic stability is typically on the scale of a few kilocalories per mole. Our results define assembly rules for NHEJ machinery and unveil the importance of weak interactions, rapidly ruptured even at sub-picoNewton forces, in regulating this multicomponent chemomechanical system for genome integrity.
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Affiliation(s)
- Jing L Wang
- Institut Jacques Monod, Université Paris Diderot, CNRS, UMR 7592, Paris, France
| | - Camille Duboc
- Institut Jacques Monod, Université Paris Diderot, CNRS, UMR 7592, Paris, France
| | - Qian Wu
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Takashi Ochi
- Department of Biochemistry, Cambridge University, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Shikang Liang
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Marc Nadal
- Institut Jacques Monod, Université Paris Diderot, CNRS, UMR 7592, Paris, France
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Tom L Blundell
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Terence R Strick
- Institut Jacques Monod, Université Paris Diderot, CNRS, UMR 7592, Paris, France.
- Ecole Normale Supérieure, PSL Research University, CNRS, INSERM, Institute of Biology (IBENS), Paris, France.
- Programme Equipes Labellisées, Ligue Contre le Cancer, Paris, France.
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15
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Ross GA, Rustenburg AS, Grinaway PB, Fass J, Chodera JD. Biomolecular Simulations under Realistic Macroscopic Salt Conditions. J Phys Chem B 2018; 122:5466-5486. [PMID: 29649876 PMCID: PMC6078207 DOI: 10.1021/acs.jpcb.7b11734] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the macroscopic concentration remains, as yet, unknown. Here, we describe the theory and implementation of a Monte Carlo osmostat that can be added to explicit solvent molecular dynamics or Monte Carlo simulations to sample from a semigrand canonical ensemble in which the number of salt pairs fluctuates dynamically during the simulation. The osmostat reproduces the correct equilibrium statistics for a simulation volume that can exchange ions with a large reservoir at a defined macroscopic salt concentration. To achieve useful Monte Carlo acceptance rates, the method makes use of nonequilibrium candidate Monte Carlo (NCMC) moves in which monovalent ions and water molecules are alchemically transmuted using short nonequilibrium trajectories, with a modified Metropolis-Hastings criterion ensuring correct equilibrium statistics for an ( Δμ, N, p, T) ensemble to achieve a ∼1046× boost in acceptance rates. We demonstrate how typical protein (DHFR and the tyrosine kinase Src) and nucleic acid (Drew-Dickerson B-DNA dodecamer) systems exhibit salt concentration distributions that significantly differ from fixed-salt bulk simulations and display fluctuations that are on the same order of magnitude as the average.
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Affiliation(s)
- Gregory A. Ross
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Present address: Schrödinger, New York, NY 10036
| | - Ariën S. Rustenburg
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY 10065
| | - Patrick B. Grinaway
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY 10065
| | - Josh Fass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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16
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Han J, Tang FM, Pu D, Xu D, Wang T, Li W. Mechanisms Underlying Regulation of Cell Cycle and Apoptosis by hnRNP B1 in Human Lung Adenocarcinoma A549 Cells. TUMORI JOURNAL 2018. [DOI: 10.1177/1430.15824] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Juan Han
- Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Feng-ming Tang
- Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Dan Pu
- Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Dan Xu
- Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Tao Wang
- Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
| | - Weimin Li
- Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, PR China
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17
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Bohrer RC, Dicks N, Gutierrez K, Duggavathi R, Bordignon V. Double‐strand DNA breaks are mainly repaired by the homologous recombination pathway in early developing swine embryos. FASEB J 2018; 32:1818-1829. [DOI: 10.1096/fj.201700800r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Naomi Dicks
- Department of Animal ScienceMcGill UniversityMontrealQuebecCanada
| | - Karina Gutierrez
- Department of Animal ScienceMcGill UniversityMontrealQuebecCanada
| | - Raj Duggavathi
- Department of Animal ScienceMcGill UniversityMontrealQuebecCanada
| | - Vilceu Bordignon
- Department of Animal ScienceMcGill UniversityMontrealQuebecCanada
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18
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Sui H, Zhou M, Imamichi H, Jiao X, Sherman BT, Lane HC, Imamichi T. STING is an essential mediator of the Ku70-mediated production of IFN-λ1 in response to exogenous DNA. Sci Signal 2017; 10:eaah5054. [PMID: 28720717 DOI: 10.1126/scisignal.aah5054] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We previously identified Ku70, a subunit of a DNA repair protein complex, as a cytosolic DNA sensor that induces the production of interferon-λ1 (IFN-λ1) by human primary cells and cell lines. IFN-λ1 is a type III IFN and has similar antiviral activity to that of the type I IFNs (IFN-α and IFN-β). We observed that human embryonic kidney (HEK) 293T cells, which are deficient in the innate immune adaptor protein STING (stimulator of IFN genes), did not produce IFN-λ1 in response to DNA unless they were reconstituted with STING. Conversely, parental HEK 293 cells produced IFN-λ1 after they were exposed to exogenous DNA; however, when STING was knocked out in the HEK 293 cells through the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 genome editing system, they lost this response. Through confocal microscopy, we demonstrated that endogenous Ku70 was located in the nucleus and then translocated to the cytoplasm upon DNA exposure to form a complex with STING. Additionally, the DNA binding domain of Ku70 was essential for formation of the Ku70-STING complex. Knocking down STING in primary human macrophages inhibited their ability to produce IFN-λ1 in response to transfection with DNA or infection with the DNA virus HSV-2 (herpes simplex virus-2). Together, these data suggest that STING mediates the Ku70-mediated IFN-λ1 innate immune response to exogenous DNA or DNA virus infection.
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Affiliation(s)
- Hongyan Sui
- Laboratory of Human Retrovirology and Immunoinformatics, Applied and Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ming Zhou
- Laboratory of Proteomics and Analytical Technologies, Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Hiromi Imamichi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaoli Jiao
- Laboratory of Human Retrovirology and Immunoinformatics, Applied and Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Brad T Sherman
- Laboratory of Human Retrovirology and Immunoinformatics, Applied and Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - H Clifford Lane
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Applied and Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
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19
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Harnor SJ, Brennan A, Cano C. Targeting DNA-Dependent Protein Kinase for Cancer Therapy. ChemMedChem 2017; 12:895-900. [DOI: 10.1002/cmdc.201700143] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/19/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Suzannah J. Harnor
- Northern Institute for Cancer Research; Newcastle University, School of Chemistry; Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Alfie Brennan
- Northern Institute for Cancer Research; Newcastle University, School of Chemistry; Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Céline Cano
- Northern Institute for Cancer Research; Newcastle University, School of Chemistry; Bedson Building Newcastle upon Tyne NE1 7RU UK
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20
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Woods ML, Barnes CP. Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair. PLoS Comput Biol 2016; 12:e1005131. [PMID: 27741226 PMCID: PMC5065155 DOI: 10.1371/journal.pcbi.1005131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/05/2016] [Indexed: 12/12/2022] Open
Abstract
DNA double-strand breaks are lesions that form during metabolism, DNA replication and exposure to mutagens. When a double-strand break occurs one of a number of repair mechanisms is recruited, all of which have differing propensities for mutational events. Despite DNA repair being of crucial importance, the relative contribution of these mechanisms and their regulatory interactions remain to be fully elucidated. Understanding these mutational processes will have a profound impact on our knowledge of genomic instability, with implications across health, disease and evolution. Here we present a new method to model the combined activation of non-homologous end joining, single strand annealing and alternative end joining, following exposure to ionising radiation. We use Bayesian statistics to integrate eight biological data sets of double-strand break repair curves under varying genetic knockouts and confirm that our model is predictive by re-simulating and comparing to additional data. Analysis of the model suggests that there are at least three disjoint modes of repair, which we assign as fast, slow and intermediate. Our results show that when multiple data sets are combined, the rate for intermediate repair is variable amongst genetic knockouts. Further analysis suggests that the ratio between slow and intermediate repair depends on the presence or absence of DNA-PKcs and Ku70, which implies that non-homologous end joining and alternative end joining are not independent. Finally, we consider the proportion of double-strand breaks within each mechanism as a time series and predict activity as a function of repair rate. We outline how our insights can be directly tested using imaging and sequencing techniques and conclude that there is evidence of variable dynamics in alternative repair pathways. Our approach is an important step towards providing a unifying theoretical framework for the dynamics of DNA repair processes.
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Affiliation(s)
- Mae L. Woods
- Department of Cell and Developmental Biology, University College London, London, England
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, England
- Department of Genetics, Evolution and Environment, University College London, London, England
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21
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Knyazhanskaya ES, Shadrina OA, Anisenko AN, Gottikh MB. Role of DNA-dependent protein kinase in the HIV-1 replication cycle. Mol Biol 2016. [DOI: 10.1134/s0026893316040075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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22
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Belov OV, Krasavin EA, Lyashko MS, Batmunkh M, Sweilam NH. A quantitative model of the major pathways for radiation-induced DNA double-strand break repair. J Theor Biol 2015; 366:115-30. [DOI: 10.1016/j.jtbi.2014.09.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/11/2014] [Accepted: 09/17/2014] [Indexed: 12/11/2022]
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23
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Zhang SM, Zhang H, Yang TY, Ying TY, Yang PX, Liu XD, Tang SJ, Zhou PK. Interaction between HIV-1 Tat and DNA-PKcs modulates HIV transcription and class switch recombination. Int J Biol Sci 2014; 10:1138-49. [PMID: 25332688 PMCID: PMC4202030 DOI: 10.7150/ijbs.10366] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/17/2014] [Indexed: 12/17/2022] Open
Abstract
HIV-1 tat targets a variety of host cell proteins to facilitate viral transcription and disrupts host cellular immunity by inducing lymphocyte apoptosis, but whether it influences humoral immunity remains unclear. Previously, our group demonstrated that tat depresses expression of DNA-PKcs, a critical component of the non-homologous end joining pathway (NHEJ) of DNA double-strand breaks repair, immunoglobulin class switch recombination (CSR) and V(D)J recombination, and sensitizes cells to ionizing radiation. In this study, we demonstrated that HIV-1 Tat down-regulates DNA-PKcs expression by directly binding to the core promoter sequence. In addition, Tat interacts with and activates the kinase activity of DNA-PKcs in a dose-dependent and DNA independent manner. Furthermore, Tat inhibits class switch recombination (CSR) at low concentrations (≤4 µg/ml) and stimulates CSR at high concentrations (≥8 µg/ml). On the other hand, low protein level and high kinase activity of DNA-PKcs promotes HIV-1 transcription, while high protein level and low kinase activity inhibit HIV-1 transcription. Co-immunoprecipitation results revealed that DNA-PKcs forms a large complex comprised of Cyclin T1, CDK9 and Tat via direct interacting with CDK9 and Tat but not Cyclin T1. Taken together, our results provide new clues that Tat regulates host humoral immunity via both transcriptional depression and kinase activation of DNA-PKcs. We also raise the possibility that inhibitors and interventions directed towards DNA-PKcs may inhibit HIV-1 transcription in AIDS patients.
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Affiliation(s)
- Shi-Meng Zhang
- 1. Department of Radiation Toxicology and Oncology; Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - He Zhang
- 1. Department of Radiation Toxicology and Oncology; Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - Tian-Yi Yang
- 1. Department of Radiation Toxicology and Oncology; Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - Tian-Yi Ying
- 2. The State Key Laboratory of NBC Protection for Civilian, 102205, Beijing, China
| | - Pei-Xiang Yang
- 3. Beijing Institute of Health Administration and Medical Information, 100850, Beijing, China
| | - Xiao-Dan Liu
- 1. Department of Radiation Toxicology and Oncology; Beijing Institute of Radiation Medicine, 100850, Beijing, China
| | - Sheng-Jian Tang
- 4. Shandong Provincial Key Laboratory of Plastic and Microscopic Repair Technology, Institute of Plastic Surgery, Weifang Medical University, 261053, Weifang, Shandong Province, China
| | - Ping-Kun Zhou
- 1. Department of Radiation Toxicology and Oncology; Beijing Institute of Radiation Medicine, 100850, Beijing, China
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24
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DNA-PK: a dynamic enzyme in a versatile DSB repair pathway. DNA Repair (Amst) 2014; 17:21-9. [PMID: 24680878 DOI: 10.1016/j.dnarep.2014.02.020] [Citation(s) in RCA: 278] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 11/23/2022]
Abstract
DNA double stranded breaks (DSBs) are the most cytoxic DNA lesion as the inability to properly repair them can lead to genomic instability and tumorigenesis. The prominent DSB repair pathway in humans is non-homologous end-joining (NHEJ). In the simplest sense, NHEJ mediates the direct re-ligation of the broken DNA molecule. However, NHEJ is a complex and versatile process that can repair DSBs with a variety of damages and ends via the utilization of a significant number of proteins. In this review we will describe the important factors and mechanisms modulating NHEJ with emphasis given to the versatility of this repair process and the DNA-PK complex.
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25
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Peters NE, Ferguson BJ, Mazzon M, Fahy AS, Krysztofinska E, Arribas-Bosacoma R, Pearl LH, Ren H, Smith GL. A mechanism for the inhibition of DNA-PK-mediated DNA sensing by a virus. PLoS Pathog 2013; 9:e1003649. [PMID: 24098118 PMCID: PMC3789764 DOI: 10.1371/journal.ppat.1003649] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 08/06/2013] [Indexed: 12/17/2022] Open
Abstract
The innate immune system is critical in the response to infection by pathogens and it is activated by pattern recognition receptors (PRRs) binding to pathogen associated molecular patterns (PAMPs). During viral infection, the direct recognition of the viral nucleic acids, such as the genomes of DNA viruses, is very important for activation of innate immunity. Recently, DNA-dependent protein kinase (DNA-PK), a heterotrimeric complex consisting of the Ku70/Ku80 heterodimer and the catalytic subunit DNA-PKcs was identified as a cytoplasmic PRR for DNA that is important for the innate immune response to intracellular DNA and DNA virus infection. Here we show that vaccinia virus (VACV) has evolved to inhibit this function of DNA-PK by expression of a highly conserved protein called C16, which was known to contribute to virulence but by an unknown mechanism. Data presented show that C16 binds directly to the Ku heterodimer and thereby inhibits the innate immune response to DNA in fibroblasts, characterised by the decreased production of cytokines and chemokines. Mechanistically, C16 acts by blocking DNA-PK binding to DNA, which correlates with reduced DNA-PK-dependent DNA sensing. The C-terminal region of C16 is sufficient for binding Ku and this activity is conserved in the variola virus (VARV) orthologue of C16. In contrast, deletion of 5 amino acids in this domain is enough to knockout this function from the attenuated vaccine strain modified vaccinia virus Ankara (MVA). In vivo a VACV mutant lacking C16 induced higher levels of cytokines and chemokines early after infection compared to control viruses, confirming the role of this virulence factor in attenuating the innate immune response. Overall this study describes the inhibition of DNA-PK-dependent DNA sensing by a poxvirus protein, adding to the evidence that DNA-PK is a critical component of innate immunity to DNA viruses.
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Affiliation(s)
- Nicholas E. Peters
- Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Brian J. Ferguson
- Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | - Michela Mazzon
- Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | - Aodhnait S. Fahy
- Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Ewelina Krysztofinska
- Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
| | - Raquel Arribas-Bosacoma
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | - Laurence H. Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom
| | - Hongwei Ren
- Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
| | - Geoffrey L. Smith
- Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London, United Kingdom
- Department of Pathology, Cambridge University, Cambridge, United Kingdom
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26
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Abdelbaqi K, Di Paola D, Rampakakis E, Zannis-Hadjopoulos M. Ku protein levels, localization and association to replication origins in different stages of breast tumor progression. J Cancer 2013; 4:358-70. [PMID: 23781282 PMCID: PMC3677623 DOI: 10.7150/jca.6289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/23/2013] [Indexed: 11/05/2022] Open
Abstract
Human origins of DNA replication are specific sequences within the genome whereby DNA replication is initiated. A select group of proteins, known as the pre-replication (pre-RC) complex, in whose formation the Ku protein (Ku70/Ku86) was shown to play a role, bind to replication origins to initiate DNA replication. In this study, we have examined the involvement of Ku in breast tumorigenesis and tumor progression and found that the Ku protein expression levels in human breast metastatic (MCF10AC1a) cells were higher in the chromatin fraction compared to hyperplastic (MCF10AT) and normal (MCF10A) human breast cells, but remained constant in both the nuclear and cytoplasmic fractions. In contrast, in human intestinal cells, the Ku expression level was relatively constant for all cell fractions. Nascent DNA abundance and chromatin association of Ku70/86 revealed that the c-myc origin activity in MCF10AC1a is 2.5 to 5-fold higher than in MCF10AT and MCF10A, respectively, and Ku was bound to the c-myc origin more abundantly in MCF10AC1a, by approximately 1.5 to 4.2-fold higher than in MCF10AT and MCF10A, respectively. In contrast, similar nascent DNA abundance and chromatin association was found for all cell lines for the lamin B2 origin, associated with the constitutively active housekeeping lamin B2 gene. Electrophoretic mobility shift assays (EMSAs) performed on the nuclear extracts (NEs) of the three cell types revealed the presence of protein-DNA replication complexes on both the c-myc and lamin B2 origins, but an increase in binding activity was observed from normal, to transformed, to cancer cells for the c-myc origin, whereas no such difference was seen for the lamin B2 origin. Overall, the results suggest that increased Ku chromatin association, beyond wild type levels, alters cellular processes, which have been implicated in tumorigenesis.
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Affiliation(s)
- Khalil Abdelbaqi
- 1. Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada H3G 1Y6; ; 2. Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6
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27
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Abstract
Nonhomologous end joining repairs DNA double-strand breaks created by ionizing radiation and V(D)J recombination. Ku, XRCC4/Ligase IV (XL), and XLF have a remarkable mismatched end (MEnd) ligase activity, particularly for ends with mismatched 3' overhangs, but the mechanism has remained obscure. Here, we showed XL required Ku to bind DNA, whereas XLF required both Ku and XL to bind DNA. We detected cooperative assembly of one or two Ku molecules and up to five molecules each of XL and XLF into a Ku-XL-XLF-DNA (MEnd ligase-DNA) complex. XLF mutations that disrupted its interactions with XRCC4 or DNA also disrupted complex assembly and end joining. Together with published co-crystal structures of truncated XRCC4 and XLF proteins, our data with full-length Ku, XL, and XLF bound to DNA indicate assembly of a filament containing Ku plus alternating XL and XLF molecules. By contrast, in the absence of XLF, we detected cooperative assembly of up to six molecules each of Ku and XL into a Ku-XL-DNA complex, consistent with a filament containing alternating Ku and XL molecules. Despite a lower molecular mass, MEnd ligase-DNA had a lower electrophoretic mobility than Ku-XL-DNA. The anomalous difference in mobility and difference in XL to Ku molar ratio suggests that MEnd ligase-DNA has a distinct structure that successfully aligns mismatched DNA ends for ligation.
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Affiliation(s)
- Chun J Tsai
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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28
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Unno J, Takagi M, Piao J, Sugimoto M, Honda F, Maeda D, Masutani M, Kiyono T, Watanabe F, Morio T, Teraoka H, Mizutani S. Artemis-dependent DNA double-strand break formation at stalled replication forks. Cancer Sci 2013; 104:703-10. [PMID: 23465063 DOI: 10.1111/cas.12144] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 02/26/2013] [Accepted: 03/02/2013] [Indexed: 11/28/2022] Open
Abstract
Stalled replication forks undergo DNA double-strand breaks (DSBs) under certain conditions. However, the precise mechanism underlying DSB induction and the cellular response to persistent replication fork stalling are not fully understood. Here we show that, in response to hydroxyurea exposure, DSBs are generated in an Artemis nuclease-dependent manner following prolonged stalling with subsequent activation of the ataxia-telangiectasia mutated (ATM) signaling pathway. The kinase activity of the catalytic subunit of the DNA-dependent protein kinase, a prerequisite for stimulation of the endonuclease activity of Artemis, is also required for DSB generation and subsequent ATM activation. Our findings indicate a novel function of Artemis as a molecular switch that converts stalled replication forks harboring single-stranded gap DNA lesions into DSBs, thereby activating the ATM signaling pathway following prolonged replication fork stalling.
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Affiliation(s)
- Junya Unno
- Department of Pediatrics and Developmental Biology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
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29
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Dolan D, Nelson G, Zupanic A, Smith G, Shanley D. Systems modelling of NHEJ reveals the importance of redox regulation of Ku70/80 in the dynamics of dna damage foci. PLoS One 2013; 8:e55190. [PMID: 23457464 PMCID: PMC3566652 DOI: 10.1371/journal.pone.0055190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 12/19/2012] [Indexed: 12/21/2022] Open
Abstract
The presence of DNA double-stranded breaks in a mammalian cell typically activates the Non-Homologous End Joining (NHEJ) pathway to repair the damage and signal to downstream systems that govern cellular decisions such as apoptosis or senescence. The signalling system also stimulates effects such as the generation of reactive oxygen species (ROS) which in turn feed back into the damage response. Although the overall process of NHEJ is well documented, we know little of the dynamics and how the system operates as a whole. We have developed a computational model which includes DNA Protein Kinase (DNA-PK) dependent NHEJ (D-NHEJ) and back-up NHEJ mechanisms (B-NHEJ) and use it to explain the dynamic response to damage induced by different levels of gamma irradiation in human fibroblasts. Our work suggests that the observed shift from fast to slow repair of DNA damage foci at higher levels of damage cannot be explained solely by inherent stochasticity in the NHEJ system. Instead, our model highlights the importance of Ku oxidation which leads to increased Ku dissociation rates from DNA damage foci and shifts repair in favour of the less efficient B-NHEJ system.
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Affiliation(s)
- David Dolan
- Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
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30
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Davis AJ, Lee KJ, Chen DJ. The N-terminal region of the DNA-dependent protein kinase catalytic subunit is required for its DNA double-stranded break-mediated activation. J Biol Chem 2013; 288:7037-46. [PMID: 23322783 DOI: 10.1074/jbc.m112.434498] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
DNA-dependent protein kinase (DNA-PK) plays an essential role in the repair of DNA double-stranded breaks (DSBs) mediated by the nonhomologous end-joining pathway. DNA-PK is a holoenzyme consisting of a DNA-binding (Ku70/Ku80) and catalytic (DNA-PKcs) subunit. DNA-PKcs is a serine/threonine protein kinase that is recruited to DSBs via Ku70/80 and is activated once the kinase is bound to the DSB ends. In this study, two large, distinct fragments of DNA-PKcs, consisting of the N terminus (amino acids 1-2713), termed N-PKcs, and the C terminus (amino acids 2714-4128), termed C-PKcs, were produced to determine the role of each terminal region in regulating the activity of DNA-PKcs. N-PKcs but not C-PKcs interacts with the Ku-DNA complex and is required for the ability of DNA-PKcs to localize to DSBs. C-PKcs has increased basal kinase activity compared with DNA-PKcs, suggesting that the N-terminal region of DNA-PKcs keeps basal activity low. The kinase activity of C-PKcs is not stimulated by Ku70/80 and DNA, further supporting that the N-terminal region is required for binding to the Ku-DNA complex and full activation of kinase activity. Collectively, the results show the N-terminal region mediates the interaction between DNA-PKcs and the Ku-DNA complex and is required for its DSB-induced enzymatic activity.
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Affiliation(s)
- Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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31
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Ferguson BJ, Mansur DS, Peters NE, Ren H, Smith GL. DNA-PK is a DNA sensor for IRF-3-dependent innate immunity. eLife 2012; 1:e00047. [PMID: 23251783 PMCID: PMC3524801 DOI: 10.7554/elife.00047] [Citation(s) in RCA: 334] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/24/2012] [Indexed: 12/17/2022] Open
Abstract
Innate immunity is the first immunological defence against pathogens. During virus infection detection of nucleic acids is crucial for the inflammatory response. Here we identify DNA-dependent protein kinase (DNA-PK) as a DNA sensor that activates innate immunity. We show that DNA-PK acts as a pattern recognition receptor, binding cytoplasmic DNA and triggering the transcription of type I interferon (IFN), cytokine and chemokine genes in a manner dependent on IFN regulatory factor 3 (IRF-3), TANK-binding kinase 1 (TBK1) and stimulator of interferon genes (STING). Both cells and mice lacking DNA-PKcs show attenuated cytokine responses to both DNA and DNA viruses but not to RNA or RNA virus infection. DNA-PK has well-established functions in the DNA repair and V(D)J recombination, hence loss of DNA-PK leads to severe combined immunodeficiency (SCID). However, we now define a novel anti-microbial function for DNA-PK, a finding with implications for host defence, vaccine development and autoimmunity. DOI:http://dx.doi.org/10.7554/eLife.00047.001 For multicellular organisms, the innate immune system is the first immunological defence against infection, rapidly recognizing and responding to the presence of any pathogen. Many different cell types contribute to the innate immunity, including fibroblasts, epithelial cells, dendritic cells and macrophages. Once alerted to injury or infection, these cells release proteins called cytokines, interferons and chemokines into the blood or directly into tissue. These proteins act as messengers and interact with receptors on the surfaces of other cells in the immune system, stimulating them to join the battle against the infection. Detecting nucleic acids such as DNA is an important part of recognizing pathogens and infectious agents, particularly viruses, and activating the innate immune system. However, while the presence of DNA in the cytoplasm is known to initiate an innate immune response, we do not fully understand how this foreign DNA is sensed, or how the innate immune system is activated once foreign DNA has been detected. Here Ferguson et al. report that a well-known complex of three proteins, collectively called DNA-dependent protein kinase, is able to activate an innate immune response when it detects foreign DNA. This enzyme, called DNA-PK for short, is best known for its ability to repair broken DNA inside the nucleus. Now Ferguson et al. have found that it is also present at high levels within fibroblasts, cells that are often primary targets of viral infection, and they go on to explain how the detection of DNA by DNA-PK triggers a sequence of events that leads to the innate immune response being activated. These events include the transcription of type I interferon, chemokines and cytokines in a manner that depends on the presence IRF-3, a transcription factor that has a central role in the response of the immune system to viral infection. By identifying a role for DNA-PK in the cytoplasm as a DNA sensor, the work of Ferguson et al. increases our understanding of innate immunity. It may also, in the future, lead to an improved understanding of autoimmunity, and might also assist in the development of more immunogenic vaccines based on DNA or microbes that contain DNA. DOI:http://dx.doi.org/10.7554/eLife.00047.002
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Affiliation(s)
- Brian J Ferguson
- Department of Virology , Imperial College London , London , United Kingdom ; Department of Pathology , University of Cambridge , Cambridge , United Kingdom
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32
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Identification of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) as a novel target of bisphenol A. PLoS One 2012; 7:e50481. [PMID: 23227178 PMCID: PMC3515620 DOI: 10.1371/journal.pone.0050481] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 10/24/2012] [Indexed: 11/21/2022] Open
Abstract
Bisphenol A (BPA) forms the backbone of plastics and epoxy resins used to produce packaging for various foods and beverages. BPA is also an estrogenic disruptor, interacting with human estrogen receptors (ER) and other related nuclear receptors. Nevertheless, the effects of BPA on human health remain unclear. The present study identified DNA-dependent protein kinase catalytic subunit (DNA-PKcs) as a novel BPA-binding protein. DNA-PKcs, in association with the Ku heterodimer (Ku70/80), is a critical enzyme involved in the repair of DNA double-strand breaks. Low levels of DNA-PK activity are previously reported to be associated with an increased risk of certain types of cancer. Although the Kd for the interaction between BPA and a drug-binding mutant of DNA-PKcs was comparatively low (137 nM), high doses of BPA were required before cellular effects were observed (100–300 μM). The results of an in vitro kinase assay showed that BPA inhibited DNA-PK kinase activity in a concentration-dependent manner. In M059K cells, BPA inhibited the phosphorylation of DNA-PKcs at Ser2056 and H2AX at Ser139 in response to ionizing radiation (IR)-irradiation. BPA also disrupted DNA-PKcs binding to Ku70/80 and increased the radiosensitivity of M059K cells, but not M059J cells (which are DNA-PKcs-deficient). Taken together, these results provide new evidence of the effects of BPA on DNA repair in mammalian cells, which are mediated via inhibition of DNA-PK activity. This study may warrant the consideration of the possible carcinogenic effects of high doses of BPA, which are mediated through its action on DNA-PK.
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33
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Liu S, Opiyo SO, Manthey K, Glanzer JG, Ashley AK, Amerin C, Troksa K, Shrivastav M, Nickoloff JA, Oakley GG. Distinct roles for DNA-PK, ATM and ATR in RPA phosphorylation and checkpoint activation in response to replication stress. Nucleic Acids Res 2012; 40:10780-94. [PMID: 22977173 PMCID: PMC3510507 DOI: 10.1093/nar/gks849] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
DNA damage encountered by DNA replication forks poses risks of genome destabilization, a
precursor to carcinogenesis. Damage checkpoint systems cause cell cycle arrest, promote
repair and induce programed cell death when damage is severe. Checkpoints are critical
parts of the DNA damage response network that act to suppress cancer. DNA damage and
perturbation of replication machinery causes replication stress, characterized by
accumulation of single-stranded DNA bound by replication protein A (RPA), which triggers
activation of ataxia telangiectasia and Rad3 related (ATR) and phosphorylation of the
RPA32, subunit of RPA, leading to Chk1 activation and arrest. DNA-dependent protein kinase
catalytic subunit (DNA-PKcs) [a kinase related to ataxia telangiectasia mutated (ATM) and
ATR] has well characterized roles in DNA double-strand break repair, but poorly understood
roles in replication stress-induced RPA phosphorylation. We show that DNA-PKcs mutant
cells fail to arrest replication following stress, and mutations in RPA32 phosphorylation
sites targeted by DNA-PKcs increase the proportion of cells in mitosis, impair ATR
signaling to Chk1 and confer a G2/M arrest defect. Inhibition of ATR and DNA-PK (but not
ATM), mimic the defects observed in cells expressing mutant RPA32. Cells expressing mutant
RPA32 or DNA-PKcs show sustained H2AX phosphorylation in response to replication stress
that persists in cells entering mitosis, indicating inappropriate mitotic entry with
unrepaired damage.
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Affiliation(s)
- Shengqin Liu
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, NE 68583, USA
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34
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Thompson LH. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography. Mutat Res 2012; 751:158-246. [PMID: 22743550 DOI: 10.1016/j.mrrev.2012.06.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 06/09/2012] [Accepted: 06/16/2012] [Indexed: 12/15/2022]
Abstract
The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.
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Affiliation(s)
- Larry H Thompson
- Biology & Biotechnology Division, L452, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-0808, United States.
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35
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Abstract
The electrophoretic mobility shift assay (EMSA) can be used to study proteins that bind to DNA structures created by DNA-damaging agents. UV-damaged DNA-binding protein (UV-DDB), which is involved in nucleotide excision repair, binds to DNA damaged by ultraviolet radiation or the anticancer drug cisplatin. Ku, XRCC4/Ligase IV, and DNA-PKcs, which are involved in the repair of DNA double-strand breaks by nonhomologous end joining, assemble in complexes at DNA ends. This chapter will describe several EMSA protocols for detecting different DNA repair protein-DNA complexes. To obtain additional information, one can apply variations of the EMSA, which include the reverse EMSA to detect binding of (35)S-labeled protein to damaged DNA, and the antibody supershift assay to detect the presence of a specific protein in the protein-DNA complex.
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36
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Meek K, Lees-Miller SP, Modesti M. N-terminal constraint activates the catalytic subunit of the DNA-dependent protein kinase in the absence of DNA or Ku. Nucleic Acids Res 2011; 40:2964-73. [PMID: 22167471 PMCID: PMC3326324 DOI: 10.1093/nar/gkr1211] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The DNA-dependent protein kinase (DNA-PK) was identified as an activity and as its three component polypeptides 25 and 15 years ago, respectively. It has been exhaustively characterized as being absolutely dependent on free double stranded DNA ends (to which it is directed by its regulatory subunit, Ku) for its activation as a robust nuclear serine/threonine protein kinase. Here, we report the unexpected finding of robust DNA-PKcs activation by N-terminal constraint, independent of either DNA or its regulatory subunit Ku. These data suggest that an N-terminal conformational change (likely induced by DNA binding) induces enzymatic activation.
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Affiliation(s)
- Katheryn Meek
- Department of Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA.
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37
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Wong ESW, Papenfuss AT, Heger A, Hsu AL, Ponting CP, Miller RD, Fenelon JC, Renfree MB, Gibbs RA, Belov K. Transcriptomic analysis supports similar functional roles for the two thymuses of the tammar wallaby. BMC Genomics 2011; 12:420. [PMID: 21854594 PMCID: PMC3173455 DOI: 10.1186/1471-2164-12-420] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 08/19/2011] [Indexed: 02/08/2023] Open
Abstract
Background The thymus plays a critical role in the development and maturation of T-cells. Humans have a single thoracic thymus and presence of a second thymus is considered an anomaly. However, many vertebrates have multiple thymuses. The tammar wallaby has two thymuses: a thoracic thymus (typically found in all mammals) and a dominant cervical thymus. Researchers have known about the presence of the two wallaby thymuses since the 1800s, but no genome-wide research has been carried out into possible functional differences between the two thymic tissues. Here, we used pyrosequencing to compare the transcriptomes of a cervical and thoracic thymus from a single 178 day old tammar wallaby. Results We show that both the tammar thoracic and the cervical thymuses displayed gene expression profiles consistent with roles in T-cell development. Both thymuses expressed genes that mediate distinct phases of T-cells differentiation, including the initial commitment of blood stem cells to the T-lineage, the generation of T-cell receptor diversity and development of thymic epithelial cells. Crucial immune genes, such as chemokines were also present. Comparable patterns of expression of non-coding RNAs were seen. 67 genes differentially expressed between the two thymuses were detected, and the possible significance of these results are discussed. Conclusion This is the first study comparing the transcriptomes of two thymuses from a single individual. Our finding supports that both thymuses are functionally equivalent and drive T-cell development. These results are an important first step in the understanding of the genetic processes that govern marsupial immunity, and also allow us to begin to trace the evolution of the mammalian immune system.
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Affiliation(s)
- Emily S W Wong
- Faculty of Veterinary Sciences, University of Sydney, Sydney, NSW 2006, Australia
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38
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Davis AJ, So S, Chen DJ. Dynamics of the PI3K-like protein kinase members ATM and DNA-PKcs at DNA double strand breaks. Cell Cycle 2011; 9:2529-36. [PMID: 20543558 DOI: 10.4161/cc.9.13.12148] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The protein kinases ATM and DNA-PKcs play critical roles in the cellular response to DNA double strand breaks (DSBs). ATM and DNA-PKcs are activated in response to DSBs and play several important roles in propagation of the damage signal and for the repair of DNA damage. Recent work from several groups, including ours, has focused on studying the dynamics of each of these proteins at DSBs and the requirements and factors which play a role(s) in this process. The use of live cell imaging of fluorescently-tagged ATM and DNA-PKcs has allowed us to study the real-time response of these proteins to laser-generated DNA damage in vivo. Here, we will extensively discuss the behavior of the ATM and DNA-PKcs proteins at DSB sites.
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Affiliation(s)
- Anthony J Davis
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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39
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Pawelczak KS, Bennett SM, Turchi JJ. Coordination of DNA-PK activation and nuclease processing of DNA termini in NHEJ. Antioxid Redox Signal 2011; 14:2531-43. [PMID: 20698792 PMCID: PMC3096510 DOI: 10.1089/ars.2010.3368] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA double-strand breaks (DSB), particularly those induced by ionizing radiation (IR), are complex lesions that can be cytotoxic if not properly repaired. IR-induced DSB often have DNA termini modifications, including thymine glycols, ring fragmentation, 3'-phosphoglycolates, 5'-hydroxyl groups, and abasic sites. Nonhomologous end joining (NHEJ) is a major pathway responsible for the repair of these complex breaks. Proteins involved in NHEJ include the Ku 70/80 heterodimer, DNA-PKcs, processing proteins including Artemis and DNA polymerases μ and λ, XRCC4, DNA ligase IV, and XLF. We will discuss the role of the physical and functional interactions of DNA-PK as a result of activation, with an emphasis on DNA structure, chemistry, and sequence. With the diversity of IR induced DSB, it is becoming increasingly clear that multiple DNA processing enzymes are likely necessary for effective repair of a break. We will explore the roles of several important processing enzymes, with a focus on the nuclease Artemis and its role in processing diverse DSB. The effect of DNA termini on both DNA-PK and Artemis activity will be analyzed from a structural and biochemical view.
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Affiliation(s)
- Katherine S Pawelczak
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 980 W. Walnut St., Indianapolis, IN 46202, USA
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40
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Kong X, Shen Y, Jiang N, Fei X, Mi J. Emerging roles of DNA-PK besides DNA repair. Cell Signal 2011; 23:1273-80. [PMID: 21514376 DOI: 10.1016/j.cellsig.2011.04.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Revised: 03/13/2011] [Accepted: 04/04/2011] [Indexed: 10/24/2022]
Abstract
The DNA-dependent protein kinase (DNA-PK) is a DNA-activated serine/threonine protein kinase, and abundantly expressed in almost all mammalian cells. The roles of DNA-PK in DNA-damage repair pathways, including non-homologous end-joining (NHEJ) repair and homologous recombinant (HR) repair, have been studied intensively. However, the high levels of DNA-PK in human cells are somewhat paradoxical in that it does not impart any increased ability to repair DNA damage. If DNA-PK essentially exceeds the demand for DNA damage repair, why do human cells universally express such high levels of this huge complex? DNA-PK has been recently reported to be involved in metabolic gene regulation in response to feeding/insulin stimulation; our studies have also suggested a role of DNA-PK in the regulation of the homeostasis of cell proliferation. These novel findings expand our horizons about the importance of DNA-PK.
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Affiliation(s)
- Xianming Kong
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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41
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Kemp MG, Lindsey-Boltz LA, Sancar A. The DNA damage response kinases DNA-dependent protein kinase (DNA-PK) and ataxia telangiectasia mutated (ATM) Are stimulated by bulky adduct-containing DNA. J Biol Chem 2011; 286:19237-46. [PMID: 21487018 DOI: 10.1074/jbc.m111.235036] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A variety of environmental, carcinogenic, and chemotherapeutic agents form bulky lesions on DNA that activate DNA damage checkpoint signaling pathways in human cells. To identify the mechanisms by which bulky DNA adducts induce damage signaling, we developed an in vitro assay using mammalian cell nuclear extract and plasmid DNA containing bulky adducts formed by N-acetoxy-2-acetylaminofluorene or benzo(a)pyrene diol epoxide. Using this cell-free system together with a variety of pharmacological, genetic, and biochemical approaches, we identified the DNA damage response kinases DNA-dependent protein kinase (DNA-PK) and ataxia telangiectasia mutated (ATM) as bulky DNA damage-stimulated kinases that phosphorylate physiologically important residues on the checkpoint proteins p53, Chk1, and RPA. Consistent with these results, purified DNA-PK and ATM were directly stimulated by bulky adduct-containing DNA and preferentially associated with damaged DNA in vitro. Because the DNA damage response kinase ATM and Rad3-related (ATR) is also stimulated by bulky DNA adducts, we conclude that a common biochemical mechanism exists for activation of DNA-PK, ATM, and ATR by bulky adduct-containing DNA.
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Affiliation(s)
- Michael G Kemp
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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Neal JA, Meek K. Choosing the right path: does DNA-PK help make the decision? Mutat Res 2011; 711:73-86. [PMID: 21376743 DOI: 10.1016/j.mrfmmm.2011.02.010] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/11/2011] [Accepted: 02/15/2011] [Indexed: 12/30/2022]
Abstract
DNA double-strand breaks are extremely harmful lesions that can lead to genomic instability and cell death if not properly repaired. There are at least three pathways that are responsible for repairing DNA double-strand breaks in mammalian cells: non-homologous end joining, homologous recombination and alternative non-homologous end joining. Here we review each of these three pathways with an emphasis on the role of the DNA-dependent protein kinase, a critical component of the non-homologous end joining pathway, in influencing which pathway is ultimately utilized for repair.
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Affiliation(s)
- Jessica A Neal
- College of Veterinary Medicine, Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
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Pang D, Winters TA, Jung M, Purkayastha S, Cavalli LR, Chasovkikh S, Haddad BR, Dritschilo A. Radiation-generated short DNA fragments may perturb non-homologous end-joining and induce genomic instability. JOURNAL OF RADIATION RESEARCH 2011; 52:309-19. [PMID: 21628845 PMCID: PMC5469405 DOI: 10.1269/jrr.10147] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cells exposed to densely ionizing radiation (high-LET) experience more severe biological damage than do cells exposed to sparsely ionizing radiation (low-LET). The prevailing hypothesis is that high-LET radiations induce DNA double strand-breaks (DSB) that are more complex and clustered, and are thereby more challenging to repair. Here, we present experimental data obtained by atomic force microscopy imaging, DNA-dependent protein kinase (DNA-PK) activity determination, DNA ligation assays, and genomic studies to suggest that short DNA fragments are important products of radiation-induced DNA lesions, and that the lengths of DNA fragments may be significant in the cellular responses to ionizing radiation. We propose the presence of a subset of short DNA fragments that may affect cell survival and genetic stability following exposure to ionizing radiation, and that the enhanced biological effects of high-LET radiation may be explained, in part, by the production of increased quantities of short DNA fragments.
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Affiliation(s)
- Dalong Pang
- Department of Radiation Medicine, Georgetown University Medical Center
| | - Thomas A. Winters
- Radiology and Imaging Sciences Department, Warren Grant Magnuson Clinical Center, National Institutes of Health
| | - Mira Jung
- Department of Radiation Medicine, Georgetown University Medical Center
| | - Shubhadeep Purkayastha
- Radiology and Imaging Sciences Department, Warren Grant Magnuson Clinical Center, National Institutes of Health
| | - Luciane R. Cavalli
- Department of Oncology/Lombardi Comprehensive Cancer Center, Georgetown University Medical Center
| | - Sergey Chasovkikh
- Department of Radiation Medicine, Georgetown University Medical Center
| | - Bassem R. Haddad
- Department of Oncology/Lombardi Comprehensive Cancer Center, Georgetown University Medical Center
| | - Anatoly Dritschilo
- Department of Radiation Medicine, Georgetown University Medical Center
- Corresponding author: Anatoly Dritschilo, MD, Department of Radiation Medicine, Georgetown University Medical Center, 3800 Reservoir Road, NW, LL Bles Washington, DC 20007
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Hendrickson CL, Purkayastha S, Pastwa E, Neumann RD, Winters TA. Coincident In Vitro Analysis of DNA-PK-Dependent and -Independent Nonhomologous End Joining. J Nucleic Acids 2010; 2010:823917. [PMID: 20706599 PMCID: PMC2919755 DOI: 10.4061/2010/823917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Accepted: 06/06/2010] [Indexed: 01/22/2023] Open
Abstract
In mammalian cells, DNA double-strand breaks (DSBs) are primarily repaired by nonhomologous end joining (NHEJ). The current model suggests that the Ku 70/80 heterodimer binds to DSB ends and recruits DNA-PKcs to form the active DNA-dependent protein kinase, DNA-PK. Subsequently, XRCC4, DNA ligase IV, XLF and most likely, other unidentified components participate in the final DSB ligation step. Therefore, DNA-PK plays a key role in NHEJ due to its structural and regulatory functions that mediate DSB end joining. However, recent studies show that additional DNA-PK-independent NHEJ pathways also exist. Unfortunately, the presence of DNA-PKcs appears to inhibit DNA-PK-independent NHEJ, and in vitro analysis of DNA-PK-independent NHEJ in the presence of the DNA-PKcs protein remains problematic. We have developed an in vitro assay that is preferentially active for DNA-PK-independent DSB repair based solely on its reaction conditions, facilitating coincident differential biochemical analysis of the two pathways. The results indicate the biochemically distinct nature of the end-joining mechanisms represented by the DNA-PK-dependent and -independent NHEJ assays as well as functional differences between the two pathways.
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Affiliation(s)
- Cynthia L Hendrickson
- Radiology & Imaging Sciences Department, Nuclear Medicine Section, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
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Lieber MR. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 2010; 79:181-211. [PMID: 20192759 DOI: 10.1146/annurev.biochem.052308.093131] [Citation(s) in RCA: 2046] [Impact Index Per Article: 136.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Double-strand DNA breaks are common events in eukaryotic cells, and there are two major pathways for repairing them: homologous recombination (HR) and nonhomologous DNA end joining (NHEJ). The various causes of double-strand breaks (DSBs) result in a diverse chemistry of DNA ends that must be repaired. Across NHEJ evolution, the enzymes of the NHEJ pathway exhibit a remarkable degree of structural tolerance in the range of DNA end substrate configurations upon which they can act. In vertebrate cells, the nuclease, DNA polymerases, and ligase of NHEJ are the most mechanistically flexible and multifunctional enzymes in each of their classes. Unlike repair pathways for more defined lesions, NHEJ repair enzymes act iteratively, act in any order, and can function independently of one another at each of the two DNA ends being joined. NHEJ is critical not only for the repair of pathologic DSBs as in chromosomal translocations, but also for the repair of physiologic DSBs created during variable (diversity) joining [V(D)J] recombination and class switch recombination (CSR). Therefore, patients lacking normal NHEJ are not only sensitive to ionizing radiation (IR), but also severely immunodeficient.
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Affiliation(s)
- Michael R Lieber
- Norris Comprehensive Cancer Center, Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, California 90089, USA.
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Bombarde O, Boby C, Gomez D, Frit P, Giraud-Panis MJ, Gilson E, Salles B, Calsou P. TRF2/RAP1 and DNA-PK mediate a double protection against joining at telomeric ends. EMBO J 2010; 29:1573-84. [PMID: 20407424 DOI: 10.1038/emboj.2010.49] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 03/04/2010] [Indexed: 11/09/2022] Open
Abstract
DNA-dependent protein kinase (DNA-PK) is a double-strand breaks repair complex, the subunits of which (KU and DNA-PKcs) are paradoxically present at mammalian telomeres. Telomere fusion has been reported in cells lacking these proteins, raising two questions: how is DNA-PK prevented from initiating classical ligase IV (LIG4)-dependent non-homologous end-joining (C-NHEJ) at telomeres and how is the backup end-joining (EJ) activity (B-NHEJ) that operates at telomeres under conditions of C-NHEJ deficiency controlled? To address these questions, we have investigated EJ using plasmid substrates bearing double-stranded telomeric tracks and human cell extracts with variable C-NHEJ or B-NHEJ activity. We found that (1) TRF2/RAP1 prevents C-NHEJ-mediated end fusion at the initial DNA-PK end binding and activation step and (2) DNA-PK counteracts a potent LIG4-independent EJ mechanism. Thus, telomeres are protected against EJ by a lock with two bolts. These results account for observations with mammalian models and underline the importance of alternative non-classical EJ pathways for telomere fusions in cells.
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Affiliation(s)
- Oriane Bombarde
- Institut de Pharmacologie et de Biologie Structurale, Toulouse, France
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Small-Molecule Drugs Mimicking DNA Damage: A New Strategy for Sensitizing Tumors to Radiotherapy. Clin Cancer Res 2009; 15:1308-16. [DOI: 10.1158/1078-0432.ccr-08-2108] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hromas R, Wray J, Lee SH, Martinez L, Farrington J, Corwin LK, Ramsey H, Nickoloff JA, Williamson EA. The human set and transposase domain protein Metnase interacts with DNA Ligase IV and enhances the efficiency and accuracy of non-homologous end-joining. DNA Repair (Amst) 2008; 7:1927-37. [PMID: 18773976 DOI: 10.1016/j.dnarep.2008.08.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 07/24/2008] [Accepted: 08/08/2008] [Indexed: 12/22/2022]
Abstract
Transposase domain proteins mediate DNA movement from one location in the genome to another in lower organisms. However, in human cells such DNA mobility would be deleterious, and therefore the vast majority of transposase-related sequences in humans are pseudogenes. We recently isolated and characterized a SET and transposase domain protein termed Metnase that promotes DNA double-strand break (DSB) repair by non-homologous end-joining (NHEJ). Both the SET and transposase domain were required for its NHEJ activity. In this study we found that Metnase interacts with DNA Ligase IV, an important component of the classical NHEJ pathway. We investigated whether Metnase had structural requirements of the free DNA ends for NHEJ repair, and found that Metnase assists in joining all types of free DNA ends equally well. Metnase also prevents long deletions from processing of the free DNA ends, and improves the accuracy of NHEJ. Metnase levels correlate with the speed of disappearance of gamma-H2Ax sites after ionizing radiation. However, Metnase has little effect on homologous recombination repair of a single DSB. Altogether, these results fit a model where Metnase plays a role in the fate of free DNA ends during NHEJ repair of DSBs.
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Affiliation(s)
- Robert Hromas
- Division of Hematology-Oncology, Cancer Research and Treatment Center, Department of Medicine, University of New Mexico Health Science Center, 900 Camino de Salud, Albuquerque, NM 87131, United States
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The Ku-dependent non-homologous end-joining but not other repair pathway is inhibited by high linear energy transfer ionizing radiation. DNA Repair (Amst) 2008; 7:725-33. [DOI: 10.1016/j.dnarep.2008.01.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 01/17/2008] [Accepted: 01/18/2008] [Indexed: 11/17/2022]
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Abstract
The DNA-dependent protein kinase (DNA-PK) is central to the process of nonhomologous end joining because it recognizes and then binds double strand breaks initiating repair. It has long been appreciated that DNA-PK protects DNA ends to promote end joining. Here we review recent work from our laboratories and others demonstrating that DNA-PK can regulate end access both positively and negatively. This is accomplished via distinct autophosphorylation events that result in opposing effects on DNA end access. Additional autophosphorylations that are both physically and functionally distinct serve to regulate kinase activity and complex dissociation. Finally, DNA-PK both positively and negatively regulates DNA end access to repair via the homologous recombination pathway. This has particularly important implications in human cells because of DNA-PK's cellular abundance.
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Affiliation(s)
- Katheryn Meek
- College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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